Crop Improvement

🧭 Overview

🧠 One-sentence thesis

Plant breeding addresses biotic and abiotic production constraints through systematic manipulation of crop reproductive systems to develop distinct, uniform, and stable cultivars suited to specific environments and end-user needs.

📌 Key points (3–5)

• Production constraints: Breeding can only address biotic (diseases, insects) and abiotic (drought, heat, poor soil) factors, not marketing, infrastructure, or policy issues.
• Reproductive systems determine breeding methods: Crops reproduce asexually (clones), autogamously (self-pollination), or allogamously (cross-pollination), and each system requires different breeding approaches.
• Cultivar types match reproductive systems: Pure-line cultivars (homogeneous, homozygous) suit self-pollinators; hybrid cultivars (homogeneous, heterozygous) suit cross-pollinators; clonal cultivars (homogeneous, heterozygous) suit vegetatively propagated crops; synthetic cultivars (heterogeneous, heterozygous) suit cross-pollinators.
• Common confusion—homogeneous vs. homozygous: Homogeneous means all individuals in a population have the same genotype; homozygous means an individual has identical alleles at a locus (A₁A₁). A clonal cultivar is homogeneous but heterozygous (A₁A₂).
• Legal cultivar definition: A cultivar must be distinct (different from existing varieties), uniform (no variation in distinguishing traits), and stable (unchanged across generations).

🌾 African crop production context

🌍 Major crops and production scale

Africa produces diverse cereals (maize, sorghum, millet, rice, wheat, barley), pulses (dry beans, groundnut, cowpeas, soybean, cocoa beans), oilseeds (seed cotton, sesame, palm), and root/tuber crops (cassava, yams, sweet potatoes, potatoes), yet contributes less than a quarter of world root and tuber production. In East Africa, bananas are extremely important—in Uganda they serve as the largest source of calories.

🚧 Production challenges breeders can address

Four main constraints reduce production:

1. Biotic constraints: living organisms (disease pathogens, insects)
2. Abiotic constraints: non-living factors (heat, drought, poor soil fertility)
3. Marketing and infrastructure: poor marketing opportunities, lack of roads/storage, unfavorable policies
4. Capital: lack of investment funds

Breeding efforts only address constraints 1 and 2. Biotic and abiotic factors also affect post-harvest storage. Continuous breeding is needed to increase production per unit land area while maintaining quality.

🌸 Reproductive systems in crops

🧬 Asexual reproduction

Asexual reproduction generates individuals that are genetically identical to the mother parent plant and are referred to as clones.

Two main forms:

• Vegetative propagation: clones from stem cuttings, suckers, tubers, runners (stolons), rhizomes, bulbs, scions. Examples: cassava and sweet potato (stem cuttings), bananas (suckers), potatoes (tubers), elephant grass (rhizomes, sets, stem cuttings).
• Apomictic reproduction: clonal seeds formed by bypassing or failing meiosis. Examples: Citrus, many perennial forages.

🌼 Sexual reproduction basics

Sexual reproduction involves union of male sperm with female egg (fertilization). Two types of pollination:

• Self-pollination: pollen from a plant pollinates a flower on the same plant.
• Cross-pollination: pollen from one plant pollinates a flower on another plant of the same species; requires wind, water, insects, birds, or other animals.

Double-fertilization (unique to flowering plants): each pollen grain contains two nuclei—one fuses with the egg cell to form a diploid zygote (embryo), the second fuses with two polar nuclei to form triploid endosperm (energy source for embryo).

🔄 Autogamous (self-pollinated) mating system

A crop is classified as autogamous when self-fertilization (union of gametes from the same plant or genotype) predominates.

Cleistogamy virtually ensures self-pollination: pollen shed occurs before the flower opens (anthesis), severely limiting cross-pollination. Observed in some legumes (groundnut, peas, some beans, soybean). In some cereals (rice, wheat, barley), most self-pollination occurs before flowers open, but some cross-pollination can occur after partial opening.

Don't confuse: Even self-pollinating species undergo small amounts of outcrossing (e.g., soybean: 0.03%–2% natural outcrossing). Environmental conditions affect mating system behavior.

Examples: sorghum, millet, rice, wheat, barley, groundnuts, cocoa, cowpeas, dry beans.

🌬️ Allogamous (cross-pollinated) mating system

A crop is classified as allogamous when it has a higher percentage of pollination and fertilization with different individuals than with itself.

Four traits/mechanisms promote cross-pollination:

Mechanism	Description	Examples
Male sterility	Non-functional pollen prevents self-pollination. CMS (cytoplasmic male sterility): mitochondrial + nuclear genes. GMS (genic male sterility): nuclear genes alone.	Used for hybrid seed production
Self-incompatibility	Viable pollen cannot fertilize flowers of same/similar genotype; rejected on stigma or in style.	Enforces cross-pollination
Imperfect flowers	Unisex flowers missing stamens or pistils. Monoecious: separate male/female flowers on same plant. Dioecious: male/female flowers on different plants.	Monoecious: maize, banana. Dioecious: papaya, date palm, spinach
Protandry/Protogyny	Protogyny: pistils mature before anthers. Protandry: anthers mature before pistils.	Protogyny: cassava, pearl millet. Protandry: sunflower, coconut

🧠 Why understanding reproductive systems matters

Breeders must understand the crop's reproductive system to make informed decisions about:

• Crossing techniques
• Population maintenance
• Isolation distances
• Line and population development methods
• Which cultivar type is appropriate (hybrid, pure-line, synthetic, clone)

🌱 Breeding populations and cultivar types

📊 Population concepts

A population is a group of individuals that share a common gene pool.

• Homogeneous population: all individuals have the same genotype (all A₁A₁, or all A₁A₂, or all A₂A₂).
• Heterogeneous population: individuals have different genotypes (mix of A₁A₁, A₁A₂, and/or A₂A₂).

How reproductive system affects population structure:

Reproductive system	Population structure	Individual genotype at loci
Cross-pollinated	Heterogeneous	Mostly heterozygous (A₁A₂)
Self-pollinated	Heterogeneous	Mostly homozygous (A₁A₁ or A₂A₂)
Asexual	Homogeneous or heterogeneous	Likely heterozygous (A₁A₂)

🧪 Clonal cultivars

Development steps:

1. Develop a genetically variable base population
2. Evaluate and select superior clones
3. Multiply the new cultivar for commercial use

Key characteristics: homogeneous and heterozygous. Offspring are identical to mother parent (in absence of mutation). Hybrid vigor is fixed and maintained, unlike seed-propagated hybrids.

Propagation methods: stem cuttings, suckers, tubers, stolons.

Examples: cassava, sweet potato, potato, cacao, yam.

🔀 Synthetic cultivars

Synthetic cultivars are produced by intermating a population of purposefully selected inbred lines, clones, hybrids, strains, or other populations of cross-pollinated plants.

Key characteristics: heterogeneous and heterozygous. Each plant is genetically different. Inbreeding depression is severe; self-pollinated seed lacks vigor of cross-pollinated seed.

Development process:

1. Select clonally propagated plants or inbred lines with desirable traits
2. Isolate and allow cross-pollination (randomly or structured) in a polycross nursery
3. Harvest seed and plant in progeny rows for evaluation
4. Select best parents based on plant traits and progeny performance (general combining ability)
5. Replant selected parents and permit cross-pollination in isolation
6. Harvest open-pollinated seed after one or more intermating cycles

Difference from open-pollinated variety: components are maintained in original form so cultivar can be reconstituted.

Example: maize population HIS1.

📏 Pure-line cultivars

Pure-line cultivars are developed for self-pollinated species. Self-pollination leads to homozygosity and homogeneity.

Key characteristics: homogeneous and homozygous.

Three basic development approaches:

Approach	Description	Notes
Introductions	Assemble varieties from other regions; identify adapted lines with desirable traits	May contain mixtures requiring roguing; need MTA awareness
Selection	Assemble landraces; identify and release best genotypes	Applicable for orphan crops; not widely used for major crops
Hybridization	Make crosses between desirable genotypes; evaluate and select superior types	Most common approach

Examples: beans, cowpea, rice, finger millet, tobacco, wheat.

🌽 Hybrid cultivars

Hybrid cultivars are produced by crossing inbred lines, typically two inbred lines in a two-way/single-cross hybrid.

Key characteristics:

• Single-cross hybrids: homogeneous and heterozygous
• Three-way hybrids: heterogeneous and heterozygous

Inbred lines are chosen for combining ability to maximize hybrid vigor. Pollen control (mechanical tools, chemicals, or genetic male sterility) is necessary for hybrid seed production.

Heterosis definitions:

• Midparent heterosis: difference between hybrid and mean of two parents
• High-parent heterosis: superiority of hybrid over the better parent

Don't confuse: Hybrid vigor is more important in allogamous species; expression is typically lower in autogamous species.

Examples: commercial single-cross maize hybrids, three-way cross maize hybrids, sunflower hybrids. Some hybrids produced for autogamous species (sorghum, tomato).

⚖️ Legal definition of a cultivar (UPOV)

📜 Three required criteria

According to The International Union for the Protection of New Varieties of Plants (UPOV), a cultivar must be:

Distinct (Article 7)

A variety is deemed to be distinct if it is clearly distinguishable from any other variety whose existence is a matter of common knowledge at the time of filing of the application.

Distinctiveness can involve morphological, physiological, molecular, or other characteristics.

Uniform (Article 8)

A variety is deemed to be uniform if, subject to the variation that may be expected from the particular features of its propagation, it is sufficiently uniform in its relevant characteristics.

No variation among individuals for distinguishing characteristics. Does not seek absolute uniformity; takes into account the nature of the variety itself. Relates only to relevant characteristics for protection.

Stable (Article 9)

A variety is deemed to be stable if its relevant characteristics remain unchanged after repeated propagation or, in the case of a particular cycle of propagation, at the end of each such cycle.

Plants remain the same from generation to generation. Ensures identity of variety is kept throughout protection period. Relates only to relevant characteristics.

🌍 UPOV background

UPOV is an intergovernmental organization based in Geneva, Switzerland, established in 1961. Mission: "provide and promote an effective system of plant variety protection, with the aim of encouraging the development of new varieties of plants, for the benefit of society."

🎯 Setting breeding objectives

🔑 Factors determining objectives

Plant breeding objectives depend on:

• Geographical adaptation
• Prevalent biotic and abiotic factors influencing production
• Uses of the cultivar
• Crop reproductive system (pure-line or hybrid)
• Factors important to farmers and end-users

✅ Prerequisites for breeding

• Genetic variation must exist for the trait being improved
• Variation must be transmissible (heritable)
• Breeding programs must be adequately set up for screening breeding material based on objectives

🧭 Overview

🧠 One-sentence thesis

Plant breeders use standardized F and S symbols with specific notation systems to communicate the generation history and selection process of breeding lines, ensuring clarity about how each line was derived and selected across generations.

📌 Key points (3–5)

• Two core symbols: F (filial) denotes generations after crossing two parents; S denotes generations of self-pollination in cross-pollinated species.
• Generation vs. line notation: F# tracks generation number (F₁, F₂, F₃…), while F x:y tracks breeding lines where x = generation of last single-plant selection and y = current generation.
• Pedigree writing conventions: Female parent listed first, male second; slashes and numbers record cross order and backcross dosage.
• Common confusion: F₂:₄ vs F₃:₄ lines—both are F₄ generation plants, but differ in which generation the single plant was selected (F₂ vs F₃).
• Selection history tracking: BCID (Breeder's Cross Identification) records year, location, cross type, and selection decisions at each generation for complete traceability.

🌱 Basic generation symbols

🌱 F# notation for filial generations

F symbol: denotes the filial (family) generation of offspring following a cross between two or more parents.

• The subscript number represents the specific generation: F₁, F₂, F₃, F₄, etc.
• F₁ = first generation immediately after crossing two parents
• Each subsequent generation advances by one number after self-pollination or sib-pollination (pollination by a sibling plant in the same progeny row)
• Example: Cross two homozygous parents → F₁ (all uniform, heterozygous) → self-pollinate F₁ → F₂ (segregating) → self-pollinate F₂ → F₃, and so on

🌾 When parents are homozygous vs heterozygous

Parent type	F₁ outcome	F₂ outcome
Both homozygous	Homogeneous (uniform) and heterozygous	Heterogeneous (segregating)
One or both heterozygous	Heterogeneous (non-uniform)	Heterogeneous
Complex cross (>2 parents, even if homozygous)	Heterogeneous and heterozygous	Heterogeneous

• Don't confuse: Homogeneous means all plants are uniform/the same; heterogeneous means plants vary. Heterozygous refers to alleles at individual loci.
• F₂ is typically the first generation when selection for simple traits begins (when parents were homozygous).

🌼 S# notation for cross-pollinated species

• In cross-pollinated species, S# is used instead of F#
• S₀ can describe progeny in two ways:
  1. Similar to F₁ in self-pollinated species (plant not derived from self-pollination)
  2. Similar to F₂ in self-pollinated species (population formed by random mating, therefore heterogeneous and heterozygous)
• Important: The breeder must clearly state which meaning is intended and use it consistently

🧬 Breeding line notation (F x:y and S x:y)

🧬 What F x:y means

F x:y notation: x = generation where a single plant was harvested separately to give rise to the derived line; y = current generation of inbreeding of plants within this derived line.

• This notation describes breeding lines (genotypes) derived from individual plants at various generations
• Also written as "Fₓ-derived Fᵧ lines" or "Fₓ-derived lines in the Fᵧ generation"
• Example: F₂:₄ line = an F₄ line derived from a single F₂ plant

🔬 F₂:₄ line development

Step-by-step process:

1. Select and harvest a single F₂ plant separately
2. Self-pollinate to produce F₃ seeds
3. Grow F₃ seeds in a single progeny row
4. Self-pollinate all or many F₃ plants in this row
5. Harvest as a bulk (all F₃ plants together) → this bulk is the F₂:₄ line

• Each individual F₂ plant gives rise to a genetically distinct F₂:₄ line
• The first subscript (2) designates the generation of the last individual-plant selection

🔬 F₃:₄ line development

Step-by-step process:

1. Start with an F₃ progeny row (produced from a self-pollinated single F₂ plant)
2. Select a single F₃ plant from that row
3. Self-pollinate to produce F₄ seed
4. Grow this seed → represents an F₃:₄ line

• Key difference from F₂:₄: The individual plant selection happened in F₃ generation instead of F₂
• Both F₂:₄ and F₃:₄ are F₄ generation plants, but selection history differs

✍️ Pedigree writing conventions

✍️ Basic cross notation

• Female parent listed first (left), male parent second (right)
• Example: (A × B) means A is female, B is male
• Alternative notation: A/B (same meaning)

🔀 Multi-parent crosses

• Three-way cross: If F₁ (A/B) is pollinated with parent C, with F₁ as female and C as male → A/B//C
• Sequential crosses use numbers to record order:
  • A/B//C/3/D/4/E/5/F/6/G
  • The number before the slash indicates the cross order
  • All listed after the number are males unless otherwise indicated

Example with mixed female/male roles:

• Step 1: A/B (first cross)
• Step 2: A/B//C (A/B is female)
• Step 3: D/3/A/B//C (D is female, A/B//C is male)
• Step 4: D/3/A/B//C/4/E (E is male, the 4-parent cross is female)

🔄 Backcross notation

• Asterisk (*) and number indicate dosage of the recurrent parent
• Placed next to the crossing symbol (/) dividing recurrent and donor parents

Notation	Meaning	Backcross generation
A*2/B	A is recurrent parent used twice	BC₁ (one backcross)
A/3*B	B is recurrent parent used three times	BC₂ (two backcrosses)

• A*2/B = A//A/B (A was female in both F₁ and BC₁)
• A/3*B could be B/3/A/B//B or A/B//B/3/B (different parent roles)
• Derived symbols follow BC designation: BC₁F₂:₄ or BC₂F₂:₄

🏷️ Cross identification and selection tracking

🏷️ Unique identity numbers

Every cross receives a unique ID including:

• Year the cross was made (e.g., 2014)
• Cross number (e.g., 1001)
• Target purpose or trait (e.g., HO for high-oil, or market segment abbreviation)

📋 BCID system components

BCID (Breeder's Cross Identification): assigns every F₁ plant, segregating line, or advanced line a unique identifier and selection history.

Components of a BCID (using CIMMYT wheat example):

1. Origin letter (e.g., CM = crusa Mexicana, "Mexican cross")
2. Cross type (e.g., BW = bread wheat × winter wheat; SS = spring × spring; SW = spring × winter)
3. Year abbreviation (e.g., 00 = 2000)
4. Location code (e.g., Y = Yaqui Valley)
5. Sequential number (e.g., 0124 = order within crossing cycle)

Example: CMBW08Y0199 = Mexican cross, bread × winter wheat, 2008, Yaqui Valley, cross #0199

📊 Selection history notation

After the BCID, numbers and letters record selection at each generation:

• Number = how many individual plants selected
• Letter = location where selection occurred
• 0 + letter (e.g., 0Y, 0M) = entire plot harvested in bulk (no individual selection)
• 0 + number + letter (e.g., 010M) = modified pedigree/bulk method (10 heads selected and bulked)

Example interpretations:

CMBW08Y0199-35Y-15M-7Y-5M-12Y-0M (pedigree method):

• F₂: 35th plant selected at location Y
• F₃: 15th plant selected at location M
• F₄: 7th plant selected at location Y
• F₅: 5th plant selected at location M
• F₆: 12th plant selected at location Y
• F₇: single plot grown at M, harvested in bulk (0M)

CMBW08Y0124-81Y-010M-010Y-010M-15Y-0M (modified pedigree/bulk):

• F₂: 81st plant selected at Y
• F₃: 10 plants selected and bulked from progeny row at M
• F₄: 10 plants selected and bulked at Y
• F₅: 10 plants selected and bulked at M
• F₆: single plant (15th) selected at Y
• F₇: progeny row at M harvested in bulk

CMSS07Y051-030Y-030M-030Y-53Y-0M (selected bulk method):

• F₂-F₄: 30 plants bulked each generation (alternating Y and M locations)
• F₅: 53rd plant selected from bulk plot at Y
• F₆: complete plot bulk harvested at M

🧭 Overview

🧠 One-sentence thesis

Genetic variation is essential for plant breeding progress, and breeders must understand how to create, access, and legally manage germplasm resources while working within natural and artificial selection frameworks.

📌 Key points (3–5)

• Why variation matters: Genetic variation is the absolute prerequisite for making progress through artificial selection in breeding programs.
• Three processes in natural selection: creating variability (mutation, recombination), rearranging variability (natural selection, genetic drift), and maintaining products (reproductive isolation).
• Gene pool concept: Germplasm is organized into primary (easy crossing), secondary (difficult crossing), and tertiary (very difficult crossing) gene pools based on ease of gene transfer.
• Common confusion: Natural selection vs. genetic drift—natural selection favors adaptive traits, while genetic drift is random and neutral to adaptation (e.g., forest fire destroying one species by chance vs. fire-resistant traits being selected).
• Legal stewardship: Material Transfer Agreements (MTAs) are legally binding contracts governing seed exchange; breeders must follow proper procedures and never distribute material without authorization.

🌱 How selection creates improvement

🌱 Natural selection framework

The excerpt describes three main processes required for natural selection to function:

1. Creating genetic variability: mutation, recombination, chromosomal segregation, gene flow
2. Rearranging genetic variability: natural selection or random genetic drift
3. Maintaining the product: reproductive isolating mechanisms

Natural selection: operates through reproductive fitness (the ability to produce offspring that contribute to the gene pool of the next generation).

• Mutations are random—not created to address organism "needs"—so they can be neutral, harmful, or beneficial.
• Somatic mutations (in non-reproductive cells) do not contribute to genetic variability.
• Gene flow becomes important when genes arrive in a population where they did not previously exist.

🎲 Genetic drift vs. natural selection

Random genetic drift: random and uncontrollable changes in gene frequency due to chance events rather than adaptive advantage.

Example from the excerpt: In a forest with 50% each of two tree species (A in the west, B in the east), a fire destroys 80% of western trees. Species B leaves more offspring purely by chance destruction of A, not because B is healthier or more productive. This is genetic drift—neutral to adaptation.

Contrast: If species B had fire-resistant wood properties, repeated fires would favor B through natural selection because the trait is genetic and adaptive.

Don't confuse: Genetic drift = random chance events; natural selection = differential reproduction based on heritable adaptive traits.

🎯 Artificial selection

Artificial selection: the deliberate choice of individuals for breeding in each generation and the advancement of select individuals.

• Directional selection: a form of artificial selection choosing phenotypically superior plants for breeding.
• Practiced for thousands of years by humans to improve plant species.
• Example: Modern maize evolved from teosinte (Zea mays ssp. parviglumis) through artificial selection.

Key morphological changes from teosinte to maize:

• Teosinte has cupulate fruit case protecting each kernel; maize has reduced cupules forming the cob.
• Teosinte ears disarticulate at maturity (seed dispersal); maize ears remain intact (easy harvest).
• Teosinte has single-spikelet cupules in two ranks; maize has four or more ranks.

📈 Evidence: Illinois long-term selection experiments

C.G. Hopkins started selection experiments in 1896 using open-pollinated corn cultivar Burr's White, establishing four strains:

Strain	Direction	Result after many generations
Illinois High Oil (IHO)	Increase oil	No upper limit reached after 100 generations; genetic variance still present
Illinois Low Oil (ILO)	Decrease oil	Reached measurable lower limit by Generation 85
Illinois High Protein (IHP)	Increase protein	Continued response
Illinois Low Protein (ILP)	Decrease protein	Reached biological/physiological limit after ~65 generations

Critical insight: Artificial selection in genetically heterogeneous populations always leads to successful outcome (mean change in the direction of selection) unless a biological constraint is reached. The mean of a trait can be altered in both directions if genetic variability exists.

Essential principle: Genetic variation is ESSENTIAL for making progress using artificial selection.

🏗️ Plant breeding process structure

🏗️ Three main phases

Phase	Focus	Parents	Commercial consideration	Outcome
Germplasm development	One trait at a time	Wild accessions, related species, elite lines	Low or non-existent	Improved parental germplasm, not a cultivar
Cultivar development	Several traits simultaneously	Elite × elite (may include germplasm line)	Primary	Genotype/population ready for release as cultivar
Technology transfer	Dissemination	N/A	High	Adoption by farmers and industry

🎯 Setting breeding objectives

Breeding objectives: based on mandate (market segment needs), organizational focus, farmer requirement, industry needs, profitability, and sustainability.

Requirements:

• Clearly defined with quantifiable descriptions (e.g., "increase yield by x% over check ABC" with head-to-head comparison).
• Based on importance, feasibility, and cost-effectiveness.
• Engagement with growers, industry, and consumers.

Two priority levels:

• 'Must to have' traits: absolutely necessary for commercial release (e.g., adequate storability).
• 'Nice to have' traits: not essential but add value to the product.

🔄 Creating breeding populations

After setting objectives and identifying parents, breeders create breeding populations by crossing two or more parents to expand genetic variability.

Major types of crosses:

1. Single cross: Line A × Line B (two elite lines)
2. Three-way cross: (Line A × Line B) × Line C (third parent should be elite/adapted for at least 50% favorable genetics)
3. Double cross: [(Line A × Line B) × (Line C × Line D)] (more genetic breadth but lower frequency of desirable recombinants)
4. Diallel cross: Each parent crossed with every other parent; n × (n – 1)/2 combinations (excluding reciprocals); mainly for genetic studies
5. Back cross: Incorporates specific trait from donor parent into elite recurrent parent through successive crossings; improved by molecular markers

🌍 Gene pools and germplasm resources

🌍 The gene pool concept

Proposed by Harlan and de Wet (1971) to provide a practical guide for breeders and geneticists wishing to make crosses. It classifies genetic resources based on ease of hybridization (ability to move genes between them), not taxonomy.

Gene pools are not static but change as more information or new technologies become available to manipulate genomes.

🥇 Primary gene pool

Who belongs: Cultivated species, landraces, farmer-developed populations, ecotypes, spontaneous races (wild or weedy).

Characteristics:

• Crossing/gene transfer is easy.
• Hybrids are generally fertile with normal chromosome pairing and gene segregation.
• Major source of genetic variation for improvement programs.
• Most breeders work exclusively within this gene pool.
• Elite breeding programs spend little direct effort on unadapted or wild relatives (due to undesirable linkage blocks, breaking of desirable linkages, epistatic interactions).

🥈 Secondary gene pool

Who belongs: Related species (usually within the same genus, though not all species in a genus; some outside the genus may qualify).

Characteristics:

• Gene transfer is possible but difficult.
• Hybrids tend to be sterile.
• Chromosomes pair poorly during meiosis.
• F₁ plants are weak and develop to maturity with difficulty.
• Recovery of desired types in advanced generations is generally difficult.

🥉 Tertiary gene pool

Who belongs: Distant relatives in other genera or distantly related species within the same genus.

Characteristics:

• Gene transfer is very difficult (requires embryo rescue, chromosome doubling, bridging species).
• Hybrid sterility is common.
• Chromosome doubling may restore fertility by providing homologues for each chromosome.
• Boundaries are poorly defined and shift as new hybridization techniques develop.

🌉 Bridging species

Bridging species: a third species that facilitates exchange of germplasm between the crop species and tertiary gene pool species by developing complex hybrids.

Example from the excerpt: Elymus × Triticum crosses failed or produced sterile hybrids even with embryo rescue. However, using Agropyron × Triticum derivative as female parent, then crossing to Elymus, allowed introgression of Elymus alleles without special techniques.

🧬 Wide hybridization examples

🧬 What is wide hybridization

Wide cross: crossing that involves individuals outside of cultivated species, typically involving secondary and/or tertiary gene pools.

Purpose: Transfer vitally important traits (especially disease resistance) not found in cultivated genotypes, even though it is difficult.

🌾 Wheat example

T1BL.1RS wheat-rye translocation (tertiary gene pool: rye to wheat):

• Widely used in bread wheat breeding programs worldwide.
• At one point, several million hectares planted to cultivars with this translocation.
• Benefits: Disease resistance cluster for leaf rust, stem rust, stripe rust, and powdery mildew; improved grain yield and kernel weight.
• Limitation: Resistance to specific genes has been overcome in some regions, showing the continual nature of plant breeding.

🍚 Rice examples

First example: Transfer of grassy stunt virus resistance gene from Oryza nivara to cultivated rice.

• 1970s epidemics transmitted by brown plant hopper caused severe yield losses.
• Thousands of accessions screened; one O. nivara accession found resistant.
• Successfully transferred through backcross breeding; resistant varieties released.

Other transfers to cultivated rice:

• Xa-21 for bacterial blight resistance from O. longistaminata
• CMS sources from O. perennis and O. glumaepatula for hybrid rice production
• Resistance to brown plant hopper, white-backed plant hopper, bacterial blight from O. officinalis
• Multiple traits from various wild Oryza species with different genome types (AA, CC, BBCC, CCDD, EE, FF, GG, HHJJ)

🔬 Artificially created variability

🔬 Mutation basics

Constitutional mutation: a germline mutation present in every cell of the offspring.

How mutations create variation:

• Novel genes produced by duplication and mutation of ancestral genes, or recombining parts of different genes.
• Lethal mutations do not carry germline forward.
• Nonlethal mutations accumulate and increase genetic variation.
• Natural selection reduces abundance of some changes while favorable mutations accumulate.

Types of chromosomal mutations:

• Deletions: loss of gene(s)
• Duplication: additive effect due to added gene(s)
• Inversion: linkage block changes; genes in close proximity co-segregate
• Insertion and translocation: gene moves to new chromosome; similar effect as duplication

Don't confuse: Germ line mutations (passed to descendants through reproductive cells) vs. somatic mutations (non-reproductive cells, not usually transmitted).

🌽 Mutation breeding example: Quality Protein Maize (QPM)

Problem: Maize endosperm protein is deficient in two essential amino acids (lysine and tryptophan).

Solution: The opaque-2 single gene mutation, together with endosperm and amino acid modifier genes, was used to develop QPM varieties.

Benefits:

• About twice as much lysine and tryptophan compared to regular maize
• 30% less leucine
• Suitable for human and animal nutrition
• Now grown on millions of hectares

Recognition: Dr. Evangelina Villegas and Dr. Surinder Vasal awarded the World Food Prize in 2000 for QPM development.

⚠️ Mutation breeding approaches and limitations

Traditional methods: Chemical or physical agents (X-rays, gamma rays, fast neutrons, ethyl methane sulfonate/EMS).

Major disadvantage: Non-targeted mutation events.

Process challenges:

• Plant breeder must increase generations to achieve homozygosity (mutant allele segregates initially).
• Constant phenotyping for traits of interest.
• Resource-intensive depending on phenotyping cost.
• Low mutation frequency at low doses (high doses cause major chromosomal aberrations and lethality).
• Large population sizes required for screening.

Important caveat: If altering only a single trait, other genome regions may have been mutated, and one change may alter other plant aspects. Extensive agronomic testing required before commercialization or use as parent.

Newer approaches: Space light ion irradiation, restriction endonucleases, Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), CRISPR/Cas-based RNA-guided DNA endonucleases—these induce site-targeted mutations.

🧪 Mutation breeding procedure

1. Seed (M₀) of inbred genotype subjected to mutagen treatment
2. Treated seed grown to form M₁ population (heterogeneous, each plant may have different mutations; heterozygous/hemizygous at numerous loci)
3. Self-fertilize M₁ plants to develop M₂ generation (allows recessive mutants to become homozygous for observable phenotypes)
4. After several M generations, mutant phenotype confirmed and established as stable (non-segregating)
5. Mutant line used in forward or backcrossing program to transfer favorable mutant to elite cultivars

Considerations: Size of M₁ and M₂ families, ploidy level, genetically effective cells (GEC) in germline, frequency of chimeras.

🧬 Transgenic approaches

Transgenic technology: transfer of cloned genes via transformation or particle bombardment so the transformed plant expresses the foreign gene.

Scope: Genes can theoretically come from virtually any living organism—from within the same primary gene pool to beyond the tertiary gene pool.

Current status: Over the past few years, mainly single genes transferred (e.g., herbicide tolerance, corn borer resistance in corn).

🏦 Genebanks and germplasm acquisition

🏦 Role of genebanks

Purpose: Preserve valuable agrobiodiversity for future generations by setting up collections of genetic resources.

Contents: 'Landraces' or local varieties of cultivated and non-cultivated wild relatives.

Benefits: Protect and preserve seed diversity; provide accessible source for plant breeders.

Global scope:

• About 1,750 institutional crop collections worldwide
• Community-based seed bank initiatives
• CGIAR maintains 706,000 samples at 15 research centers (cereals, legumes, roots, tubers, trees, staple crops)
• All CGIAR accessions are international public good under the International Treaty on Plant Genetic Resources for Food and Agriculture

🇺🇸 National Plant Germplasm System (USA)

Functions:

• Acquiring crop germplasm
• Preserving crop germplasm
• Evaluating crop germplasm
• Documenting crop germplasm
• Distributing crop germplasm

GRIN (Germplasm Resources Information Network):

• Search for genotypes of interest via query interface
• Place order to receive seed via order form
• Involves paperwork (agreements, seed import/export permits, customs documents)
• Planning ahead is critical for timely seed receipt

Tip: Contact the curator or other genebank scientists for suggestions on specific traits or accessions, but do groundwork first.

📜 Legal considerations and stewardship

📜 Material Transfer Agreement (MTA)

Material Transfer Agreement (MTA): an agreement that allows for transfer of seed or plant part without transfer of title; a legally binding contract between provider and recipient.

Key principle: Provider maintains ownership at all times; recipient uses material according to contract terms.

Critical rule: Plant breeders should NEVER give out material without going through proper steps. Work with organizational Intellectual Property and Commercialization office or IP/Technology Transfer office.

Signatories: Sending breeder + organizational representative + recipient breeder + recipient organizational representative.

Responsibility: Plant breeder/researcher utilizing the material is ultimately responsible for fulfilling MTA obligations.

📋 MTA sections

Section	Content
Introduction	Type of material or purpose
Parties	Sender, recipient, organizational affiliations
Definitions	Scientific terms (material, seed, genotype)
Description of use	Conditions on what can/cannot be done
Confidential information	Specific confidentiality clauses
Intellectual Property rights	Licensing, royalties, inventions conditions
Warranties	Material does not come with warranties (protects sender)
Liability/indemnification	Recipient assumes all liability; sender not liable
Publication	Publication rights for receiver
Governing law	Which jurisdiction laws apply (state, country)
Termination	Agreement end date; what to do with leftover material (usually destroy original)
Signatures	Agreement not executed until all signatures obtained; material should not be sent until MTA is signed
Exhibits/appendices	List of material or accompanying data

🌐 International Treaty provisions

Standard Material Transfer Agreement (SMTA):

• Mandatory model for providing/receiving material under the Multilateral System
• Result of lengthy negotiations among Contracting Parties
• May not be varied or abbreviated
• Private agreements between providers and recipients, but Governing Body (through FAO as Third Party Beneficiary) has recognized interest

👨‍🌾 Farmers' Rights (Article 9)

The International Treaty recognizes the enormous contribution of local and indigenous communities and farmers for conservation and development of plant genetic resources.

Government responsibilities for implementing Farmers' Rights:

• Protection of traditional knowledge relevant to plant genetic resources
• Right to equitably participate in sharing benefits from utilization of plant genetic resources
• Right to participate in decision-making at national level on conservation and sustainable use

Support measures:

• Funding strategy with priority for farmers in developing countries, least developed countries, and countries with economies in transition
• Support for farmers who conserve and sustainably utilize plant genetic resources

✅ Uses of germplasm

Two main approaches:

1. Direct release as cultivars: Less likely in species with active breeding efforts; more likely in orphan crops where some selection may be done on plant introduction or landrace before release.
2. Introgression of single-gene traits: More appropriate use—transferring traits from wild species or unadapted germplasm into elite cultivars.

🧭 Overview

🧠 One-sentence thesis

Genetic variation is the foundation of plant breeding success, and understanding population structures, heritability, and selection theory enables breeders to predict and maximize genetic improvement across generations.

📌 Key points (3–5)

• Why genetic variation matters: Without sufficient variability among individuals in breeding populations, genetic improvement cannot occur; understanding underlying genetic interactions helps breeders manipulate variation effectively.
• Population vs. Mendelian genetics: Population genetics applies to all matings in a population (not just one cross) and focuses on increasing the frequency of desirable alleles.
• Heritability determines selection effectiveness: Higher heritability means phenotype better reflects genotype, making selection more effective; it depends on genetic variance relative to total phenotypic variance.
• Common confusion—broad vs. narrow sense heritability: Broad sense includes all genetic effects (additive + dominance + epistasis); narrow sense includes only additive effects that can be fixed in breeding.
• The breeder's equation: Response to selection depends on selection intensity, heritability, and phenotypic variability—breeders must balance these factors to maximize genetic gain.

🧬 Population structures in breeding

🧬 What defines a population in breeding

Population: any group of individuals sharing a common gene pool.

Gene pool: the sum total of all genes present in a population.

• Population genetics principles apply to the total products of all matings in the population, not just one specific mating (unlike Mendelian genetics).
• Breeding methods are designed to increase the frequency (proportion) of desirable alleles in the population.

🌱 Simple populations (2–4 parents)

Two-way cross (single cross)

• The simplest segregating population: cross two elite lines to produce F₁, then self-fertilize F₁ to produce F₂.
• Each parent contributes 50% genetically.
• F₂ and higher filial generations are used for selection in self-pollinating crops (wheat, rice, soybean).
• In cross-pollinated crops like maize, single cross hybrids (F₁) from inbred parents are the commercial product.

Backcross population

• Cross F₁ back to one parent to produce BC₁F₁, then self to create a segregating population.
• Useful when one parent is superior in most traits and the goal is to transfer one or two genes from an unadapted parent into an elite line.
• Each backcross F₁ seed is heterogeneous, requiring phenotypic testing or marker-assisted selection.

Three-way cross

• Cross a single-cross F₁ to a third parent (inbred line), then self-pollinate.
• The third parent contributes 50% of alleles; the first two parents each contribute 25%.
• The third parent should generally be one of the best parents.
• Useful when one parent is less desirable and one or two are more desirable.

Double cross (four-parent cross)

• Cross two single-cross F₁ hybrids (each from two inbred lines).
• Each of the four parents contributes 25% genetically.
• Each resulting individual is genetically distinct.

🔬 Complex populations (more than four parents)

Why use complex populations

• Develop information for parents and full-sib families.
• Identify heterotic groups.
• Estimate general and/or specific combining ability.
• Estimate additive, dominant, and epistatic genetic effects and genetic correlations.

Nested designs (North Carolina Design I)

• Each male parent is mated to a different subset of female parents.
• Example: 4 males × 8 females, each male mated to 2 different females.

Factorial designs (North Carolina Design II)

• Each member of a group of males is mated to each member of a group of females.
• Example: 4 males × 8 females = 32 crosses.

Diallel cross

• All pairwise crosses among parents, including reciprocals and self-pollinations.
• Each parent is mated with every parent in the population (including selfs).
• Complete diallel is usually used only as a research tool.
• Don't confuse: Selfs don't contribute interesting recombination if parents are inbred; reciprocal crosses are functionally the same in terms of recombination in later generations (unless maternal/paternal effects exist).

Half-diallel cross

• Each parent mated with every other parent, excluding selfs and reciprocals.
• More practical than complete diallel for breeding purposes.

Partial diallel

• Only selected subsets of full diallel crosses are made.
• Allows incorporation of germplasm diversity without making a massive number of crosses.
• Example: Partial diallel among parents, followed by diallel among single crosses.

Polycrosses

• Used to intercross selected plants in cross-pollinating species.
• Natural conditions (wind or insects) make the crosses; no control on specific parental pairings.
• Considerations: flowering time synchronization, wind effects, insect pollinator activity.
• Planting arrangements: Latin Square (each parent in each row and column) or randomized complete block design.

Polycross harvest procedures (to ensure equal contributions):

1. Bulk harvest entire plot (easiest but unequal contributions).
2. Bulk each parent's seed across replications, then composite equal amounts (most common but some inequality).
3. Composite equal amounts from each clone in each replication (most balanced, recommended).

📊 Trait types and gene action

📊 Qualitative vs. quantitative traits

Qualitative traits

• Controlled by single or few genes.
• Phenotypes classified into distinct categories (presence/absence, yes/no, different colors).
• Generally not influenced by environment.
• Examples: awned vs. awnless wheat, purple vs. white flowers, round vs. wrinkled seeds.
• Expression is the same regardless of environment.

Quantitative traits

• Controlled by several genes.
• Phenotypes form a continuum, cannot be classified into distinct categories.
• Influenced by environment—same genotype produces different phenotypes in different environments.
• Examples: yield, protein %, oil %, seed weight.
• Most traits breeders work to improve are quantitative.

Don't confuse: Plant height can seem qualitative (short vs. tall) but is actually quantitative because it occurs across a range of values and is controlled by several genes. Disease resistance can be either qualitative or quantitative depending on genetic control, environmental influence, and phenotypic expression.

⚙️ Additive gene action

Additive gene action: when substituting one allele for another at a gene locus always causes the same effect.

• Formula: A₁A₁ – A₁A₂ = A₁A₂ – A₂A₂
• The effect of substituting A₁ for A₂ is the same whether the substitution occurs in genotype A₂A₂ or in genotype A₁A₂.
• Linear regression with common slope between genotypes describes additive effects.
• When a gene acts additively, maximum trait expression occurs in the genotype possessing all favorable alleles.
• Example: If A₁A₁ = 8, A₁A₂ = 4, A₂A₂ = 0, then substituting A₁ with A₂ always changes the value by +4.

⚙️ Non-additive gene action

Dominance effects (intra-locus interactions)

• Deviations from additivity: A₁A₁ – A₁A₂ ≠ A₁A₂ – A₂A₂
• The heterozygote is similar to one parent rather than the mean of the homozygotes.
• Non-linear regression with non-common slope between genotypes.
• Example: If A₁A₁ = 6, A₁A₂ = 6, A₂A₂ = 1, the heterozygote equals the dominant homozygote.

Epistatic effects (inter-locus interactions)

• Interactions between genes at different loci (e.g., A₁/B₁ or A₂/B₂).
• Can be additive×additive, dominance×dominance, or additive×dominance.
• Non-parallel lines in graphical representation indicate epistatic interaction.
• These interactions are important for most traits.

Implications for breeding

• In self-pollinated species (cultivar = inbred line): non-additive gene effects can rarely be fixed; selection response is unpredictable for traits controlled by non-additive genes.
• In cross-pollinated species (hybrid cultivars): non-additive gene effects, especially dominance, are important and exploitable.

Selection challenge with dominance

• When selecting based only on phenotype in early generations, breeders cannot distinguish homozygous from heterozygous individuals.
• Example: With complete dominance at two loci, a breeder selecting for maximum phenotype will select 9/16 plants, but only 1/16 is the desired homozygous dominant genotype.

🌍 Phenotype, environment, and interactions

🌍 The phenotype equation

Basic relationship

• Phenotype (P) = Genotype (G) + Environment (E)
• For populations: Phenotypic variance (Vₚ) = Genotypic variance (Vɢ) + Environmental variance (Vₑ)
• Genetic variability is heritable and can be manipulated by breeders.
• Environmental variability is not heritable and can mask true trait expression.

With interactions

• Phenotype = Genotype (G) + Environment (E) + Genotype × Environment interaction (GxE)
• Not all phenotypic variation is accounted for by G and GxE; remaining variation is attributed to error.

🌍 Understanding environment

Micro-environment vs. macro-environment

• Micro-environment: unique set of factors altering development of a single plant.
• Macro-environment: a class of micro-environments; groups of plants experiencing similar conditions at the same time and space.
• Example: In a water-logged field, individual plants suffer slightly different levels (micro), but all suffer some degree (macro).
• Breeders focus on macro-environments, classified as location, year, or location × year.

Environmental factors

• Soil differences, temperature, humidity, rainfall, day length, solar radiation, wind, salinity, pathogens, pests, etc.

🌍 Genotype × Environment (GxE) interaction

Three types of GxE interaction

Type	Description	Graphical pattern	Breeding implication
No interaction	Genotypes perform consistently across environments	Parallel lines	Same genotype selected everywhere
Non-crossover	Change in magnitude but not rank	Non-parallel lines, no crossing	Ranking preserved
Crossover	Change in rank	Lines cross	Most important: different genotypes selected in different environments

Crossover interaction example

• Environment 1 is disease-free; Environment 2 has pathogen A.
• Genotype 2: high yielding, disease susceptible → best in Environment 1.
• Genotype 1: lower yielding, disease resistant → best in Environment 2.
• Breeder's goal: combine better response to both environments into a single genotype.
• Challenge: determine if yield and disease resistance are mutually exclusive (linkage vs. pleiotropy).

🌍 Practical considerations for breeders

Testing strategy based on mandate

• International institutions (CGIAR): wider adaptation mandate, use many diverse locations (>20).
• State/provincial institutes: localized mandate, use fewer environments representative of one or two macro-environments.

Resource allocation

• Understand relative importance of G×Location, G×Year, and G×Location×Year interactions.
• Helps decide how many locations and years to use for testing.

Mega-environments

• Stability analysis (e.g., AMMI) identifies similar environments.
• Within a mega-environment: little or no GxE interaction.
• Breeders gain little by testing in more similar environments.
• Should test across dissimilar environments for stable performance.
• Sample one or more locations from each mega-environment.

Site selection factors

1. Good correlation with farmer growing conditions.
2. Infrastructure to handle different tests and mitigate threats.
3. Low environmental error (higher heritability) to differentiate desirables from discards.
4. Infrastructure for timely planting, maintenance, harvest, processing.

Adaptation philosophy

• Wide vs. specific adaptation debate depends on program mandate, target region, and farmers.
• Breeder's job: ensure cultivar helps farmers profit and meets end-user requirements.
• Think of cultivar as a "package" with all necessary ingredients for adoption.

📈 Heritability concepts

📈 Definition and types

Heritability: the degree to which characteristics of a plant are repeated in its progeny; mathematically, the proportion of total variability due to genetic causes.

Broad sense heritability (H²)

• H² = Vɢ / Vₚ
• Includes all genetic variance (additive + dominance + epistasis).
• Less valuable because it includes non-additive effects that cannot be fixed in homozygous condition.

Narrow sense heritability (h²)

• h² = Vₐ / Vₚ (where Vₐ = additive genetic variance)
• More valuable because it indicates how much variability is due to additive gene action.
• Additive effects can be selected for effectively and fixed in homozygous condition.

Don't confuse: Broad sense tells you environment's effect is small but doesn't distinguish fixable (additive) from non-fixable (dominance, epistasis) genetic effects. Narrow sense specifically measures the fixable portion.

📈 The Johannsen experiment (1903)

Setup

• Studied seed weight in beans (Phaseolus vulgaris, highly self-pollinated).
• Started with variable seed lot from cultivar 'Princess'.
• Selected for large and small seeds, grew individually, measured progeny.

Results

• Selection was effective in the original unselected population: large-seeded parents → large-seeded progeny; small-seeded parents → small-seeded progeny.
• Selection within a line was NOT effective: regardless of parent seed size, progeny always showed the average seed weight of the parent line.

Conclusion

• Original seed lot was a mixture of different genotypes/purelines (each homozygous for seed weight genes).
• Even when progeny differed phenotypically, each seed of a line possessed the same genotype for seed weight.
• This demonstrated that genetic variability is essential for selection to be effective; environmental variability is not heritable.

📈 Importance for breeding

Why heritability matters

• Selection response is related to heritability.
• Higher heritability → phenotype better reflects genotype → more effective selection.
• More extensive testing (more environments, more replications) reduces phenotypic variance and increases heritability.
• More locations are more effective than more years (smaller variance component for G×Year vs. G×Location).
• In most cases, selection doesn't need more than one year of data (except when selecting each generation toward true-breeding status).

Traits with high heritability

• Can be selected on single-plant basis in early generation.
• Can be selected in fewer (even single) environments.

Context matters

• Each heritability estimate is unique to: method of calculation, testing environment, generation used, genotypes studied.
• Breeders should consider a range of heritability (not absolute value) with confidence intervals.
• High narrow sense heritability (e.g., ≥0.7) means early generation selection can be effective.

📈 Estimation methods

1. Variance component method

• Compare segregating and homogenous populations.
• Applicable to self-pollinated or clonally propagated species.
• Estimates broad sense heritability.
• In self-pollinated species: Parent 1, Parent 2, and F₁ are genetically uniform, so their variance equals environmental variance (Vₑ).
• F₂ or other segregating generation variance = Vɢ + Vₑ, so Vɢ can be calculated.

2. Covariance between relatives

• Examples: parent-offspring regression, half-sib and full-sib covariance, inbred family covariance.
• Uses special mating designs (half-sib, full-sib, North Carolina designs).
• Analysis of trials across environments.

3. Realized heritability

• Calculated from actual response to selection (see Selection Theory section).

Multi-location, multi-year example

• Heritability on genotypic mean basis accounts for replications and environments.
• Formula adjusts for number of replications (r) and environments (e).
• If genotypes are randomly chosen, the ratio is heritability; if selected genotypes, it's called repeatability (measures precision and proportion of genetic variation).

🎯 Selection theory and response

🎯 Truncation selection

The process

• Individual selection based on phenotypic value.
• Truncation point (T) separates selected from unselected individuals.
• μ = mean of unselected population (generation 0).
• μₛ = mean of selected parents.
• μ' = mean of offspring generation (generation 1).
• Generally: μₛ > μ' > μ

Why μₛ > μ'

• Some selected parents had favorable genotypes → pass favorable genes to offspring (why μ' > μ).
• Some selected parents had superior phenotype due to favorable environment, not favorable genotype.
• Alleles (not genotypes) are transmitted; favorable genotypes may segregate or recombination may break favorable linkages.

🎯 Key equations

Selection differential (S)

• S = μₛ – μ
• The difference between selected parents and the original population.

Response to selection (R)

• R = μ' – μ
• The difference between offspring generation and original population.

Prediction equation

• R = h²S
• Response depends on heritability and selection differential.

Alternative form with selection intensity

• R = ih²σₚ
• Where i = standardized selection differential, σₚ = phenotypic standard deviation.

🎯 The breeder's equation

Formula: R = ih²σₚ

What it shows

• Selection response depends on three factors:
  1. Selection intensity (i): proportion of population selected (lower % selected → higher i).
  2. Heritability (h²): proportion of phenotypic variance due to additive genetic effects.
  3. Phenotypic variability (σₚ): amount of variation present in the population.

Selection intensity examples

% selected	Standardized selection differential (i)
0.01%	3.959
1%	2.665
5%	2.063
10%	1.755
25%	1.271
50%	0.798

Maximizing response

• Start with high trait expression.
• Maximize heritability through proper testing.
• Apply high selection intensity (but beware diminishing returns and increased variability of response).

🎯 Variability of response

Formula: CV(R) depends on n (number of lines), p (proportion selected), h², and i.

Examples showing trade-offs

• n=1000, p=0.01, h²=0.2, i=3.959 → CV=39%
• n=100, p=0.01, h²=0.2, i=3.959 → CV=124% (smaller starting population increases variability)
• n=1000, p=0.01, h²=0.7, i=3.959 → CV=8% (higher heritability reduces variability)
• n=1000, p=5%, h²=0.7, i=2.063 → CV=2% (less intense selection reduces variability)

Lesson: Balance expected response (desirable) with variability of response (undesirable).

🎯 Practical strategies

Maximizing genetic standard deviation

• Cross diverse parents to increase genetic variance.
• Trade-off: Diverse crosses may have lower mean than elite × elite crosses.
• Most cultivar development programs use best × best or at least 75% elite (e.g., (best × exotic) × best).

Optimizing selection intensity

• Can increase by selecting fewer lines (but increases response variability).
• Better: test more units but select fewer (requires more resources).
• Don't compromise on proper trait measurement protocols—this lowers correlation between phenotype and genotype (lowers h).

Expected genetic gain formula

• ΔG = (ic h² σₐ) / y
• Adds parental control (c) and years per cycle (y) to the basic equation.

Ways to increase genetic gain

Increase numerator:

• Increase genetic variance (larger populations, diverse but mostly elite parents).
• Increase selection intensity (without genetic drift).
• Increase parental control (c=1 for self-pollinated; c=0.5 if male gametes from unselected; c=2.0 if selected seed of selected genotypes used).

Decrease denominator:

• Decrease seasons per cycle (y): use off-season nurseries, greenhouses, or marker-assisted selection.
• Decrease phenotypic variance: increase locations and replications (locations more effective than replications).
• Use proper experimental designs (augmented designs, moving means, incomplete lattice, RCBD).

Different progeny types

• Theoretical proportion of additive variance to total genotypic variance:
  • Half-sib: 0.25
  • Full-sib: 0.5
  • S₁ progenies: 1.0

🎯 Reducing environmental effects

Recommendations to increase heritability

1. Use best quality land (uniform, highly productive).
2. Use best management practices (recommended fertilizer, irrigation, rotation, planting time, weeding, harvesting).
3. Avoid pest/pathogen control if naturally present (provides another selection trait).
4. Use check cultivars frequently (better handle on variability).
5. Use appropriate statistical designs (lattice, RCBD, augmented designs).
6. Use replication (improves precision) and randomization (improves accuracy).

🎨 Multiple trait selection strategies

🎨 Tandem selection

• Select sequentially for each trait in successive generations.
• Improve population first for one trait, then next trait, and so on.
• Disadvantages: Long selection cycle; potential reduction in first trait selected.
• Generally not followed in commercial plant breeding.

🎨 Independent culling (truncation selection)

• Most common strategy deployed by breeders worldwide.
• Selection practiced successively in the same generation.
• Discard all individuals failing to meet desired level for one trait, regardless of other trait values.
• Repeat for second trait, then continue until all selections made.
• Experienced breeders may allow relaxation for major traits when culling for less important traits.
• Issue: Each successive cull reduces population size and genetic variability.

🎨 Index selection

• Simultaneous selection for every trait in the same generation.
• Index based on combination of heritability and economic value of each trait.
• Each line receives an index score based on trait expression and trait weight.
• Most breeders use "mental" index selection (overall assessment of multiple traits, then keep or discard).
• Example: In space-planted nursery, mentally assess height, seed fill, plant health, lodging, inflorescence.
• More sophisticated methods exist (Pesek-Baker index) but require variance and covariance estimation.
• Using economic weights is a good compromise.

🔗 Combining ability and heterosis

🔗 General and specific combining ability

General Combining Ability (GCA): the average performance of a line in hybrid combinations, expressed as deviation from the overall mean of crosses.

Specific Combining Ability (SCA): instances where hybrid performance is better or poorer than expected based on average performance of parent lines; the deviation from expected value.

Key distinctions

Aspect	GCA	SCA
Definition	Average performance across all crosses	Performance in specific combination
Genetic basis	Additive effects (and additive×additive interactions)	Non-additive effects (dominance and epistasis)
Importance	More important for unselected lines; important for synthetics	More important for previously selected lines; important for hybrids
Calculation	Deviation of parent mean from population mean	Deviation of specific cross from expected value (sum of parental GCAs)

Historical finding (Sprague and Tatum, 1942)

• For unselected inbred lines: GCA relatively more important than SCA.
• For previously selected lines: SCA more important than GCA.

🔗 Calculation examples

GCA calculation

• GCA of parent A = (mean of all crosses with A) – (overall mean of all crosses)
• In a diallel: GCA = [Total of crosses with parent / (n-2)] – [Grand total / n(n-2)]
• Where n = number of parents.

SCA calculation

• Expected value of cross A×B = GCA_A + GCA_B + overall mean
• SCA_AB = Observed value of A×B – Expected value of A×B

Example interpretation

• If GCA_A = -7.2 and GCA_B = 2.1, with overall mean = 91.4:
• Expected A×B = -7.2 + 2.1 + 91.4 = 86.3
• If observed A×B = 91, then SCA_AB = 91 – 86.3 = 4.7 (positive SCA indicates better than expected performance)

🔗 Heterosis

Heterosis: the superior performance of crosses relative to their parents.

Mid-parent heterosis

• Difference between hybrid and mean of two parents.
• Formula: Heterosis = μ_hybrid – μ_mid-parent

High-parent heterosis

• Superiority of hybrid over the better parent.

Genetic basis

• Dependent on presence of dominance.
• Dependent on summation of allele frequency differences across loci.
• Important in maize and other cross-pollinated crops for heterotic group identification and exploitation.

🧭 Overview

🧠 One-sentence thesis

Cultivar development follows specific, sequential (or parallel) steps tailored to the crop's mode of propagation—clonal, self-pollinated, or cross-pollinated—to ensure breeding objectives are met efficiently and the resulting cultivars meet producer, processor, and consumer needs.

📌 Key points (3–5)

• Cultivar types differ by propagation and genetics: clonal cultivars are heterozygous and homogeneous (maintained vegetatively); pure-line cultivars (self-pollinated) are homozygous and homogeneous; hybrids and synthetics (cross-pollinated) are heterozygous and vary in homogeneity.
• Four-step framework applies broadly: (1) define objectives, (2) form genetic base / create segregating populations, (3) perform selection, (4) conduct trials and seed multiplication.
• Clonal crops face unique challenges: maintaining disease-free stock (especially viruses) is critical; micropropagation and tissue culture are used for rapid, clean multiplication; somaclonal variation can arise but is not always desirable.
• Common confusion—pure lines vs inbred lines: pure lines (self-pollinated crops) are released as cultivars; inbred lines (cross-pollinated crops) suffer inbreeding depression and are used only as parents for hybrids or synthetics, not for direct commercial planting.
• Hybrid systems require special mechanisms: cytoplasmic male sterility (CMS), environmental-sensitive male sterility (two-line systems), or detasseling enable economical hybrid seed production; heterosis must justify the cost of hybrid seed production.

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🌱 Clonal (asexually propagated) cultivars

🧬 What clones are

Clone: genetically identical copies of a genotype, produced by asexual (vegetative) propagation.

• A population of clones is homogeneous (all identical) but each individual is highly heterozygous.
• Heterosis is fixed indefinitely as long as vegetative propagation continues.
• Clones can result from inter-generic or inter-specific crosses, even if the hybrid is sterile, because sexual reproduction is not needed.

🦠 Disease management challenge

• Viruses and other pathogens transmit through vegetative parts, so keeping parental lines and breeding stocks disease-free is essential.
• Detection methods:
  • Serological (e.g., ELISA)
  • Nucleic acid-based (e.g., Real Time-PCR)
• Elimination methods:
  • Tissue culture from terminal growing points (often pathogen-free)
  • Heat treatment (longer for viruses)
  • Chemical surface sterilization
  • Use of apomictic seed (if available)
• Example: virus-indexing in potato uses meristem tissue culture to produce disease-free plantlets.

🧪 Micropropagation and somaclonal variation

• Micropropagation: culturing apical shoots, axillary buds, or meristems on sterile nutrient medium to rapidly produce clones year-round in small space.
• Somaclonal variation (SV): genetically stable variation arising from tissue culture; can expand germplasm diversity but may also cause unwanted changes.
  • Example of success: aluminum tolerance in rice.
  • SV is characterized by chimerism (tissue mosaicism)—an individual has two or more genetically different cell types, maintained only by vegetative propagation (not transferred sexually).
• Don't confuse: SV is mitotic variation, not meiotic; it does not pass to sexual progeny.

🔄 Five-step development process

1. Selection and maintenance of stock plants for culture initiation.
2. Initiation and establishment of culture from an explant (e.g., shoot tip) on suitable nutrient medium.
3. Multiple shoot formation from the cultured explant.
4. Rooting of in vitro developed shoots.
5. Transplanting and hardening (acclimatization) before field planting.

🌾 Examples of clonal cultivars

• Crops: potato, cassava, sweet potato, banana, sugarcane, many ornamentals and fruit trees.
• Vegetative tissues used: tubers, stem cuttings, rhizomes, bulbs.

🌿 Apomixis (special case)

Apomixis: formation of seeds without meiosis.

• Two forms:
  1. Gametophytic apomixis: asexual embryo from unfertilized egg.
  2. Adventitious embryony: asexual embryo from nucellus tissue.
• Seeds are genetically identical to the parent.
• Breeding strategy: population improvement by sexual reproduction, then variety development by apomixis.
• Example: Kentucky bluegrass.

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🌾 Pure-line cultivars (self-pollinated crops)

🧬 What pure lines are

Pure line: homogeneous and homozygous cultivar developed in self-pollinating species, maintained indefinitely by selfing.

• Don't confuse with inbred lines: inbred lines are developed in cross-pollinated species through forced inbreeding, suffer inbreeding depression, and are used only as parents for hybrids or synthetics—not released to farmers.
• Pure lines can be maintained by natural selfing; inbred lines require artificial selfing or sib-mating each generation.

📋 Four-step development framework

🎯 Step 1: Define objectives

• Objectives must be clearly defined and biologically feasible.
• Consider:
  • Needs of producer, processor, and consumer (visit farms, attend meetings, read industry news).
  • Available resources (disease nurseries, marker labs, crossing facilities).
• Clear objectives enable strategic decisions: parent choice, breeding method, selection strategy, traits to select and when.

🧬 Step 2: Form genetic base (choose parents)

• Parent sources:
  • Advanced lines from own or other breeding programs
  • Released cultivars
  • Germplasm from gene banks or pre-breeding programs
  • Introductions from other countries
  • Mutant lines or populations
  • Wild relatives (if crossable or embryo rescue available)
• Crops with long breeding history rely on elite lines and cultivars; crops with less breeding rely on populations and introductions.
• All desired traits must be present in the parents; selection is based on reliable, complete data (yield, adaptation, stress, quality).
• Cross configuration:
  • Two pure-lines → F₁ is heterozygous and homogeneous.
  • Three-way cross → F₁ is heterozygous and heterogeneous, requiring larger F₁ population.
• Debate: fewer crosses with large populations per cross vs. many crosses with smaller populations. Witcombe and Virk (2001) suggest fewer, carefully chosen crosses with large populations increase probability of recovering superior genotypes.

🔬 Step 3: Perform selection

• When to start: as early as F₂ (generation of maximum variability); minimum population size to observe desirable types is lowest in F₂.
• Selection in each generation eliminates undesirable types and enriches desirable ones.
• Molecular markers: if tightly linked to trait (or on the gene) and robust, markers enable confident early selection (not influenced by environment).
  • Example: eliminate homozygous recessive genotypes for a trait controlled by recessive gene—these will never segregate to give the dominant allele.
• Early generations (F₂–F₄):
  • Select for high to moderate heritability traits (plant type, branching, disease reaction).
  • Grow in selection environment similar to target region or representative of target environments.
  • Eliminate controllable variation (weeds, non-uniform land, animal damage, uneven chemical application).
  • Single replication yield plots may be used with statistical approaches (running mean, partial rep, augmented designs) if resources are limited.
• Later generations (F₄–F₆ or F₈):
  • More detailed evaluation, multi-location testing, replication.
  • Select for lower heritability traits (yield, end-use quality).
  • Techniques requiring small samples (e.g., NIRS) can be used in earlier generations for quality traits.

🧪 Step 4: Conduct trials and seed multiplication

• Final stages: lines are pure (non-segregating).
• Extensive testing of few best recombinants: agronomic performance, end-use quality, adaptation, stability.
• Multi-environment testing (locations × years).
• Designs: lattice (incomplete block if many entries) or RCBD.
• Detailed observations on more traits (fewer lines allow more detailed assessment).
• Proactive seed multiplication: initiate alongside advanced yield testing to ensure sufficient certified seed for timely launch.
• Doubled haploid (DH): steps 3 and 4 are closely aligned; once DH is generated, lines go directly into multi-location replicated testing (if seed quantity permits).

🌾 Examples of self-pollinated crops

• Common bean, soybean, cowpea, groundnut, rice, wheat, barley, millet, sorghum.

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🌻 Synthetic cultivars (cross-pollinated crops)

🧬 What synthetics are

Synthetic cultivar: mixture of heterogeneous and heterozygous individuals derived from parental lines (clones or inbreds) assessed for general combining ability and crossed in a polycross configuration.

• Parental lines are maintained so synthetics can be re-constituted when needed.
• S₀: seed from polycross nursery.
• S₁: produced by intermating S₀ plants; maximum heterosis observed here; can be sold as synthetic cultivar in asexually propagated crops (e.g., alfalfa).
• S₂, S₃, S₄: in annual crops (e.g., maize), progression from Breeder Seed → Foundation Seed → Certified Seed.
• Don't confuse with open-pollinated variety (OPV): OPV is developed by mass selection without preliminary combining ability testing; equivalent to a landrace. Synthetics have known, tested parents in predetermined configuration; OPV does not.

🌾 When synthetics are preferred

• Crops that show heterosis but hybrid production is difficult or uneconomical.
• Synthetics have hybrid vigor and produce usable seed for succeeding seasons.
• Examples: forage crops (alfalfa), some maize in developing countries.

🔄 Four-step development framework

1. Define objectives (same principles as pure-line breeding).
2. Assemble parental lines: from previous synthetic, experimental populations, clones (forages), or inbred lines (maize).
3. Selection and polycross:
   • Grow clones in source nursery (space-planted grid) to reduce environmental variance.
   • Select for high heritability traits (disease, morphology).
   • Grow superior clones in polycross nursery to facilitate random or equal pollination among clones.
   • Harvest seed equally per clone per replication.
   • In perennials, clones may be grown multiple years with seed harvest each year.
4. Progeny testing: test polycross seed in performance trials (multiple locations, replications, years).
   • Identify superior clones based on progeny performance.
   • Cross superior clones to produce the synthetic.
   • Syn1 or Syn2 released in forages; in maize, 2–3 more pollination rounds needed for sufficient commercial seed.

🔬 Selection methods in synthetics

• Half-sib selection: widely used in perennial forages; polycross mating generates half-sib families from selected clones; families evaluated in replicated rows for 2–3 years; effective for high heritability traits (e.g., oil, protein in maize).
  • Half-sib: common but unknown pollen parent; female identifiable; less effective for low heritability traits.
• Full-sib mating: crossing pairs of plants; control exerted on both male and female parents.
• Recurrent selection methods:
  1. Simple recurrent selection (mass selection): phenotypic selection alone, no progeny testing.
  2. Recurrent selection for general combining ability: wide genetic base cultivar (population) as tester; half-sib progeny test; selections based on test cross progeny performance.
  3. Recurrent selection for specific combining ability: narrow genetic base line (inbred) as tester; half-sib progeny test; selections based on test cross progeny performance.
  4. Reciprocal recurrent selection: two heterozygous populations, each serves as tester for the other; exploits both general and specific combining ability.

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🌽 Hybrid cultivars (cross-pollinated crops)

🧬 What hybrids are

Hybrid cultivar: F₁ offspring of a planned cross between inbred lines, cultivars, clones, or populations.

• Types: single cross (A × B), three-way cross ((A × B) × C), double cross ((A × B) × (C × D)).
• Absolute requirements:
  1. Superior performance over parents (heterosis).
  2. Economical hybrid seed production.
• Example success story: hybrid maize in USA (replaced open-pollinated varieties by 1930s).
• Advantages: higher yield, improved stalk lodging tolerance, improved drought response.

🌾 Hybrid seed production mechanisms

🌽 Detasseling (maize)

• Configuration of male and female rows.
• Female rows detasseled; seed collected only from female rows.
• Male rows destroyed post-pollination to prevent contamination.
• Male must: be good combiner (high SCA), produce good pollen, flower synchronously with female (good nicking).

🧬 Cytoplasmic male sterility (CMS)

CMS: plants with sterile cytoplasm plus nuclear non-restorer genes are male sterile; plants with sterile cytoplasm plus nuclear restorer genes produce fertile pollen.

• Plants with normal cytoplasm are male fertile regardless of nuclear genes.
• Fertility restoration not needed if vegetative part is of economic value.
• Useful in field crops (wheat, barley, rye, sunflower, grain sorghum) where hand emasculation is too expensive.

🌾 Three-line system (e.g., hybrid rice in China)

• A line (male sterile line): CMS controlled by cytoplasm and nucleus; used as female in hybrid seed production.
• B line (maintainer line): pollinator to maintain male sterility; has viable pollen, sets normal seed.
• R line (restorer line): restores fertility in F₁ when crossed to CMS line.
• History: research initiated 1964, commercialization started 1976, area exceeded 10 million ha by 1987.

🌾 Two-line system (e.g., hybrid rice)

• Male sterile line: nuclear gene(s) and environmental conditions (photoperiod and/or temperature) control male sterility.
  • Types: EGMS, PGMS, TGMS, PTGMS.
• R line (restorer line): any cultivar that restores fertility in F₁.
• Advantages over three-line:
  1. Simpler (no maintainer needed).
  2. More applicable in diverse genetic backgrounds, easier to implement.
  3. Reduced cost of breeding and seed production.
  4. No detrimental CMS effects.
• Disadvantage: dependency on environmental conditions; requires environments with consistent temperature and day length at critical growth times.

🌽 Hybrid maize cultivar development

🔄 Four-step framework

1. Develop inbred lines.
2. Make crosses to produce hybrids.
3. Test hybrids.
4. Develop seed for commercial production.

🧬 Inbred line development

• Traditional method: inbreeding selected heterozygous plants until sufficient homozygosity without severe inbreeding depression; sib-mating may be used.
• Doubled haploid (DH) technology: provides 100% genetic homozygosity in one generation; minimizes inbreeding depression; better response to marker-assisted selection; significantly reduces time.
  • Haploids carry single copy of every gene; deleterious genes have immediate effects, quickly eliminated.
  • Only one round of recombination → minimizes breakage of desirable linkages but also reduces chances to break undesirable linkages → larger population sizes may be useful.
• Sources of inbred lines: historically OPVs; now advanced lines from breeding programs, recurrent selection programs (public), or crosses within heterotic groups (private).

🧬 Heterotic groups (North America example)

• Inbred lines classified into heterotic groups (e.g., Stiff Stalk and Non-Stiff Stalk).
• Modern hybrids result from crossing lines from different heterotic groups.
• Classification based on: pedigree, molecular markers, performance in hybrid combinations.
• Conventional inbred development: crosses within a heterotic group; testers from different heterotic groups used during population advancement.

🔬 Pedigree method (most common in North America)

• Two-parent cross (parents from same heterotic group):
  • Form F₂ population.
  • Several rounds of inbreeding using ear-to-row (each family traces to different F₂ plant).
  • Eliminate genotypes with obvious defects during inbreeding.
• Early generation testing (around F₃ or F₄):
  • Form topcross hybrids between F₄ lines and inbred from contrasting heterotic group.
  • Cross made in off-season nursery.
  • Test topcross hybrids in summer in 2+ environments.
  • Select based on yield, lodging, maturity, test weight, height, other traits.
  • Advance inbred lines through another round of inbreeding in same season.
• Lines producing merit hybrids (similar or better than commercial checks) advanced through another round of breeding and crossing.
• Superior inbreds forwarded to hybrid development teams for commercial testing with specific testers in more environments.

🧪 Hybrid commercialization

• Early testing phase: more hybrid combinations in fewer environments.
• Later testing phases: fewer hybrid combinations in more environments.
• Testing involves more locations, fewer replications → more vigorous evaluation for adaptation.
• Requirements for good parents:
  • Female: vigorous, produces high quality healthy seed.
  • Male: produces abundant, good quality pollen.
• Tester choice: from complementary heterotic group, maximizes variance among test crosses, possesses high mean.

🌾 Practical considerations for hybrid systems

1. Field crops (wheat, barley, rye, sunflower, grain sorghum): large seed amounts needed, low return per unit area → expensive hand emasculation not preferred; CMS useful.
2. Pollination: must be field-scale (wind or bees); males shed abundant pollen, females receptive, synchronous flowering.
3. Female inbred: generally more productive, higher seed production capacity.
4. Male and female: superior specific combining ability, distinct (different heterotic groups or origins, e.g., stiff stalk vs. non-stiff stalk in maize; indica vs. japonica in rice).
5. Heterosis expression: must be sufficient to overcome development and seed production costs.
   • Example: wheat heterosis insufficient; floral morphology prevents easy pollination.

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🌾 Multi-line and blend cultivars (self-pollinated crops)

🧬 Multi-line cultivars

Multi-line: set of isolines (traditionally created by backcrossing or transformation) that differ for one or more traits, grown as a mixture in self-pollinating crops.

• Used to control prevailing pathogens (e.g., multi-line wheat with different rust resistance genes).
• Theoretically provides better protection against pathogen races, prevents total crop loss.
• Pure lines are phenotypically uniform for morphological and agronomic traits (height, maturity, photoperiod) plus genetic resistance to specific disease (or other trait, e.g., abiotic stress).
• Backcrossing develops isogenic lines, then combined in predetermined ratio.

🧬 Blend (composite) cultivars

Blend: mixture of different genotypes with greater genetic distance than multi-line components.

• Multi-line = closely related isolines; blend = different types of cultivars.
• Two strategies:
  1. Minimize differences in maturity, growth habit, lodging, disease resistance → uniformity.
  2. Pick phenotypically different blends to maintain certain percentages (if intention is diversity).
• Example: WB Seed Company provides commercial examples.

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🌱 Special considerations for clonal crops (cassava example)

🧬 Biological seed vs. vegetative cuttings

• Biological (botanical) seed: F₁ obtained from crossing.
• Vegetative (clonal) parts: plant parts from F₁ for further testing; identical to F₁ plant.
• Several cuttings from single F₁ are identical to each other and to F₁; cuttings from different F₁ plants are dissimilar.
• Root systems differ considerably between plants from biological seed and vegetative cuttings → low correlation for traits like starch content.
• Solution: germinate biological seed, then transplant → develops root system similar to vegetative cuttings.

🌾 Cutting source and performance

• Area of plant used for cutting influences performance.
• Example (cassava): mid-section cuttings perform better than top or bottom.
• Variation in physiological status of cutting → larger experimental errors.
• Consistency in vegetative cutting is important to remove unwanted error.
• Breeders must know number of cuttings per plant (constraint for multi-location trials).

🌾 Crossing block and selection timeline (cassava example)

• Crossing block can be in field over a year (cassava: up to 18 months for flowering synchronization).
• Average 1–2 seeds per directed cross.
• Year 3: first selection in nurseries with plants from botanical seed.
• Select only for high heritability traits (plant type, branching, disease reaction) due to low correlation between individual plant and yield plot performance.
• Reduce population by 60–80% using visual assessment (spray paint, tags).
• From ~100,000 F₁ plants → 2,000–3,000 clones for clonal evaluation trials (6–10 plants per clone from vegetative cuttings).

🌾 Plot considerations

• Ensure equal plot size (length, width) to avoid bias.
• Use GPS planter, trimmer, or careful pre-planting measurements.
• Inter-plot competition: increase row distance, reduce plant-plant distance, or leave empty row between plots → increases within-genotype competition, reduces between-genotype competition.
• Divide fields into smaller blocks; conduct selection within block with commercial/elite checks regularly across field.
• Record all trait data to assess within-family and among-family performance; indicates parent quality.

🌾 Trait assessment and advancement

• Clonal evaluation trials: un-replicated single row; select for intermediate to lower heritability traits (root/tuber dry matter).
• Clones advance through stages: clonal evaluation → preliminary yield tests → advanced yield tests → regional tests.
• Number of entries reduces at each stage; vigor of testing increases (locations, replication, traits).
• Processing and consumer preference (end-use quality) tested only on most advanced material (expensive, cumbersome).
• Start stock multiplication for commercial planting while evaluating most promising material.
• PYT and AYT stages: testing at more locations more beneficial than more replications; 2–3 replications per entry suffice.

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📊 Summary table: cultivar types and characteristics

Cultivar type	Heterozygosity	Homogeneity	Propagation	Crop examples
Clonal	Heterozygous	Homogeneous	Asexual (vegetative)	Potato, cassava, banana, sugarcane
Pure-line	Homozygous	Homogeneous	Sexual (selfing)	Wheat, rice, soybean, common bean
Inbred line	Homozygous	Homogeneous	Sexual (forced selfing/sib-mating)	Maize (as parents, not for commercial planting)
Synthetic	Heterozygous	Heterogeneous	Sexual (open pollination of selected parents)	Alfalfa, some maize
Hybrid (single cross)	Heterozygous	Homogeneous	Sexual (controlled cross)	Maize, rice, sunflower, sorghum
Hybrid (three-way, double cross)	Heterozygous	Heterogeneous	Sexual (controlled cross)	Maize
Multi-line	Homozygous (each line)	Homogeneous (each line)	Sexual (selfing); mixture of isolines	Wheat (rust resistance)
Blend	Homozygous (each line)	Variable (mixture of cultivars)	Sexual (selfing); mixture of cultivars	Various self-pollinated crops

🧭 Overview

🧠 One-sentence thesis

Different breeding strategies are deployed to maximize genetic superiority per unit cost and time, with method choice depending on the crop's mating system (self-pollinated, cross-pollinated, or clonal), available resources, and breeding objectives.

📌 Key points (3–5)

• Method selection depends on mating system: self-pollinated crops use pedigree/bulk/SSD/doubled haploid methods to develop pure-line cultivars; cross-pollinated crops use recurrent selection or hybrid development; clonal crops exploit fixed heterosis through vegetative propagation.
• Trade-offs between methods: pedigree allows early selection and record-keeping but is resource-intensive; bulk relies on natural selection and is low-cost; SSD/doubled haploid rapidly achieve homozygosity but require specialized facilities or conditions.
• Innovations enhance efficiency: marker-assisted backcrossing reduces linkage drag and accelerates genome recovery; early generation testing eliminates inferior lines before homozygosity; doubled haploid achieves true homozygosity in one generation.
• Common confusion—recurrent selection types: phenotypic recurrent selection evaluates individual plants directly; genotypic recurrent selection evaluates progeny performance (combining ability); mass selection may or may not control pollen source.
• Hybrid vs open-pollinated cultivars: hybrids exploit heterosis but require annual seed purchase; open-pollinated varieties (OPVs) and synthetics allow seed recycling but yield less and show inbreeding depression over generations.

🌾 Methods for self-pollinated crops

🧬 Pedigree method

The pedigree method involves selection on individual plants in early generations for highly heritable traits, with yield testing conducted once homozygous lines are developed.

• How it works: Select individual F₂ plants → grow F₃ rows → select within and among rows → advance through F₄, F₅, F₆ until homogenous → bulk harvest and yield test.
• Record-keeping: Pedigree information is maintained to track family performance, allowing breeders to select more plants from superior families or advance entire families for yield testing.
• Modified pedigree: Early generation testing (EGT) starts yield trials in F₃ or F₄ while within-family selection continues, allowing elimination of inferior lines earlier.
• Example: A breeder selects 100 F₂ plants, grows them as F₃ rows, selects the best 30 rows and 2–3 plants per row, advances to F₄ yield plots, and repeats until F₆ lines are homozygous and ready for multi-location testing.
• Don't confuse: Pedigree tracks individual plant ancestry; bulk does not track individuals within populations.

🌾 Bulk method

Bulk method allows natural selection to remove undesirable genotypes by advancing entire populations (per cross) to homozygosity through bulks, with artificial selection applied only after homozygosity.

• How it works: F₂ population → bulk harvest and plant F₃ → repeat bulking through F₅ or F₆ → select individual plants from homozygous bulk → yield test selected lines.
• Natural selection: The growing environment dictates which traits are selected for or against; disease or stress nurseries can be used to select for specific traits.
• Low cost and technical demand: No individual plant tracking; entire population seed is harvested and replanted (or a subsample).
• Modified bulk: Single plants or inflorescences are selected at each generation, or markers are used to select for desirable traits within bulks.
• Example: A breeder plants 10,000 F₂ seeds, harvests all seed in bulk, plants F₃ bulk in a disease nursery to allow natural selection against susceptible plants, repeats through F₅, then selects 200 individual plants for yield testing.

🌱 Single seed descent (SSD)

Single seed descent rapidly advances lines to homozygosity by planting one seed per plant (or 2–3 in modified SSD) in successive generations, deferring selection until lines are homozygous.

• Purpose: Maintain large population size to preserve F₂ genetic variation; reduce time to develop cultivars by completing 2–3 generations per year in controlled environments (greenhouse).
• How it works: F₂ → collect one seed per plant → F₃ → one seed per plant → repeat to F₅ or F₆ → yield test homozygous lines.
• Modified SSD: Plant 2–3 seeds per hill, collect 2–3 seeds per hill to reduce population loss from poor germination.
• No record-keeping: Individual plants are not tracked during advancement; selection is deferred until homozygosity.
• Example: A small-grain breeder plants 300 F₂ seeds in a greenhouse, collects one seed per plant, plants F₃ in a second greenhouse cycle, repeats for F₄ and F₅ in 18 months, then yield-tests 250 homozygous F₅ lines.
• Don't confuse: SSD defers selection; pedigree selects in early generations.

🧪 Doubled haploid (DH)

Doubled haploids are created by generating haploid plants from microspores (androgenesis) or unfertilized eggs (gynogenesis), then doubling chromosome number with colchicine to produce homozygous diploid plants in a single generation.

• True homozygosity: DH genotypes are completely homozygous; only one generation of meiosis occurs (at F₁).
• Speed: Can advance to yield trials in season 3 if sufficient seed is available; fastest method to develop cultivars.
• Requirements: Specialized lab or service provider; large population size is critical because only one meiotic generation occurs.
• Suitability: Ideal for marker-assisted breeding to select for fixed traits; becoming preferred for maize inbred line development.
• Example: A breeder crosses two elite lines, generates 500 DH lines from F₁ microspores, selects 100 DH lines with target markers, and enters them into yield trials in the third season.
• Not applicable to legumes: Legume crops are recalcitrant to tissue culture and haploid induction/rescue.

🔄 Backcross breeding and innovations

🎯 Backcross method

Backcross breeding introgresses a single gene (or 2–3 genes) from a donor parent into an elite cultivar (recurrent parent) by repeatedly crossing to the recurrent parent, recovering the majority of the recurrent parent genome while retaining the target gene.

• When to use: Transferring disease resistance, herbicide tolerance, or other qualitative traits into an adapted cultivar.
• How it works: Cross donor (rr) × recurrent (RR) → F₁ (Rr) → backcross to recurrent → select Rr individuals → repeat 5–6 backcrosses → self to fix rr.
• Recessive genes: If the target gene is recessive, F₁ must be selfed to identify Rr types before the next backcross (or use markers to identify Rr without selfing).
• Linkage drag: Undesirable genes linked to the target gene may be inadvertently transferred, especially from unadapted or related species; larger populations and recombinant selection are needed.
• Example: A breeder wants to add a recessive disease resistance gene from a wild relative into an elite soybean line; after 6 backcrosses and marker-assisted selection for recombinants, the new line has >99% recurrent parent genome plus the resistance gene.

🧬 Marker-assisted backcrossing innovations

Three types of marker selection accelerate backcross breeding:

Selection type	Purpose	How it helps
Target gene/QTL selection	Screen for the target trait	Useful for recessive alleles or traits with laborious phenotyping
Recombinant selection	Select progeny with target gene and flanking markers	Minimizes linkage drag by identifying recombinants near the target
Background selection	Select against donor genome with background markers	Accelerates recovery of recurrent parent genome

• Marker-assisted recurrent selection (MARS): One generation of phenotypic selection in target environment → markers predict individual plant performance → several generations of marker-only selection in year-round nursery.
• Comparison: Conventional backcrossing requires 6 backcrosses over 12+ seasons; marker-assisted backcrossing can achieve the same genome recovery in 3–4 backcrosses over 6–8 seasons.

📊 Early generation testing (EGT)

Early generation testing selects superior lines or families before homozygosity by yield-testing segregating (F₃ or F₄) plots, allowing elimination of inferior materials earlier.

• Two uses: (1) Yield-test individual lines in early generations (modified pedigree); (2) yield-test early-generation bulks to remove entire inferior populations.
• Trade-off: Requires more resources (replicated plots, multiple locations) but eliminates inferior lines before investing in later-generation testing.
• Lower heritability traits: EGT allows selection for traits like yield that have low heritability at the individual plant level.
• Example: A breeder plants 500 F₃ lines in 2-row yield plots at 3 locations, discards the lowest-yielding 300 lines, and advances only 200 lines to F₄ for continued selection.

🌽 Methods for cross-pollinated crops

🔁 Recurrent selection overview

Recurrent selection improves the mean performance of a population while maintaining genetic variability by selecting and inter-mating superior individuals over indefinite cycles, increasing the frequency of desirable genes.

• Goal: Improve population mean; maintain variability for continued selection.
• Used for: Open-pollinated varieties (OPVs) and synthetics in cross-pollinated species (e.g., maize).
• Cycle: Select individuals → evaluate → inter-mate selected individuals → next cycle.
• Don't confuse mass vs phenotypic recurrent selection: Mass selection uses unselected and selected pollen; phenotypic recurrent selection controls both male and female parents (expected genetic gain is doubled).

🌾 Phenotypic vs genotypic recurrent selection

Aspect	Phenotypic recurrent selection	Genotypic recurrent selection
Basis	Phenotype of the individual plant	Progeny performance (combining ability)
Evaluation	Individual plants assessed directly	Progeny tested in replicated, multi-location trials
Environmental control	Difficult; micro-environment variability limits accuracy	Replication provides accurate breeding value
Suitable traits	High heritability (flowering time, morphology, disease resistance)	Lower heritability (yield, combining ability)

• Phenotypic recurrent selection problems: Micro-environment variability, competition effects from uneven planting, missing neighbors.
• Solutions: Gridding designs (select within grids); avoid selecting plants with missing neighbors.

🧬 Recurrent half-sib selection

An intra-population improvement method where individuals are crossed to a common tester (population or inbred line), half-sib progeny are evaluated, and the best individuals are intercrossed.

• How it works: Season 1—cross individuals to tester, divide seed into Part 1 (testing) and Part 2 (remnant) → Season 2—evaluate half-sib families in replicated trials → Season 3—intercross remnant seed of selected families.
• Tester choice: Population per se (bulk seed) or inbred line; inbred tester provides more precise combining ability estimates.
• Parental control: Controlling both parents (male and female) increases genetic gain per year but requires an extra season to evaluate and recombine.
• Example: A maize breeder self-pollinates 200 plants, uses pollen from each to pollinate a tester, evaluates 200 half-sib families for yield, selects the top 30 families, and intercrosses their selfed progeny to form the next cycle.

🧬 Recurrent full-sib selection

Full-sib families are created by pairwise crosses, evaluated in field tests, and the best families are intercrossed using remnant seed.

• Cycle: Season 1—make paired crosses, divide seed into Part 1 (testing) and Part 2 (remnant) → Season 2—evaluate full-sib families → Season 3—intercross selected families using Part 2 seed.
• Advantage: One cycle per year.
• Disadvantage: Less recombination between cycles compared to half-sib or selfed family methods.
• Example: A breeder makes 100 pairwise crosses, evaluates full-sib families at 3 locations, selects the top 20 families, and intercrosses them to start cycle 2.

🧬 Recurrent selection among selfed families

S₀ plants are selfed to produce S₀:₁ lines, selfed progenies are evaluated, and remnant S₁ seed from selected lines is intercrossed.

• Cycle: Season 1—self S₀ plants → Season 2—evaluate S₀:₁ lines → Season 3—intercross remnant S₁ seed of selected lines.
• Variation: More than one generation of selfing can be used if more seed is needed for evaluation.
• Example: A breeder selfs 300 S₀ plants, evaluates 300 S₀:₁ lines for disease resistance and yield, selects 50 superior lines, and intercrosses their S₁ seed.

🔄 Reciprocal recurrent selection (RRS)

RRS improves both general and specific combining ability of two populations simultaneously by mating plants from one population to a tester from the other population, selecting based on hybrid progeny performance, and intercrossing selected individuals within each population.

• Purpose: Exploit both additive and dominance genetic effects.
• How it works: Population #1 plants are selfed and outcrossed to Population #2 as tester; Population #2 plants are selfed and outcrossed to Population #1 as tester → evaluate testcross progenies → select superior plants based on testcross performance → intercross selfed seed of selected plants within each population.
• Cycle length: One generation for selection, one generation for intermating.
• Example: A breeder maintains two maize heterotic groups; plants from Group A are testcrossed to Group B, plants from Group B are testcrossed to Group A; the top 30 plants in each group (based on testcross yield) are intercrossed within their group to form the next cycle.

🌱 Hybrid and clonal cultivar methods

🌽 Hybrid cultivar development

Hybrids are produced by crossing inbred lines from dissimilar heterotic groups; inbred lines are developed within heterotic groups and evaluated for specific combining ability by crossing to testers from other groups.

• Process: Develop inbred lines within heterotic group (using pedigree, SSD, DH, etc.) → cross to testers from other heterotic groups → evaluate hundreds or thousands of hybrids → release the most superior hybrid(s).
• Hybrid seed production: Plant 6–8 female inbred rows interspersed with 1–2 male inbred rows → de-tassel female rows before pollen shed → harvest cobs from female rows (these are the hybrid seed).
• De-tasseling: Manual or mechanical removal of male inflorescences from female plants to prevent selfing; male rows are often destroyed after pollination to avoid contamination.
• Example: A company crosses 50 elite inbreds from Heterotic Group A with 50 inbreds from Heterotic Group B, evaluates 2,500 hybrids over 3 years, and releases 5 hybrids targeted to different maturity zones.

🌾 Open-pollinated varieties (OPVs) and synthetics

OPVs are developed using recurrent selection; synthetics are formed by mixing clones or inbred lines in predetermined proportions and allowing random pollination.

OPV advantages and disadvantages:

Advantages	Disadvantages
Seed can be recycled (if grown in isolation or middle field harvested)	Yields lower than hybrids
Broader adaptability than hybrids	Not competitive in fertile, high-input areas
Less costly; may require fewer inputs	Plants less uniform
More accessible where hybrids unavailable or seed channels poor	Yield reduction over generations due to inbreeding depression

• Synthetics: Formed from clones or inbred lines chosen for general combining ability; farmers can use for several generations but must eventually obtain reconstituted seed from breeder to avoid inbreeding depression.
• Example: A breeder creates a maize synthetic by mixing equal seed amounts from 8 inbred lines with high general combining ability; farmers plant the synthetic, harvest seed from the middle of the field (to reduce outcrossing), and replant for 2–3 generations before purchasing new seed.

🌿 Clonal cultivar methods

Clonal crops exploit fixed heterosis by propagating F₁ hybrids vegetatively; each F₁ from a cross is unique, and selection identifies superior clones for release.

• Advantages: (1) Heterosis is fixed in F₁ and preserved through vegetative propagation; (2) farmers can harvest and use vegetative parts to grow the next crop (e.g., potato tubers, sugarcane stalks, cassava stems).
• Breeding process: Cross two clones → generate large F₁ population (each F₁ is unique) → screen F₁ clones over multiple cycles → select superior clone for release.
• Simultaneous testing: Since clones breed true, a single clone can be evaluated in multiple tests simultaneously (yield trials, disease nurseries, etc.).
• Step-wise reduction: Each season, undesirable clones are discarded; remaining clones are propagated for more extensive testing.
• Example (sugarcane cultivar CP 03-1912): 2000—cross made; 2002—100,000 true seed transplanted; 2003—15,000 advanced to stage 1; 2004–2006—successive culling (≈10% per season) through stages 2, 3, 4 at multiple locations; 2011—one clone released as cultivar.

🌾 Cytoplasmic male sterility (CMS) systems

CMS systems are used to produce hybrids in crops with some outcrossing (rice, sorghum, cotton); breeders develop 'B-lines' (maintainers) and 'R-lines' (restorers) using self-pollinated breeding methods, then cross 'A-lines' (male-sterile) with 'R-lines' to produce hybrid seed.

• Gene pools: 'S' and 'F' genes are in the cytoplasm; 'R' and 'r' genes are in the nucleus.
• Hybrid seed production: Cross A-line (male-sterile) × R-line (restorer) → F₁ hybrid seed is fertile and sold to farmers.
• B-line development: Use backcross method to develop A-lines (male-sterile) from available CMS genes.
• Separate gene pools: A/B and R gene pools are maintained as separate reproductive pools, analogous to heterotic groups in maize.
• Example: A sorghum breeder develops a new R-line with improved drought tolerance using pedigree method, crosses it to an elite A-line, and evaluates the hybrid for yield and male fertility restoration.

🧩 Key distinctions and common confusions

🧩 Pedigree vs bulk vs SSD

• Pedigree: Select individuals in early generations; track family records; resource-intensive.
• Bulk: Defer selection until homozygosity; natural selection acts; low cost; no individual tracking.
• SSD: Defer selection until homozygosity; rapid advancement; maintain large population; no individual tracking.
• Don't confuse: Pedigree and modified pedigree (with EGT) select early; bulk and SSD defer selection.

🧩 Phenotypic vs genotypic recurrent selection

• Phenotypic: Evaluate individual plants directly; suitable for high-heritability traits; environmental variability is a problem.
• Genotypic: Evaluate progeny performance (half-sib, full-sib, or selfed families); suitable for low-heritability traits; more accurate breeding value.
• Don't confuse: Mass selection (may or may not control pollen) vs phenotypic recurrent selection (controls both parents).

🧩 Hybrids vs OPVs vs synthetics

• Hybrids: Exploit heterosis; highest yield; uniform; require annual seed purchase; narrow adaptation.
• OPVs: Developed by recurrent selection; seed can be recycled; lower yield; broader adaptation; inbreeding depression over generations.
• Synthetics: Formed from inbred lines; seed can be recycled for a few generations; intermediate yield; must be reconstituted by breeder to avoid inbreeding depression.
• Don't confuse: OPVs are populations improved by recurrent selection; synthetics are mixtures of specific inbred lines or clones.

🧩 Backcross vs recurrent selection

• Backcross: Introgress one or a few genes into an elite cultivar; recover recurrent parent genome; used for qualitative traits.
• Recurrent selection: Improve population mean for quantitative traits; maintain variability; used for open-pollinated varieties.
• Don't confuse: Backcross aims to preserve the recurrent parent; recurrent selection aims to improve the population.

🧭 Overview

🧠 One-sentence thesis

Participatory plant breeding (PPB) and participatory variety selection (PVS) emerged as alternative breeding approaches that involve farmers and other stakeholders throughout the breeding process to better serve resource-poor farmers in marginal, high-stress environments where conventional breeding has often failed to meet their needs.

📌 Key points (3–5)

• Why PPB emerged: Formal/conventional breeding programs benefit farmers with good environments or resources to modify conditions, but often fail farmers in marginal soils and high-stress conditions with limited resources.
• What makes it "participatory": Different actors (scientists, farmers, consumers, extension agents, cooperatives, vendors, traders, processors, government and non-government organizations) have significant research roles in all major breeding stages.
• Two main approaches: Formal-led PPB (initiated and managed by research institutions) vs. Farmer-led PPB (scientists support farmer-controlled breeding systems).
• Common confusion—PPB vs. PVS: PPB involves farmers throughout the breeding cycle from setting objectives to selection; PVS is a continuation where farmers test finished or near-finished cultivars on their own fields, usually at the end of the process.
• Key outcomes: Faster cultivar release (3–4 years vs. longer conventional timelines), higher adoption rates, better adaptation to marginal environments, and enhanced farmer knowledge and biodiversity.

🌾 Why participatory breeding was needed

🌾 Limitations of conventional breeding

Formal or conventional plant breeding programs (centralized breeding programs) are designed to meet specific requirements of different groups of farmers in different growing environments.

• Conventional programs have been more beneficial to farmers who either:
  • Have good crop growing environments, or
  • Can modify environments through additional inputs (fertilizer, pesticides, irrigation).
• The gap: Results may not meet requirements of farmers growing crops under marginal soils and high-stress environmental conditions.

🎯 Target contexts for PPB

PPB is implemented in areas where:

• Technology transfer or adoption of modern cultivars is low (farmers not comfortable taking risks to replace traditional varieties).
• Modern cultivars are not available.
• Low yield potential, high stress (drought), and heterogeneous environments exist.
• Resources and modern technologies are limited (mainly developing countries, remote regions).

Example: A farmer in a drought-prone region with degraded soil cannot afford fertilizer and irrigation; conventional high-yielding varieties bred for optimal conditions fail in this environment, so PPB addresses this gap by breeding directly in the target environment with farmer input.

🤝 Categories and types of participation

🤝 Two main PPB categories

Category	Who leads	Description
Formal-led PPB	Research institutions (NARS, IARC)	Farmers are asked to join activities initiated, managed, and executed by formal breeding programs
Farmer-led PPB	Farmers	Scientists/development workers support farmer-controlled, managed, and executed breeding systems; scientists support varietal selection and seed systems

🔄 Five types of participation (from least to most farmer control)

1. Conventional: No farmer participation.
2. Consultative: Farmers consulted at every stage but breeder makes decisions; farmers participate in joint selections with breeder in breeders' plots on station.
3. Collaborative: Decisions made jointly by farmer and breeder; two-way communication; both must agree to change joint decisions; usually effective for self-pollinated crops.
4. Collegial participation: Farmers grow genotypes in their fields and make their own selections (group or individual); organized communication with breeder; farmers voluntarily supply seeds of selected genotypes to breeder for further evaluation and multiplication.
5. Farmer experimentation: Breeders do not participate in selection or research activities; farmers make own decisions without organized communication with breeders.

Don't confuse: The type chosen depends on resources available and crop type—collaborative participation is more easily done for self-pollinated species.

🎯 Goals, stages, and requirements

🎯 Three main goals of PPB

1. Increase production and productivity in non-commercial crops in unpredictable environments under abiotic/biotic stress.
2. Enhance biodiversity and germplasm access to local farmers (especially disadvantaged groups like women and poor farmers); makes breeding cost-effective and output-oriented through decentralization addressing more niches.
3. Increase farmer skills to speed up farmer selection and seed production efforts.

📋 Diagnostic survey (first activity)

Before starting PPB, a diagnostic survey enables effective discussion between breeders and farmers and helps breeders understand:

• Agricultural problems of local farming conditions
• Farmers' crop management practices
• Farmers' specific needs and preferences

🔢 Five stages of participation in PPB process

1. Set breeding objectives/targets: Begins from participatory rural appraisal.
2. Generate genetic variability: Access from local landraces or collections for testing with complementary characteristics.
3. Determine approach: Choose consultative/collaborative based on resources and crop type; select among segregating populations.
4. Evaluate cultivar and cull: Discard inferior genotypes (this is PVS if farmer is involved in genotype selection).
5. Collaborate with seed system: Cultivar release, popularization, diffusion, seed multiplication, and distribution.

✅ Essential requirements for success

• Local farmers must be interested in active participation during breeding/selection.
• Breeders and farmers must collaborate at each stage.
• Better chance of success if:
  • Locally adapted parents are used in crosses for PPB
  • Selection of superior genotypes is made in local environments
  • Cultivars selected by farmers have traits important to farmers

👨‍🌾 Farmer roles and contributions

👨‍🌾 Six key farmer roles

1. Technical leadership: Test cultivars in specific environmental niches; contribute knowledge and experiences.
2. Organization: Organize farmer research groups.
3. Information provision: Provide information on cultivar preferences and important traits to maintain or introduce to existing landraces.
4. Skill building: Involved through farmer-farmer interactions.
5. Genetic material: Provide their landraces or genetic materials for further breeding work.
6. Resources: Provide land for testing PPB genotypes.

Example: A farmer group provides local drought-tolerant landrace seeds, tests new crosses on their fields, shares observations about which lines perform best under local drought conditions, and teaches neighboring farmers about the new varieties.

📈 Outcomes and impacts

📈 Five major possible outcomes

1. Production gain: Significant gains through increased yield, increased stability, faster uptake of released cultivars, wider diffusion, better identification of farmer-preferred quality traits (taste, ease of processing).
2. Biodiversity enhancement: Farmer communities get more access to different germplasm, more information and knowledge, increased inter- and intra-cultivar diversity.
3. Cost-efficiency and effectiveness: Selection time is short (cultivars identified in 3–4 years); reduces research cost; released cultivars disseminate faster, less expensive diffusion.
4. Farmer knowledge and capacity enhancement: Facilitates development of more PPB lines, gain in extensive experience, increased agricultural knowledge dissemination (including agronomic practices).
5. Farmers' needs met: Increased farmer satisfaction; broader range of users reached (women, men, elders, young).

🌟 Four key impacts of PPB

1. Higher adoption rate of PPB products (new cultivars, agronomic and crop protection practices).
2. Improved cultivars acceptable by farmers for highly stressed marginal areas.
3. Immediate adoption and yield increase in remote areas of developing countries where soil is degraded and drought is a major problem.
4. Significant changes in cultivar release procedure and seed multiplication system: Time from testing to release is shorter than conventional breeding.

⏱️ Timeline comparison (beans example)

According to Figure 2 in the excerpt:

• PPB system involves fewer years for selection to next cycle or variety release compared to conventional system.
• This demonstrates the cost-efficiency outcome mentioned above.

Don't confuse: Faster release does not mean lower quality—it means selection happens in the target environment with farmer input from the start, eliminating mismatches between breeder priorities and farmer needs.

🌱 Participatory Variety Selection (PVS)

🌱 What PVS is

Participatory variety selection (PVS) is an approach where selection of finished or near-finished cultivars is made by the farmer on her/his own fields.

• Finished products/genotypes include: Released cultivars, advanced stage cultivars, advanced non-segregating lines (self-pollinated crops), or advanced populations (cross-pollinated crops).
• PVS is generally a continuation of PPB; once potential cultivars are identified through PPB, farmers test them using PVS.
• Farmers usually participate at the end of the cyclical process.

🔍 Three phases of PVS

1. Clear identification of farmers' needs.
2. Search for suitable advanced lines or cultivars to test in farmers' conditions.
3. Implementing the experiment on farmers' own fields and dissemination of preferred cultivars.

🎯 Four importance points of PVS

1. Provide access to local farmers' choice of large number of cultivars; increase crop diversity.
2. Increase production and productivity to ensure food security.
3. Speed up dissemination and enhance adoption of pre-released and released cultivars in diversified environments.
4. Enable cultivar selection in targeted environmental niches in short period with less cost.

Don't confuse PVS with PPB: PVS involves research and extension methods to deploy genotypes (promising advanced lines/released cultivars) on farmers' fields, whereas PPB involves farmers throughout the entire breeding cycle from crossing to selection. PVS tests nearly finished products; PPB creates them with farmer input from the start.

🧭 Overview

🧠 One-sentence thesis

Common bean (Phaseolus vulgaris) breeding programs use diverse germplasm from two major domestication centers and multiple breeding methods to develop improved cultivars that address both biotic and abiotic production constraints while meeting market demands for specific seed types.

📌 Key points (3–5)

• Two domestication centers: Common bean was domesticated independently in the Andean and Middle American regions, creating distinct gene pools that form the basis of modern breeding programs.
• Multiple classification systems: Beans are classified by utilization (snap, green shell, dry), seed characteristics (color, size, shape), growth habit (bush vs. climbing), and maturity duration.
• Production constraints are both biotic and abiotic: Fungal diseases and pests cause significant losses, but abiotic stresses (drought, heat, soil fertility problems) are the major constraints in tropical regions.
• Common confusion—photoperiod sensitivity: Most bean cultivars are short-day plants (flower when nights are long), but day-neutral types also exist; photoperiod effects increase with temperature, so both factors interact.
• CIAT coordinates global improvement: The International Center for Tropical Agriculture leads bean breeding efforts worldwide, focusing on disease resistance, abiotic stress tolerance, and priority market classes.

🌍 Origin and genetic diversity

🗺️ Domestication centers

• Common bean was domesticated in two major centers: Andean region and Middle America (Mexico and Central America).
• The wild ancestor (Phaseolus vulgaris L.) grows as a viny herbaceous annual from northern Mexico to northern Argentina.
• This dual domestication created genetically distinct populations that breeders now use as complementary sources of variation.

🧬 Gene pool structure

Bean gene pools: Four wild bean gene pools exist, centered in (1) Middle America, (2) Colombia, (3) Western Ecuador and Northern Peru, and (4) the southern Andes.

• The cultivated bean gene pool derives mainly from the southern Andean and Middle American wild gene pools.
• DNA marker analysis (AFLP) revealed this structure, showing that domestication drew from geographically separated wild populations.
• Don't confuse: Wild gene pools (four centers) vs. domesticated gene pools (primarily two sources).

🎨 Race differentiation

• Within the major gene pools, beans are divided into different races based on:
  • Plant morphology
  • Adaptation range
  • Agronomic traits
  • Seed characteristics (size, shape, color)
• Example: Andean beans typically have larger seeds than Middle American types.

🌱 Biology and development

📅 Growth phases and stages

Two main phases:

• Vegetative phase: From seed germination to first floral buds (determinate types) or first racemes (indeterminate types).
• Reproductive phase: From first floral buds/racemes to maturity.

Key difference by growth habit:

• Indeterminate types: Continue producing vegetative structures (leaves, branches, stem) even after flowering begins—can have flowers and pods simultaneously.
• Determinate types: Vegetative phase ends completely when floral buds appear.

Four growth stage groups:

1. Emergence & Early Vegetative Growth (VE, VC, V1-V3)
2. Branching & Rapid Vegetative Growth (V4-Vn)
3. Flowering & Pod Formation (R1-R4)
4. Pod Fill & Maturation (R5-RH)

☀️ Photosynthesis pathway

C3 photosynthetic pathway: Maximum leaf photosynthetic rates range from 12 to 35 mg CO₂ per square decimeter per hour at ambient CO₂ concentrations.

• This is lower than soybean photosynthetic rates.
• Recent measurements show relatively high rates, possibly due to improved measurement techniques.

🌡️ Photoperiod and temperature responses

Photoperiod sensitivity:

• Most common bean cultivars show a short-day response for flowering (flower when night length exceeds their critical photoperiod).
• Day-neutral genotypes also exist but are less common.
• Large-seeded and highland germplasm tend to be more photoperiod-sensitive.

Temperature interactions:

• Photoperiod effects on phenology increase with temperature.
• Higher temperatures cause greater overall rate of growth and development.
• Both factors have strong effects on growth and development.
• Inheritance is controlled by few major genes.

📊 Classification systems

🍽️ By utilization

Type	Harvest stage	Consumption form
Green/snap beans	Immature pods	Fresh or processed pods
Green shell/fresh beans	Full-sized immature seeds	Fresh seeds
Dry beans	Mature seeds	Dried ripe seeds

🎨 By seed characteristics

• Most commonly used classification system for dry beans.
• Seed size: Ranges from 17 grams per 100 seeds (navy beans) to 100 grams per 100 seeds (Faba beans).
• Seed shape: Round, oblong, kidney-shaped, and many combinations.
• Color: Rainbow array of colors and patterns with varying brilliance.
• Surface texture: Shiny (brilliant), opaque, or intermediate.

🌿 By growth habit

Three categories:

• Bush beans: Determinate, dwarf growth.
• Semi-climbing beans: Intermediate habit.
• Climbing beans: Very vigorous, indeterminate.

⏱️ By maturity duration

• Varieties grouped as early or late.
• Range varies by region and growth habit: 60 to 300 days to maturity.
• Difference is both varietal (genetic) and environmental (especially day-length and temperature).

🌍 Adaptation and importance

🗺️ Geographic adaptation

• Widely cultivated in tropical and subtropical areas worldwide.
• Grows in latitudes between 52°N to 32°S.
• Adapted to humid tropics, semi-arid tropics, and cold climatic regions.
• Short-day tropical crop requiring 300-600 mm precipitation to complete life cycle (depending on soil, climate, cultivar).

Optimal conditions:

• Temperature: 21-24°C during growing season.
• Soil pH: 6.3-6.7.

🌾 Production statistics

• World production: approximately 27.7 million tons (FAO, 2021).
• Latin America: Largest producing region.
• Top three producers in western hemisphere: Brazil, Mexico, USA.
• Africa: Production concentrated in eastern and southern highlands (Ethiopia to South Africa); Kenya is largest producer.
• Mostly dryland production (rainfall-dependent), with smaller area under irrigation.

🍲 Nutritional role

Protein and mineral source: Common bean provides approximately 25% protein content plus important minerals (especially iron) and fiber.

• Provides protein and fiber to more than 100 million people in Africa.
• Plant protein is the largest protein source for poor people in developing countries.
• Consumed mainly as mature grain; also immature seeds, young pods, and leaves in some regions (sub-Saharan Africa, Latin America).

🌾 Cropping systems

In Africa:

• Traditionally grown by smallholder farmers.
• East and Central Africa: 23% monocropped, 77% intercropped with maize, sorghum, bananas, or other crops.
• Southern Africa: 53% monocropped, 47% intercropped.

Benefits in rotation:

• Breaks disease and pest cycles associated with cereals.
• Range of growth habits (determinate bush to vigorous climbers) and growth cycles (3-10 months) allows beans to fit many production niches.

🌱 Nitrogen fixation benefits

Atmospheric nitrogen fixation: Climbing beans can fix 16-42 kg per hectare of atmospheric nitrogen per season, which can be increased with good agronomic practices.

Documented benefits:

• East Africa: Sorghum yield improvements of 40-57% when grown in rotation with climbing beans.
• Eastern Central Africa: Cereal crop yields increased by 25-40% after climbing beans.
• Critical for smallholder farmers who cannot afford inorganic fertilizers or lack animals for manure.
• Improves soil health and maintains soil fertility.

⚠️ Production constraints

🦠 Biotic constraints

Fungal diseases (universal constraints):

• Widely distributed: Anthracnose, rust, angular leaf spot.
• Locally intense: Rhizoctonia web blight (warm-moist environments), ascochyta blight.
• Emerging problem: Root rots caused by Pythium spp. and Fusarium spp.

Insect pests (occasional problems):

• Central America: Bean pod weevil (Apion godmani and A. aurichalceum) is most important.
• East Africa: Bean stem maggot, aphids, and pod borers cause serious problems.

🌡️ Abiotic constraints

Major constraint: Abiotic stress is the major constraint to bean productivity in most tropical countries.

Key abiotic stresses:

• Drought (extreme limited water stress): Causes yield loss in Mexico, Brazil, Central America, Eastern and Southern Africa.
• Heat stress: Adversely affects cultivation in Central and Southern America and Africa.
• Nutrient deficiencies: Phosphorous (P) and nitrogen (N) reduce yield.
• Soil toxicity: Aluminum and Manganese toxicity associated with acid soil; low Calcium availability.

Comparison table:

Limitation	Frequency	Intensity	Risk to farmers
Pests and diseases	+++	+++	++++
Drought	++	++++	++
Low soil fertility	+++++	+++	+
High temperatures	+++++	+++	+

(Scale: + = very low; +++++ = very high)

Key insight: While pests and diseases are frequent and intense, abiotic stresses (especially high temperatures and low soil fertility) are more frequent but pose lower risk to farmers because they are more predictable.

🏛️ International breeding infrastructure

🌐 CIAT's role and mission

International Center for Tropical Agriculture (CIAT): Established in Cali, Colombia, in 1971 under the CGIAR system with the mandate to work on common bean.

Primary mission: Contribute to global food security by making bean production more profitable for small-scale farmers in Africa, Latin America, and the Caribbean.

Coordination function:

• Coordinates all common bean research programs at the national level.
• Strong collaborative breeding programs throughout the tropics of the Americas and Africa.
• Interchanges improved germplasm among countries.

🎯 Breeding focus areas

Historical achievements:

• Successfully developed varieties with genetic resistance to major diseases and pests, minimizing yield losses.

Recent focus:

• Breeding for improved tolerance to abiotic stresses (drought and soil problems).
• Gained significance due to more erratic climatic conditions changing patterns and intensity of both abiotic and biotic stresses.
• Strategy focuses on priority bean grain (market class) types.

🔬 Tools and approaches

Supporting broad goals through:

• Biodiversity exploitation: More than 35,000 accessions in CIAT collection.
• Biotechnology: Particularly marker-assisted selection.
• Gene discovery: Advanced molecular tools.

Network structure:

• CIAT outlines technical contributions and responsibilities for regional centers:
  • ECABREN: East and Central Africa Bean Research Network
  • SABREN: South African Bean Research Network
• Also coordinates with national bean breeding programs, universities, and advanced research institutions.

🧬 Breeding methods and strategies

🌾 Common breeding methods

Self-pollinating crop: Common bean is autogamous, so breeding methods follow those applied to other self-pollinating crops.

Methods used (in order of frequency):

Method	Use case	Notes
Pedigree selection	General improvement	Most commonly used system
Back cross	Highly heritable traits	Usually single gene control
Inbred back cross	Trait introgression	1-2 backcrosses followed by selfing
Congruity back crossing	Maintaining heterozygosity	Alternate crossing to each parent
Recurrent selection	Population improvement	Cyclical improvement
Single seed descent	Elite line development	Among closely related elite lines
Gamete selection	Multiple parent crosses	Individual F₁ plants give rise to families

🏗️ Three-tiered breeding strategy

Purpose: Accommodate gene exchange between distantly related parents and achieve integrated genetic improvement.

Structure (from the breeding pyramid):

• Tier 1 (Base): Wide crosses between gene pools to create genetic diversity.
• Tier 2 (Middle): Selection and evaluation in target environments.
• Tier 3 (Top): Elite line development and cultivar release.

General breeding steps:

1. Define breeding objectives
2. Select parents
3. Make crosses
4. Generate segregating populations
5. Select in early generations
6. Evaluate advanced lines
7. Conduct multi-location trials
8. Release cultivars

🎯 Integrated improvement approach

Key principle: Success requires integrating:

• Gene exchange between distantly related parents (Andean × Middle American crosses)
• Selection for multiple traits simultaneously (disease resistance, abiotic stress tolerance, seed quality)
• Evaluation across diverse target environments
• Collaboration between international centers, regional networks, and national programs

Don't confuse: Simple pedigree selection (within one gene pool) vs. integrated improvement (deliberately crossing gene pools to combine complementary traits).

🧭 Overview

🧠 One-sentence thesis

Cowpea breeding programs worldwide focus on developing high-yielding, stress-resistant cultivars through conventional methods (bulk, backcross, pedigree) and increasingly through marker-assisted selection, with success depending on integrating farmer, consumer, and market preferences alongside agronomic performance.

📌 Key points (3–5)

• What cowpea is: A warm-season legume (2n=22) ranked second after groundnut, grown globally for food and feed, with 25% protein content and vital for food security.
• Breeding objectives: Higher grain yield, improved quality, resistance to biotic stresses (insects, diseases, parasitic weeds, nematodes) and abiotic stresses (drought, heat, low phosphorus).
• Methods used: Primarily bulk, backcross, and pedigree breeding for pure-line cultivars; self-pollinating crop with up to 5% outcrossing.
• Common confusion: Agronomic excellence alone does not guarantee adoption—varieties must satisfy farmers' production needs, consumers' taste/quality preferences, and market standards (seed size, color) simultaneously.
• Key institutions: IITA (International Institute of Tropical Agriculture) holds the global mandate and the world's largest germplasm collection (>15,000 cultivated + 560 wild accessions).

🌱 Biology and classification

🌱 Botanical characteristics

• Family: Leguminosae (Vigna unguiculata L. Walp., 2n=2x=22).
• Appearance: Annual herbaceous plant similar to common bean but with darker green, shinier, rarely pubescent leaves.
• Growth habit: Ranges from erect/semi-erect to prostrate (trailing) or climbing; indeterminate to determinate (most accessions are indeterminate).
• Root system: Strong taproot reaching up to 95 inches depth after 8 weeks.
• Flowers and pods: Borne on long peduncles (15–30 cm), a unique feature among legumes facilitating hand harvest; typically 2–3 pods per peduncle (up to 4+ under favorable conditions).
• Seeds: Smooth or wrinkled, diverse colors (white, cream, yellow, red, brown, black), often with a marked hilum and dark arc ("eye bean" types like blackeye).

🌍 Domestication and diversity

• Origin: Domesticated in Southern Africa, later spread to East/West Africa and Asia; wild relatives found throughout Africa.
• Five cultivar groups (Baudoin and Marechal, 1985):
  1. Unguiculata: Major group; thick, shiny seed testa.
  2. Textilis: Long inflorescence peduncle; mostly West Africa.
  3. Sesquipedalis: Fleshy pod, wrinkled when ripe; mainly East Africa.
  4. Melanophthalmus: Thin, often wrinkled testa; flower and seed partly white; West Africa origin.
  5. Biflora: Thick, shiny testa; flower and seed often colored; Southeast Asia.

📊 Classification systems

Classification basis	Categories	Notes
Utilization	Food (leaves, immature pods, seeds, dried seeds), feed (forage, hay, silage), green manure, cover crop	Dual-purpose varieties provide both grain and fodder
Seed characteristics	Size (150–300 g/1000 seeds), shape (kidney or globular), color (white, cream, green, buff, red, brown, black, speckled, mottled)	Large seed size important for productivity and market quality
Growth habit	Erect to semi-erect, prostrate (trailing), climbing; indeterminate to determinate	Non-vining types tend to be more determinate
Maturity duration	Early (55 days), medium, late (up to 240 days)	Varies by variety and environment (photoperiod, temperature)

☀️ Photosynthesis and environmental responses

• Photosynthetic pathway: C3 (like other grain legumes).
• Photoperiod: Short-day plant; genotypes range from day-neutral to photoperiod-sensitive (delay in flowering varies).
• Temperature: Warmer temperatures speed flowering in both sensitive and insensitive genotypes; optimum 20–35°C.
• Flowering: Initiation ranges 30–90 days after planting; physiological maturity 55–240 days.
• Adaptation significance: Understanding photoperiod and temperature responses helps breeders match genotypes to specific environments (e.g., pod ripening timed to escape excessive rainfall/disease).

Don't confuse: Photoperiod sensitivity is not a defect—it allows adaptation to local climates by timing reproduction to favorable conditions.

🌍 Adaptation and economic importance

🌍 Geographic distribution and production

• Cultivation zones: Tropics and subtropics (35°N to 30°S) across Africa, Asia, Oceania, Middle East, Southern Europe, Southern USA, Central and South America.
• Climate requirements: Hot and dry tropical conditions; drought-tolerant compared to other legumes; 400–700 mm annual precipitation; soil pH 5.5–8.3.
• Soil preference: Wide range of textures, but prefers sandy soil; low salt tolerance, somewhat tolerant to aluminum; sensitive to waterlogging and chilling.
• Global production: ~14 million ha planted annually; ~6 million MT total production; average yield ~0.45 tonnes/ha (FAOSTAT, 2010).
• Major producers: Nigeria and Niger dominate (4+ million ha each; 45% and 15% of world production respectively); also Brazil, Haiti, India, Myanmar, Sri Lanka, Australia, USA.

🍽️ Nutritional and cropping value

• Nutrition: 25% protein, rich in tryptophan (compared to cereals), several vitamins, minerals, fibers; low fat content.
• Uses at all growth stages: Young leaves, immature pods, immature seeds, dried seeds (Africa); stems/leaves/vines as animal feed.
• Cropping systems: Major component of traditional intercropping in Africa, Asia, Central/South America; common mixtures include millet-cowpea (22% of fields in Sudan savanna, Nigeria), sorghum-cowpea (10%), millet-cowpea-groundnut (8%).
• Intercropping trade-offs: Grain yield lower than sole crop due to low plant population, shading, nutrient competition.
• Soil benefits: Used as green manure (nitrogen provision to subsequent crops), erosion control, weed suppression.

Example: A farmer in the Sudan savanna might plant millet-cowpea mixture to obtain both cereal grain and legume protein/fodder while improving soil nitrogen for the next season.

⚠️ Production constraints

🐛 Biotic constraints

• Insect pests: Aphids (main pest; vectors of cowpea mosaic virus), flower thrips, pod borers.
• Diseases: Fungal (Cercospora leaf spot, ashy stem blight), bacterial (bacterial blight), viral (blackeye cowpea mosaic polyvirus BICMV, cowpea mosaic comovirus).
• Parasitic weeds: Striga and Alectra (attach to cowpea roots, tap nutrients; major problem in Tanzania and Malawi).
• Nematodes: Root damage causing significant yield loss (e.g., root-knot nematodes Meloidogyne incognita, M. javanica).

🌡️ Abiotic constraints

• Extreme drought and heat.
• Soil acidity.
• Low phosphorus availability.

Don't confuse: Cowpea is drought-tolerant compared to other legumes, but extreme drought still limits yield.

🏛️ International breeding centers and strategy

🏛️ IITA's global mandate

• Role: International Institute of Tropical Agriculture has global mandate for cowpea improvement; develops and distributes improved varieties to >65 national programs in Africa.
• Regional centers: Additional scientists/breeding centers in Philippines, Nigeria, Burkina Faso, Cameroon, Congo, Brazil to address regional constraints.
• Germplasm collection: World's largest and most diverse—>15,000 cultivated varieties from >100 countries + 560 wild cowpea accessions.

🎯 Breeding strategy

• Target traits: Diverse maturity (extra early 60–70 days, medium 75–90 days), non-photosensitive, plant type, growth habit, seed types, combined resistance to biotic and abiotic stresses, quality (fodder and grain).
• Identified genes: Plant architecture, physiological traits (root architecture, photosensitivity, nitrogen fixation), quality, abiotic stress (heat, drought), biotic stress (bacterial/fungal/viral diseases, nematodes, aphids, bruchid, thrips, parasitic weeds).
• Flexibility: Varieties suitable for sole crop or intercrop in multiple cropping systems.

🧬 Breeding methods and strategies

🧬 Genetic and reproductive system

• Chromosome number: 2n = 2x = 22 (true diploid).
• Mating system: Primarily self-pollinating (autogamous); up to 5% outcrossing possible (insect-mediated pollen transfer).
• Cultivar type: Most farmer-grown cultivars are pure lines.

🛠️ Breeding methods

• Primary methods: Bulk, backcross, and pedigree breeding (used by IITA and national programs).
• Why these methods: Suitable for handling large segregating populations in a self-pollinating crop.
• Primary objective: Higher grain yield and improved grain quality.
• Secondary objectives: Wide range of abiotic and biotic stress resistance.

🎯 Breeding program focus

• Maturity classes: Extra early (60–70 days) and medium (75–90 days).
• Photoperiod: Non-photosensitive lines for broad adaptation.
• Dual purpose: Good grain quality + possibility for dual-purpose use (grain or fodder).
• Cropping system fit: Suitable for sole crop or intercrop.

Don't confuse: "Pure line" means genetically uniform (homozygous), not that the crop never outcrosses—cowpea is predominantly self-pollinating but occasional outcrossing occurs.

📋 Example cultivar development: CB27

📋 CB27 development process (University of California Riverside, 1989–1999)

• Released: 1999.
• Target characteristics:
  1. High yielding.
  2. Reproductive-stage heat tolerance.
  3. Broad-based Fusarium wilt resistance (races 3 and 4).
  4. Broad-based root-knot nematode resistance (non-aggressive and aggressive M. incognita, M. javanica).
  5. Semi-dwarf, less vegetative shoot biomass.
  6. Bright white seed coat.
  7. Good seed weight.
  8. Non-leaky pigments during boiling, excellent canning quality.

🔬 Trial progression (1989–1998)

• 1989: Preliminary Blackeye Trials (PYT) at Kearney Agricultural Center (KAC)—selected lines H8-14, H8-9, H8-8, H8-7, H8-4 from cross 336 x 1393 (heat-tolerant origin).
• 1990–1992: Advanced Blackeye Trials (AYT) at UCR and KAC—evaluated yield, seed weight, seed density, lodging, earliness, vigor under single and double flush management.
• 1992: Heat tolerance screening in hot glasshouse (34/30°C day/night); H8-9 showed 92% podding (best), H8-8 70%, H8-14 57%.
• 1992: Nematode resistance screening—H8-8 sublines tested for association between heat tolerance and root-knot nematode resistance (non-aggressive M. incognita).
• 1993: Screening for resistance to aggressive M. incognita and M. javanica; H8-8 sublines (e.g., H8-8-6, H8-8-13, H8-8-15, H8-8-16, H8-8-27, H8-8-35) showed resistance to both non-aggressive and aggressive strains.
• 1993: Heat tolerance confirmed in hot glasshouse and Coachella Valley; H8-8 sublines produced flowers and pods, while checks CB5 and CB46 did not.
• 1994–1996: Advanced and Uniform Yield Trials (UYT) at multiple locations (KAC, UCR, Shafter, Stanislaus, Tulare, Westside)—H8-8-27 and H8-8-15 consistently high-yielding.
• 1996: Field trials in nematode-infested fields (KAC, Muller Farm-Chance Field)—H8-8-27 and H8-8-15 showed resistance to Rk gene-virulent strains of M. javanica and M. incognita, plus Fusarium wilt races 3 and 4.
• 1997: Strip trial near Wasco, CA—H8-8-27 had lower total damage (2.0%) and higher grade (UN No. 1) than CB46 (4.2% damage, US No. 3).
• 1998: Uniform trials—H8-8-27 yielded 4466 lb/ac (mean across 4 locations) vs. CB46 4271 lb/ac; similar seed weight (~23 g/100 seeds); lower % split seedcoat (13% vs. 18%).
• 1999: Final performance summary—CB27 (H8-8-27) superior to checks CB5 and CB46 for Fusarium wilt (races 3 and 4), root-knot nematodes (avirulent and virulent M. incognita, M. javanica), heat tolerance, and chill tolerance.

📊 Key data insights

• Yield stability: H8-8-27 performed well across years (1989–1998) and locations (KAC, UCR, Shafter, Stanislaus, Tulare, Westside).
• Seed weight: Maintained good seed weight (206–247 mg/seed across trials; ~22–24 g/100 seeds in later trials).
• Harvest index: H8-9 had highest harvest index (51%) in 1991 UCR trial, indicating efficient conversion of biomass to grain.
• Plant type: H8-8-27 classified as medium growth habit, medium-large plant size, low to medium vinyness, lower Pythium incidence than checks.

Example: In 1996, H8-8-27 yielded 21.0 cwt/ac in a field infested with Rk gene-virulent M. javanica and M. incognita (Muller Farm), while CB88 (lacking broad nematode resistance) yielded only 10.2 cwt/ac—demonstrating the value of stacking multiple resistance genes.

🤝 Participatory varietal selection and market-led breeding

🤝 Participatory approach example (Burkina Faso, IITA)

• Released varieties: IT99K-573-2-1 and IT98K-205-8.
• Selection process: Local farmers and researchers chose varieties from multiple options after 2 years of trials in central and northern Burkina Faso.
• Selected traits: Early maturing (60 days), high yielding (2170 kg/ha), resistant to parasitic weed Striga, big seed size, preferred color, cooking qualities matching farmers' taste.
• Climate adaptation: Better adaptability to climate change; can grow in drier regions with low rainfall.

📊 Trait importance (Tanzania and Malawi example)

• Farmer priorities (from participatory market-led breeding study):
  • Agronomic traits (6 traits): High yield, early maturity, resistance to Alectra, resistance to diseases, tolerance to pests, drought tolerance.
  • Consumer/market traits (5 traits): Brown seed color, white seed color, good taste, large seed, many leaves, tender leaves.
• Most important trait: Large seed size (marketing perspective).
• Key agronomic traits: High yield, early maturity, resistance to Alectra vogelii (parasitic weed causing considerable damage in Tanzania and Malawi).

🔄 Value chain approach (pathway to cultivar release)

• Problem solved: Past varieties with excellent agronomic traits failed because they did not satisfy farmers, consumers, and market preferences simultaneously.
• Solution: Integrate preferences of all stakeholders (farmers, consumers, market) from the start.
• Example cultivar: IT99K-573-2-1 developed using this approach.

Alectra vogelii: A parasitic weed that attaches to cowpea plants and taps nutrients, causing considerable damage; major problem in Tanzania and Malawi cowpea-growing areas.

Don't confuse: "Farmer preference" vs. "consumer preference"—farmers prioritize agronomic traits (yield, maturity, disease resistance) for production, while consumers prioritize quality traits (seed size, color, taste) for consumption and market value.

🧬 Marker-assisted selection (MAS)

🧬 Current status and future

• Development stage: MAS approaches being developed; high-density marker maps and SNP markers becoming available.
• Investment: Increasing as cowpea gains global acreage.
• Genetic mapping: Loci controlling important pest/disease resistance genes and agronomic traits placed on genetic map (e.g., Kelly et al., 2003).
• Linked markers: Closely linked markers to some biotic traits identified (Gowda et al., 2002).
• Good MAS candidates: Traits governed by major genes (simply inherited).
• Future potential: Genomic selection approach offers usefulness for complex traits.

🤝 Collaborative efforts

• Partners: IITA, Bean/Cowpea Collaborative Research Support Program (Bean/Cowpea CRSP), advanced laboratories (USA, Australia), African Agricultural Technology Foundation (AATF), Network for Genetic Improvement of Cowpea for Africa (NGICA), Monsanto Corporation.
• Goal: Exploit biotechnology tools to complement conventional breeding for improving disease and insect resistance.

Example: A breeder could use MAS to select for Fusarium wilt resistance (race 4) and root-knot nematode resistance simultaneously in early generations, reducing the need for extensive field screening and accelerating cultivar development.

🧭 Overview

🧠 One-sentence thesis

Pearl millet breeding has evolved from simple selection to hybrid development using cytoplasmic-nuclear male sterility systems, aiming to improve yield, stress tolerance, and resistance to biotic and abiotic constraints in semi-arid tropical regions.

📌 Key points (3–5)

• Ancient staple crop: Millets, especially pearl millet, were domesticated over 7,000 years ago in Africa and are adapted to semi-arid tropics where other cereals fail.
• Four pearl millet races: Classified by grain shape (typhoides, Nigritarium, Globosum, Leonis), each with distinct morphology and geographic distribution.
• Protogynous flowering enables outcrossing: Pearl millet flowers are hermaphroditic but stigmas mature before anthers, resulting in >85% cross-pollination naturally.
• Common confusion—vegetative vs reproductive phases: The vegetative phase runs from emergence to panicle initiation; the reproductive phase begins with spikelet formation and ends at pollination; grain filling follows fertilization.
• Breeding breakthrough: Discovery of A1 cytoplasmic-nuclear male sterility (CMS) in the USA enabled commercial F₁ hybrid development, transforming pearl millet breeding.

🌾 Crop identity and distribution

🌾 What millets are

Millets are tall and vigorous grasses with panicles containing small seeds, grouped in the cereal family Gramineae, same category as sorghum and maize.

• Four widely grown species: pearl millet (Pennisetum glaucum), finger millet (Eleusine coracana), foxtail millet (Setaria italica), and proso millet (Panicum miliaceum).
• Adapted to semi-arid tropics of Africa and Asia where other crops generally cannot be grown.
• Used as staple food in these regions.

🗺️ Origin and global production

• Domestication: Believed to be one of the first domesticated cereals, cultivated over 7,000 years ago during the Neolithic era in Africa, then spread worldwide.
• Gene bank collections: 161,708 accessions preserved globally, 98.1% cultivated types.
• Major producers:
  • Asia: India, China, Nepal, Pakistan, Myanmar
  • Sub-Saharan Africa: Nigeria, Niger, Senegal, Cameroon, Burkina Faso, Mali, Uganda, Kenya, Namibia, Tanzania, Togo, Chad, Zimbabwe
• Production scale: Grown in over 90 countries (2004–2008), contributing 32.3 million tons annually.
• Geographic specialization: Pearl millet mainly in South Asia and Sub-Saharan Africa; finger millet in South/Southeast Asia and East Africa; foxtail millet in South/Southeast Asia; proso millet in Asia, Europe, and North America.

🏛️ Research institutions

• ICRISAT (International Crops Research Institute for the Semi-Arid Tropics): CGIAR center with millet mandate, coordinates all millet research in semi-arid tropics, maintains large germplasm collection in Patancheru, India.
• Regional gene banks: East Africa (Ethiopia, Kenya), West Africa (Nigeria, Senegal).
• USA gene banks: Fort Collins (Colorado), Griffin (Georgia), Ames (Iowa), Pullman (Washington).

🔬 Pearl millet morphology and classification

🔬 Origin and diversity

• Common name: Bulrush millet.
• Origin: Semi-dry land tropics of western Africa.
• Diversity hotspot: Western Sudan to Senegal; highest morphological diversity south of the Sahara desert.
• Stress adaptation: Evolution under high temperature and drought pressures made pearl millet tolerant to moisture stress, high temperatures, and low soil fertility—critical for hot desert farming in Africa and Asia.

🧬 Four races based on grain shape

Race	Grain (caryopsis) shape	Inflorescence shape	Geographic distribution
Typhoides	Obovate; obtuse and terete cross-section	Cylindrical; most diverse morphology	Widely across Africa; widely grown in India
Nigritarium	Angular cross-section with 3–6 facets; longer grain protruding beyond floral bracts	Candle-like	Western Sudan, Nigeria
Globosum	Spherical	Candle-like	Central Nigeria, Niger, Ghana, Togo, Benin
Leonis	Acute and terete; acute apex with remnants of stylar base	Candle-like	Sierra Leone, Senegal, Mauritania

Don't confuse: Race classification is based on grain shape (caryopsis morphology), not plant height or panicle size.

🌱 Plant biology

• Photosynthesis: C₄ type—high efficiency carbon fixation, high dry matter production.
• Photoperiod: Short-day plant requiring long nights before flower initiation.
• Soil tolerance: Grows on light textured, sandy, acidic, less fertile soils.
• Chromosome number: 2n = 2x = 14 (diploid).
• Flower type: Hermaphrodite with protogynous development (stigma receptive before anthers shed pollen), resulting in >85% outcrossing.

🌿 Growth phases and development

🌿 Vegetative phase (emergence to panicle initiation)

• Germination: 2–3 days under optimum temperature and moisture.
• Root system: Monocotyledonous—primary root plus adventitious roots; deep penetration up to 180 cm for water absorption.
  • Heavy-tillering plants: more horizontal spread than deep penetration.
  • Drought-tolerant cultivars (3–15 days after sowing): 35% more root length than susceptible cultivars.
• Stem: Upright annual grass, 1–2 cm diameter, solid, 2–4 m tall, round/oval shape; slightly swollen nodes with adventitious roots at base; internodal length increases upward.
• Leaves: Single leaf per node in alternate orientation; open sheaths, hairy ligules.
• Tillering: High potential to produce effective tillers from different branches, each potentially bearing productive panicles—important during unfavorable conditions like extreme drought.

🌸 Reproductive phase (panicle initiation to pollination)

• Initiation: Dome-like structure forms, leading to spikelets, florets, glumes, stigma, anthers.
• End point: Stigma emergence (flowering) and pollination.
• Critical period for grain number: Between panicle initiation and anthesis.
• Inflorescence (panicle): Compound terminal spike; compact and cylindrical or conical; 2–3 cm diameter, 15–45 cm long; size and shape consistent for a given genotype.

🌾 Grain filling phase (fertilization to maturity)

• Process: Fertilization in main shoot panicle continues until maturity; plant dry weight increases in grain.
• Tiller flowering: In some cultivars, tillers elongate and flower during this phase, causing dry matter translocation to non-grain components (mainly tiller stems).
• Maturity marker: Dark layer of tissue develops on grain at physiological maturity, typically 20–25 days after flowering for most cultivars.

Example: If a cultivar flowers on day 60, the dark layer marking maturity appears around day 80–85.

🌍 Adaptation, uses, and production

🌍 Global cultivation area

• Total: ~29 million ha annually in dry land tropical regions.
  • Africa: 16 million ha (60%)
  • Asia: 11 million ha (35%, primarily India)
  • Latin America: 2 million ha
  • Europe: 4%
  • North America: 1% (mainly forage and poultry feed)
• Pearl millet accounts for about half of the world's millet production.
• Sub-Saharan Africa: Third major cereal crop, staple food in Nigeria, Niger, Burkina Faso, Chad, Mali, Mauritania, Senegal, Sudan, Uganda.

🍞 Economic importance and uses

• Food use: 93% of grain used as food in developing countries of Africa and Asia.
• Feed use: 7% used for animal and poultry feed in USA, Australia, South Africa.
• Traditional products: Flat bread, stiff roti, porridge.
• Modern products: Bakery products, snacks.
• Subsistence crop: Referred to as staple food of poor people in semi-arid and arid environments.

🌾 Soil and climate adaptation

• Best soil: Light sandy soil.
• Rainfall: 350–700 mm per annum.
• Drought tolerance: High; can regrow and produce tillers to compensate for drought losses, enabling faster regeneration.
  • Favorable conditions: 4,000–5,000 kg/ha yield.
  • Severe drought: 500–600 kg/ha yield.
• Reliability: More reliable than sorghum and maize in marginal areas.
• Limitations: Less tolerant to waterlogging and flooding.

Don't confuse: Pearl millet's drought tolerance does not mean it thrives in waterlogged conditions—it is specifically adapted to dry environments.

⚠️ Production constraints

🦠 Biotic stress (diseases and pests)

Bacterial diseases:

• Bacterial spot (caused by Pseudomonas syringae)
• Bacterial leaf streak (caused by Xanthomonas campestris pv. pennamericanum)

Fungal diseases (cause more yield loss than bacterial):

• Downy mildew (Sclerospora graminicola, Plasmopara penniseti)
• Blast (Pyricularia grisea)
• Smut (Moesziomyces penicillariae, Tolyposporium penicillariae)
• Rust (Puccinia substriata var. penicillariae)

Insect pests:

• Millet head miner
• Stalk borer

Parasitic weeds (serious in sub-Saharan Africa):

• Striga hermonthica
• Striga asiatica

Other pests:

• Parasitic nematodes

🌡️ Abiotic stress

• Drought: In all pearl millet growing regions.
• High soil salinity and acidity.
• Extreme high temperature: At seedling stage and during flowering.

🧬 Breeding methods and objectives

🧬 Breeding history

• Asia (India): Began early 1930s, emphasis on high yield and productivity.
• USA: Focus on forage and biomass yield.
• West Africa: Started 1950s, emphasis on grain yield increases.
• Breakthrough: Discovery of A1 cytoplasmic-nuclear male sterility (CMS) system in Tifton, Georgia, USA; enabled breeding of commercially viable male-sterile line (A-line), leading to first F₁ grain hybrid released in India.

🔬 Male sterility system

Cytoplasmic-nuclear male sterility (CMS) provides control over outcrossing, enabling application of testcross method where a large number of inbred lines can be crossed with few, better, high general- and specific-combining ability CMS inbred lines.

• Why it matters: CMS allows efficient hybrid production by preventing self-pollination in the female parent, ensuring all seed is hybrid.
• Testcross method: Breeders can evaluate many inbred lines by crossing them with a few elite CMS lines.

Don't confuse: Natural protogyny (stigma matures first) causes high outcrossing in open-pollinated populations; CMS is a breeding tool that guarantees outcrossing for hybrid seed production.

🎯 Breeding objectives at ICRISAT

1. High grain yield: Compact head, more tillers, earliness, reduced plant height.
2. High forage yield: High biomass, good digestibility.
3. Resistance: To diseases, insect pests, and (implied from context) abiotic stresses.

Example: A breeder might cross a CMS line with compact heads and early maturity with an inbred line resistant to downy mildew to produce a high-yielding, disease-resistant hybrid.

🧭 Overview

🧠 One-sentence thesis

Rice breeding leverages both conventional pureline methods and hybrid systems (using male sterility mechanisms) to develop improved cultivars that address yield, adaptation, and stress resistance across diverse production ecosystems worldwide.

📌 Key points (3–5)

• Two cultivated species: Oryza sativa (Asian rice, with indica and japonica subspecies) and Oryza glaberrima (African rice); domesticated independently in different regions and times.
• Heterosis and hybrid rice: F₁ hybrids can yield 15–20% more than the best pureline cultivars; commercial hybrid production relies on male sterility systems (CGMS three-line or EGMS two-line).
• Male sterility systems: CGMS uses three lines (A, B, R) with cytoplasmic factors; EGMS uses two lines with environment-sensitive sterility (temperature or photoperiod).
• Common confusion: CGMS vs. EGMS—CGMS requires a maintainer line and restorer line (three lines total), while EGMS eliminates the maintainer line but depends on environmental conditions for sterility expression.
• Production ecosystems: Rice is grown in four major systems (irrigated, rainfed lowland, upland, flood-prone), with irrigated lowland contributing ~75% of total production.

🌾 Rice species and domestication

🌍 Origin and domestication timeline

• Three cultivated species:
  • Oryza glaberrima: domesticated in West Africa ~1500–800 BC (2,000–3,000 years ago).
  • Oryza sativa japonica: domesticated in central China ~7000 BC (8,200–13,500 years ago).
  • Oryza sativa indica: domesticated in the Indian subcontinent ~2500 BC.
• Wild ancestor: Oryza rufipogon existed across a broad geographic range in Asia; human selection transformed it into cultivated rice.

🔄 Transformation from wild to cultivated

Domestication of O. rufipogon resulted in complete transformation of morphological and physiological traits.

• Changes in cultivated rice (O. sativa):
  • Reduced dormancy, grain shattering, outcrossing.
  • Loss of pigmentation in hull and seed coat.
  • Better synchronization of tiller development and panicle formation.
  • Increased secondary panicle branches, higher grain yield and weight, improved photoperiodic response.
• Example: Wild O. rufipogon has shattering seeds and irregular panicle development; cultivated O. sativa has non-shattering seeds and synchronized panicle formation.

🌾 NERICA rice

NERICA stands for "New Rice for Africa," developed using interspecific hybridization of O. glaberrima (African rice) and O. sativa (Asian rice) at the Africa Rice Center (WARDA).

• Purpose: Raise the yield of African rice cultivars.
• Development method: Embryo-rescue technique (interspecific crosses do not produce viable seed naturally).
• Benefits: Higher yield (increased grain size, better growth), resistance to biotic (diseases, pests) and abiotic (drought) stresses.
• Recognition: Dr. Monty Jones won the 2004 World Food Prize for creating this cultivar suited to African drylands (Guinea, Nigeria, Côte d'Ivoire, Uganda).

🌾 Major rice categories

Category	Grain type	Cooking behavior
indica	Long-grain	Non-sticky when cooked
japonica	Short-grain	Sticky when cooked
aromatic	Medium to long-grain	Nut-like aroma and taste when cooked
glutinous	—	Especially sticky and glue-like when cooked

🌱 Biology and development

🌱 Three developmental stages

1. Vegetative (germination to panicle initiation): subdivided into germination, early seedling growth, tillering.
2. Reproductive (panicle initiation to heading): subdivided into stem elongation, panicle initiation, panicle development, flowering.
3. Ripening (milky stage to maturity): subdivided into milk grain, dough grain, mature grain.

• In tropical environments, approximately half of the growth days are in the vegetative phase, and one-quarter each in the reproductive and ripening phases.

🌱 Seedling development (S0–S3)

• S0: Unimbibed seed.
• S1: Coleoptile or radicle emergence (whichever emerges first).
• S2: Both coleoptile and radicle have emerged.
• S3: Prophyll (first leaf, lacks blade and collar, only sheath) emerges from coleoptile.

🌿 Vegetative development (V1–VN)

• Stages labeled V1, V2, … VN, where N = final number of leaves with collars on the main stem.
• VF denotes the flag leaf; VF-n denotes the nth node before the flag leaf.

🌾 Reproductive development (R0–R9)

• R0: Panicle development initiated.
• R1: Panicle branches formed.
• R2: Flag leaf collar formation.
• R3: Panicle exertion from boot (tip above collar of flag leaf).
• R4: One or more florets on main stem panicle reach anthesis.
• R5: At least one caryopsis elongating to end of hull.
• R6: At least one caryopsis elongated to end of hull.
• R7: At least one grain has yellow hull.
• R8: At least one grain has brown hull (grain has begun to dry).
• R9: All grains that reached R6 have brown hulls.

🌾 Yield components

• Four components:
  1. Number of panicles/m².
  2. Number of grains/panicle.
  3. Percentage of ripened grains.
  4. 1000 gm weight.
• Best measure: Plot yield weight remains the best way to determine yield of lines or genotypes.

☀️ Photosynthesis and photoperiod

• C3 plant: Rice uses the C3 photosynthetic pathway, which is less efficient than C4 at transforming inputs to grain.
• Ongoing efforts: Development of C4 rice to enhance photosynthetic capacity and increase yield.
• Photoperiod: Oryza sativa is a short-day plant (requires long nights to flower).
  • Heading date accelerates under short-day conditions.
  • Heading date delays under long-day conditions.

🌍 Production systems and adaptation

🌾 Four major production ecosystems

Ecosystem	Description	Production area (%)	Total rice production (%)
Irrigated rice	Well-watered, flooded throughout growing season	55–60	~75
Rainfed lowland rice	Dependent on rainfall, land prepared to preserve rainwater	~30	~20
Upland rice	No irrigation, relies completely on rainfall	~10	<5
Flood-prone rice	Deep water rice in river areas, no water control system	—	—

• Key insight: Irrigated lowland contributes the majority of total rice production despite not being the largest area.

🌾 Diversity and adaptation

• Huge diversity in Oryza species for shape, color, and size.
• Rice is grown on all six continents except Antarctica.
• Staple food in numerous countries, particularly in Asia.

🍚 Processing and nutrition

• Milling and polishing: Produces white rice by removing outer layers and germ; results in product deficient in thiamine.
• Fortification and parboiling: Retain adequate quantities of thiamine and other B vitamins.
  • Parboiling: Unhusked rice is steamed so water is absorbed by the whole grain, providing even distribution of vitamins.
  • Conventional method: Paddy is dried and dehusked prior to milling.

🏛️ International breeding centers (CGIAR)

1. IRRI (International Rice Research Institute): Global mandate, headquarters in Los Baños, Laguna, Philippines.
2. WARDA (West Africa Rice Development Association): Mandate for rice in West Africa.
3. CIAT (International Centre for Tropical Agriculture): Regional mandate for rice in Latin America.

🌾 Heterosis and hybrid rice

🌾 What is heterosis

Heterosis refers to the superiority of the F₁ hybrids resulting from a cross of diverse parents, over their parents in performance of desired traits (e.g., vigor, yield, number of productive tillers, panicle size, number of spikelets per panicle).

• Commercial hybrid rice: F₁ hybrid developed from cross of two genetically diverse pureline parents.
• Yield advantage: Good rice hybrids can yield 15–20% higher than the best pureline cultivar under similar conditions.

🌾 Types of heterosis (in decreasing order)

1. Intersubspecific heterosis: O. sativa ssp. indica × O. sativa ssp. japonica

   • Shows maximum heterosis in F₁ hybrid.
   • Limitations: High spikelet sterility and long growth duration.
   • Solution: Discovery of wide compatibility (WC) genes overcomes these problems.

2. Intrasubspecific heterosis: Most commonly used; provides ~15–20% more yield than best check.

   • Examples: indica × indica; japonica × japonica.

3. Interspecific heterosis: Crosses between O. sativa and O. glaberrima.

   • Very high yield heterosis but plant stature remains a problem.
   • F₁ hybrids cannot be used commercially.
   • Used to generate genetic variability and bring together biotic and abiotic stress resistance genes.

🌾 Why hybrid rice

• Self-pollinated crop: Rice requires male sterility system to develop commercial hybrids.
• Commercial interest: Companies profit from farmers returning each year to buy new seed.
• Higher seed cost: Partly due to increased cost of developing the parents used to make hybrids.

🧬 Male sterility systems

🧬 Three forms of male sterility

Male sterility is defined as the inability of a plant to produce functional pollen grains.

1. Cytoplasmic genetic male sterility (CGMS): Three-line system.
2. Environment-sensitive genic male sterility (EGMS): Two-line system.
   • TGMS: temperature-sensitive genetic male sterility.
   • rTGMS: reverse temperature-sensitive genetic male sterility.
   • PGMS: photoperiod-sensitive genetic male sterility.
   • rPGMS: reverse photoperiod-sensitive genetic male sterility.
   • PTGMS: photothermosensitive genetic male sterility.
3. Chemically induced male sterility (CIMS).

🧬 CGMS three-line system

Three lines involved:

1. Cytoplasmic male sterile line (A line):

   • Male sterility controlled by interaction of sterile cytoplasm (S) and fertility-restoring genes (rf) in recessive form in nucleus.
   • Used as female parent in hybrid production.

2. Cytoplasmic male fertile line / maintainer (B line):

   • Iso-cytoplasmic to A-line (similar nuclear genes but has normal cytoplasmic factor N).
   • N gene makes B-line self-fertile.
   • Used in crossing with sterile A-line to maintain A-line seed production.

3. Restorer line (R line):

   • Possesses dominant fertility-restoring genes (Rf).
   • Genetically dissimilar from A-line for heterosis expression.
   • Restorer gene in dominant homozygous (RfRf) or heterozygous (Rfrf) state restores fertility in F₁ hybrid.

🧬 CGMS hybrid seed production (two steps)

Step 1: A-line multiplication (A×B):

• Seed of CMS line (A) multiplied by crossing with maintainer line (B).
• Field pattern: 6 or 8 rows of A-lines alternating with 2 rows of B-lines.
• Example pattern: … B B A A A A A A B B A A A A A A B B …

Step 2: Hybrid seed production (A×R):

• Hybrid seed produced by crossing A-line with R-line in isolation.
• Field pattern: 8–10 rows of A-lines interspersed with 2 rows of R-line.
• Example pattern: … R R A A A A A A A A R R A A A A A A A A R R …

Additional practices:

• Stagger planting dates to synchronize flowering.
• Use ropes or sticks for better pollen dispersal and seed set.
• Hormone treatment (Gibberellic acid) increases female receptivity by improving panicle emergence from sheath.

🧬 EGMS two-line system

• Male sterile line: Male sterility controlled by recessive gene; sterility expression influenced by environment (temperature, photoperiod, or both).
• Male fertile line: Pureline selected to be good pollen producer.
• No maintainer line required: Any fertile line can be used as pollen source parent.

🧬 Types of EGMS systems

1. TGMS (Thermo-sensitive genetic male sterility):

   • Sterility/fertility controlled by temperature (regardless of photoperiod).
   • Highly sterile under high temperature; highly fertile under low temperature.
   • Example: Remei variety (gamma ray induced mutation): sterility at 31–24°C, partial fertility at 28–21°C, complete fertility at 25–15°C.

2. PGMS (Photoperiod-sensitive genetic male sterility):

   • Sterility/fertility controlled by daylength.
   • Male sterile under long-day conditions; fertile under short-day conditions.
   • Example: Nongken 58S (NK58S), first spontaneous PGMS mutant (1973): male sterility under long day length (>13.75 h), partial/complete fertility under short day length (<13.5 h).

3. rPGMS (Reverse photoperiod-sensitive genic male sterility):

   • Sterility under short day length; fertile under long day length.

4. PTGMS (Photo-thermosensitive genetic male sterility):

   • Sensitive to both photoperiod and temperature.
   • Temperature is the important factor; PTGMS lines become completely sterile or fertile beyond a threshold temperature range, without photoperiod influence.
   • Effect of temperature and photoperiod difficult to separate under natural conditions.

🧬 EGMS advantages vs. disadvantages

Advantages:

1. No requirement for seed multiplication of maintainer line (cheaper).
2. No need for backcross breeding to develop CMS A-line from B-lines.
3. Higher hybrid breeding efficiency (any fertile line can be pollen source).
4. No undesirable effects of sterility-inducing cytoplasm.
5. Ideal for developing indica × japonica hybrids (no restorer line requirement).

Disadvantages:

1. Sterility trait controlled by environmental factors; any variation (temperature fluctuation from storm, rain) impacts EGMS line sterility.
2. Seed production constrained by latitude with optimal photoperiod length; limits location options.
3. Seed multiplication (lines and hybrids) constrained by space and season.

Don't confuse: CGMS is more stable (cytoplasmic control) but requires three lines; EGMS is simpler (two lines) but vulnerable to environmental fluctuations.

🌾 Conventional rice breeding

🌾 Conventional breeding process

• Method: Two parents are crossed; segregating generations screened for trait of interest (e.g., disease resistance, maturity, height, protein).
• Selection: Uniform lines tested for yield; along with resistance, desirable varieties selected and released.
• Timeline: Development process from initial cross to variety release follows standard pureline breeding steps (cross → F₁ → F₂ → … → uniform lines → yield testing → release).

🧭 Overview

🧠 One-sentence thesis

Sorghum is a multipurpose cereal crop of global importance that combines exceptional drought and heat tolerance with diverse uses (food, feed, fuel, forage) and is supported by advanced genomic resources, making it a vital tool for addressing food security challenges in both tropical and temperate regions.

📌 Key points (3–5)

• Origin and diversity: Sorghum originated in North Eastern Africa ~5,000 years ago and is classified into five morphological races (durra, kafir, guinea, bicolor, caudatum) that differ mainly in panicle morphology and grain characteristics.
• Unique drought adaptations: Sorghum possesses motor cells that roll leaves during stress, extensive root systems, waxy leaves, and the ability to pause and resume growth, enabling survival where other crops fail.
• Multiple classification systems: Sorghum is classified by utilization (grain, sweet, broom, grass), by agronomic groups (kafir, milo, hegari, feterita, dura, shallu, kaoliang), and by intended purpose (food, feed, biofuel).
• Common confusion—tillering: Lower plant density causes more tillering (undesirable late-forming tillers with high moisture), while higher density suppresses it; tillers from upper stem nodes are problematic because they delay harvest and cause storage issues.
• Breeding approaches: Two main cultivar types are developed—open-pollinated/pure-line varieties (mainly for developing countries) using recurrent selection or pedigree methods, and hybrids (mainly for industrialized countries) using a 3-line cytoplasmic male sterility system (A-line, B-line, R-line).

🌍 Origin, classification, and biology

🌱 Domestication and geographic diversity

• Origin: North Eastern Africa, domesticated in Ethiopia and parts of Congo approximately 5,000 years ago by selecting from wild sorghum.
• Secondary centers: India, Sudan, and Nigeria are considered secondary centers of origin.
• Greatest diversity: The genus Sorghum has 20–30 species; the areas of origin still harbor the greatest diversity of wild and cultivated species today.
• Early distribution to Asia and other continents generated further genetic diversity.

🌾 Five morphological races

All cultivated sorghums (Sorghum bicolor spp.) are grouped into five races plus ten intermediate races:

Race	Origin/Distribution	Key characteristics
Durra	Ethiopia, horn of Africa → Nigeria, West Africa	Panicle morphology, grain size, yield potential differ
Kafir	Eastern and southern Africa	Grows well in that region
Guinea	West and Central Africa	Developed and grows well in that region
Bicolor	East Africa	Less important to African production
Caudatum	(Not detailed in excerpt)	One of the five races

• Races differ mainly in panicle morphology, grain size, and yield potential.

🌿 Plant biology and structure

• Family and form: Annual grass, Graminae family, reaches up to 5 m in height with one to several tillers.
• Tillering behavior:
  • Tillers emerge first from the base; later tillers can form on stem nodes when conditions are favorable.
  • Upper or lower node tillers are undesirable: they form late, produce small amounts of unripe grain with high moisture content, causing delayed harvest and storage/delivery problems.
  • Don't confuse: Lower plant density (sparse planting) → more tillering; higher density → suppresses tillering. Unfavorable conditions also suppress tillering.
• Root system: Fibrous, mostly concentrated in top 90 cm of soil, but can extend twice that depth (up to ~180 cm) in dry environments.
• Leaves: Alternate, 15–35 cm long, total number varies 7–24 depending on variety and environment.
  • Unique feature: Rows of motor cells along the midrib on the upper leaf surface allow leaves to roll up rapidly during drought stress to minimize water loss.

🌡️ Temperature and photoperiod requirements

• Germination: Optimum 27–35°C.
• Growth and development: Requires high temperature, 27–30°C.
• Tolerance: Can tolerate as low as 21°C without significant effect; increased day/night temperature beyond requirements delays flower initiation and reduces yield.
• Photoperiod: Short-day plant requiring long nights before flower initiation.
  • Optimum for flower initiation: 10–11 hours.
  • Photoperiod beyond 12 hours stimulates vegetative growth.
  • Tropical cultivars are more photoperiod-sensitive than short-season (quick-maturing) cultivars.

🌾 Inflorescence and pollination

• Panicle: The inflorescence (head) may be loose or dense; under favorable conditions, initiation occurs after one-third of the growth cycle.
• Grain number: Each fully developed panicle contains 800–3,000 grains, each usually enclosed by glumes; seed color is variable.
• Flowering: Flowers open at night or early morning, starting at the top of the panicle; takes 6–9 days for the whole panicle to flower.
• Pollination: Predominantly self-pollinated due to flower structure, but natural cross-pollination occurs at approximately 2–25%.

🌱 Growth stages and photosynthesis

📈 Three distinct growth stages

After seedling emergence, sorghum goes through three stages:

Stage	Name	Key events	Stress tolerance
GS I	Vegetative growth	Develops leaves, internodes, tillers; prepares for grain formation	Can tolerate drought, heat, freezing
GS II	Reproductive phase	Panicle initiation → flowering; maximum seed set	Most critical period; high water requirement; severe moisture stress hinders panicle initiation, delays flowering, reduces seed set and grain yield
GS III	Grain filling	Flowering → grain filled with dry matter	(Not detailed in excerpt)

• Don't confuse: GS II is the most critical for determining grain production level; water stress at this stage causes the greatest yield loss.

☀️ Photosynthesis efficiency

C4 grass: Sorghum is one of the C4 grasses with high photosynthetic efficiency.

• This contributes to its ability to thrive in warm, dry environments.

🌾 Classification systems

🍽️ Classification by utilization (mode of consumption)

🍞 Human food

• Africa and Asia: Consumed as unfermented and fermented pancakes (breads), porridges, dumplings, snacks, malted alcoholic and nonalcoholic beverages.
• Grain color preference: White grain for cooking; red and brown grain for beer making.
• Bird pressure: In areas like Lake Victoria, farmers grow red/brown grain sorghum (rich in tannin, bitter tasting) to prevent bird feeding losses.
• USA: Primarily grown as fuel crop (ethanol); few food products available, but researchers are developing sorghum products and exploring health benefits.
  • Example: Sorghum grain did not show toxicity to celiac patients; several gluten-free sorghum products have been developed.

🐄 Animal feed

• USA, Central/South America, Europe, Australia, China: Sorghum grain used as cattle, pig, and chicken feed.
• Sweet sorghum: Used as cattle feed (similar to silage corn) in Europe.
• Problem: Presence of prussic acid (HCN) in fresh sweet sorghum can cause death in cattle; eliminated through cultivar choice and proper agronomic practices.

⚡ Renewable energy

• Unique biofuel crop: Used in various forms—starch and sugar converted to ethanol; lignocellulose (cellulose, hemicellulose, lignin—inedible parts) converted to biogas.
• Sweet sorghum is unique because it serves as food, fodder, and biofuel.

🌾 Classification by intended purpose

Four major groups:

1. Grain sorghum: Staple food in tropical Africa and Asia; raw material for alcoholic beverages, sweets, glucose.
2. Sweet sorghum: Produced for sugar production; sugar used to make sweet syrup similar to molasses.
3. Broom sorghum: Long panicles with fine, elastic branches (fibers) with seed on tips; used for making brooms.
4. Grass sorghum: Grown for green feed and forage.

🌾 Classification by agronomic groups

Seven commercial grain sorghum groups:

Group	Origin	Stalk/Leaves	Panicle	Seed	Other traits
Kafir	South Africa	Thick, juicy stalk; large leaves	Cylindrical, no awn	Medium size; white, pink, or red	—
Milo	East Africa	Less juicy than kafir; light green leaves	Short, compact, oval	Large; yellow or white	More tillers; more heat/drought tolerant than kafir
Hegari	Sudan	More leaves than kafir	Nearly oval	Chalky white	Sweeter juice, desirable for forage
Feterita	Sudan	Few leaves, dry stems	Oval, compact	Large, chalky white	—
Dura	Mediterranean, Middle East	Dry stems	Erect, compact or loose	Flat, pubescent glumes	Grown in North Africa, India, Near East
Shallu	India	Tall, slender, dry stalks	Loose	Pearly white	Late maturing, requires long growing period
Kaoliang	China, Japan	Slender, dry, woody stalks; sparse leaves	Open, semi-compact	Small; white or brown; bitter taste	—

🌍 Adaptation and cropping systems

🌡️ Environmental adaptation

• Climate: Adapted to wide range, particularly warm weather; grown between 40°N and 40°S in arid, semi-arid tropics and subtropics.
• Altitude: Up to 2,300 m above sea level in tropics.
• Rainfall: Annual rainfall 300–1,200 mm.
• Temperate regions: Widely grown in South China, USA, some parts of Europe; cold-tolerant sorghums grown in Central America.
• Maturity: Short-day plant requiring 90–140 days to mature depending on climate and cultivar type.
• Soil: Wide range from vertisol (clay) in tropics to light sandy soil; pH 5.0–8.5; tolerant to salinity compared to corn.
• Outstanding characteristics: Heat and drought tolerance; can produce grain in poor soil where other crops fail.

🌾 Drought tolerance mechanisms

Morphological and physiological characteristics:

• Extensive root system.
• Wax on leaves (minimizes water loss).
• Ability to stop growth during moisture stress and resume growth when moisture increases (from rain).
• Motor cells in leaves that roll up rapidly during drought stress.

🌱 Intercropping systems

Intercropping: A cropping system involving growing two or more crops in the same space at the same time.

• Common practice: Among small-scale farmers in semi-arid Africa and Asia to increase productivity per unit area.
• Sorghum combinations:
  • With legumes: sorghum-chickpea, sorghum-common bean, sorghum-pigeon pea, sorghum-cowpea, sorghum-mung bean.
  • With cereals: sorghum-millet, maize-sorghum.
• Yield benefits: Significant yield increases reported compared to pure stands.
  • Example: Sorghum yield increased 8–34% in sorghum-legume intercropping vs. sole sorghum.
  • Example: In Ethiopia, sorghum-mung bean intercropping gave extra yield of 495 kg/ha vs. sole sorghum; also reduced Striga infestation.
• Other benefits: Efficient use of space and time; diversification (harvest two or more crops from same land); better weed control; reduced disease and pest incidence.

🐛 Production constraints

🦠 Biotic constraints (diseases and pests)

🍄 Fungal diseases

• Smut (caused by Sphacelotheca spp.): May cause more yield losses than other fungal diseases; widely important in eastern, central, southern Africa.
  • Types: loose smut, kernel smut, head smut, long smut.
  • Control: Seed treatment with fungicides; use of resistant cultivars.
• Rust (caused by Puccinia purpurea): Widely distributed in many sorghum-producing regions, particularly Africa.
• Grain mold: Caused by several fungi (Curvularia lunata, Fusarium spp.).
  • Infects grain during development; causes severe discoloration and loss of seed quality.
  • Increased by continued rainfall throughout grain maturity period; causes delayed harvest.
  • Control: Use of resistant cultivars; adjustment of planting time to avoid long maturation during prolonged rainy season.
• Anthracnose (Colletotrichum graminicola): One of the most important sorghum diseases.
• Others: Downy mildew, ergot, bacterial streak are occasional important constraints.

🐛 Insect pests

• Tropical Africa: Stem borer (particularly Busseola fusca and Chilo partellus) and shoot fly (Antherigona soccata).
  • Yield losses significantly high; problem widespread in major sorghum-producing African countries.

🌿 Other biotic constraints

• Striga: Rated as causing high yield losses in all regions in Africa.
  • Example: Yield losses estimated >50% in some countries (Rwanda, Kenya).
• Weeds and quelea: Also major production constraints.

🌡️ Abiotic constraints

• Extreme drought: In all sorghum-growing regions.
• Saline soil: Some parts of India and Middle East countries.
• Acidic soil: Mostly in Latin America.

🧬 Breeding programs and methods

🏛️ International breeding center and collections

🌍 ICRISAT

• Full name: International Crops Research Institute for the Semi-Arid Tropics, member of CGIAR.
• Location: Patancheru, India; established 1972 with sorghum as one of five mandate crops.
• Collections: 36,774 accessions from 90 countries maintained in gene bank; exhibit 80% of diversity present in the crop.
• Mission: Reduce poverty, hunger, environmental degradation in dry land tropics; coordinates all sorghum research in semi-arid tropics worldwide.
• Collaboration: Strong collaboration and active breeding programs covering >55 countries in Asia and sub-Saharan Africa.
• Focus areas:
  • Developing cultivars with genetic resistance to major diseases and insect pests.
  • Developing intermediate breeding products (e.g., wide range of male sterile lines for hybrid development).
  • Diversification of breeding populations through incorporation of abiotic and biotic resistance traits not previously used.
  • Current emphasis: Tolerance to drought, heat, aluminum toxicity, salt; resistance to head and stem pests, grain molds; earliness with high grain and biomass yield; tillering capacity.

🌍 Additional collection locations

• Temperate regions: USA (National seed storage lab), China.
• Tropical Africa: Zimbabwe (SADC/ICRISAT sorghum and millet improvement program, Matopos), Ethiopia (Institute of Biodiversity Conservation, Addis Ababa), Kenya (National gene bank, Crop Plant Genetic Center, KARI), Uganda (Serere Agricultural and Animal Production Research Institute).
• All accessions are valuable genetic resources for further germplasm development.

🧬 Breeding opportunities and objectives

🧬 Genomic resources

• Chromosome number: 2n=2x=20.
• Pollination: Predominantly self-pollinated with 2–25% outcrossing.
• Genome size: Small (730 Mbp) compared to maize or sugarcane.
• Sequencing: Fully sequenced genome provides many opportunities to plant breeders and genomics researchers.

🎯 Breeding objectives

• High grain and fodder yield potential.
• Resistance to diseases (smut, rust, grain mold, bacterial blight, anthracnose, downy mildew, etc.).
• Resistance to insect pests (stalk borer, shoot fly, midge).
• Resistance to drought and extremely acidic soil.
• Wide adaptation.
• Improved quality (for use in bread, porridge, snacks, beverages).

🌾 Two kinds of cultivars

1. Open-pollinated (OP) or pure-line cultivars: Mainly for developing countries.
2. Hybrid cultivars: Mainly for industrialized countries where seed systems are well developed.

• Don't confuse: Breeding methods for OPV differ from pure-line or hybrid development; OPV uses recurrent selection schemes, while pure-lines use methods for self-pollinating crops.

🌾 Open-pollinated and pure-line cultivar development

🔄 Population improvement

• Most common method in developing countries (Africa).
• Definition: Includes a group of sorghum plants sharing a common gene pool.
• Purpose: Develop broad-based gene pools through recurrent selection methods.
• Mechanism: Increases frequency of genes affecting trait(s) under selection; maintains genetic variability by recombining superior genotypes for continuous improvement.
• Two types:
  • Intra-population improvement: Practiced within specific population for its improvement.
  • Inter-population improvement: Selection based on intercross performance between two populations.
• Most convenient methods: Mass selection, S1 and S2 progeny testing.

🌳 Pedigree method

• Process: Hybridize between desirable complementary parental lines → select desirable plants from segregating populations until homozygosity is achieved.
• Application: Improving specific traits (disease and insect pest resistance, plant height, early maturity, etc.).
• Outcome: Leads to development of pure-line cultivars.
• Note: Also used to develop B-line and R-lines for hybrid development and production programs.

🔙 Backcross breeding

• Purpose: Transfer favorable single or few genes from donor genotype (generally poor agronomic performance) into elite genotype (recipient).
• Traits transferred: Resistance to diseases (grain mold, rust, smut); resistance to insect pests (stalk borer, shoot fly).
• Note: Used to develop A-line version of B-lines for hybrid development and production programs.

🌾 Hybrid cultivar development (hybrid breeding)

🌽 Comparison to maize hybrid breeding

• Similarity: Closely resembles hybrid corn breeding.
• Two major differences:
  1. Heterotic groups: Not well defined in sorghum as in maize; groups based on fertility restorer genes; more recently, reproductive groups emerging with differentiation and use of nuclear fertility genes.
  2. Male sterility system: Sorghum utilizes cytoplasmic male sterility (3-line system) to facilitate hybrid seed production, unlike maize which uses manual detasseling (detassel female inbred, allow male inbred pollen to pollinate to create hybrid seed on female ears).

🧬 Three-line system (CMS system)

• A-line (CMS line): Cytoplasmic male sterile; serves as seed-bearing parent.
• B-line (maintainer line): Has recessive form of fertility restorer gene; used as maintainer for the A-line.
• R-line (restorer line): Has dominant form of fertility restorer gene in the nucleus; capacity to restore fertility in the A system; used as pollen parent.

🔬 Breeding process

1. Develop B-line (maintainer) and R-line (restorer) under two separate reproductive groups (to maximize heterosis) using pedigree, Single Seed Descent, or any method suitable for self-pollinating crops.
2. Once new and superior B-lines are developed, use backcross breeding to convert them to A-lines (CMS lines).
3. As backcross breeding continues, assess general combining ability (GCA) or specific combining ability (SCA) to decide which B-line conversion to continue and to generate information on suitable R-line parent in combination.

• Don't confuse: The A-line is the female (seed-bearing) parent in hybrid seed production; the R-line is the male (pollen) parent; the B-line is used only to maintain the A-line, not in the final hybrid.

🧭 Overview

🧠 One-sentence thesis

Sweetpotato breeding in Sub-Saharan Africa focuses on developing improved varieties through accelerated breeding schemes that maximize evaluation across multiple environments while addressing constraints like viral diseases, limited access to clean planting material, and the genetic complexity of this hexaploid, clonally propagated crop.

📌 Key points (3–5)

• Genetic complexity: Sweetpotato is a hexaploid (2n=6x=90) that is self-incompatible and highly heterozygous, making it difficult to fix recessive traits even when their frequency exceeds 70%.
• Major constraints in Africa: Five main limitations keep yields at 5.6 t/ha (far below the 40-50 t/ha potential): lack of virus-free planting material, lack of improved varieties, weevil damage, poor agronomic practices, and limited market access.
• Accelerated Breeding Scheme (ABS): This method reduces variety development time from 7-8 years to 4 years by evaluating many genotypes across multiple locations without replication in early stages, exploiting the fact that spatial (location) variation exceeds temporal (year) variation.
• Common confusion: Clonal propagation fixes heterozygosity and vigor for the life of the clone, but viral infections accumulate rapidly (within weeks to a year) because propagation is vegetative, not from seed.
• Breeding goals: Include virus and disease resistance, improved yield and dry matter content, orange-fleshed varieties high in beta-carotene to combat vitamin A deficiency, weevil resistance, and drought tolerance.

🌱 Biology and importance of sweetpotato

🌍 Origin and diversity

Sweetpotato (Ipomoea batatas (L.) Lam., Convolvulaceae): a hexaploid species (2n=6x=90) that originated in Central and South America.

• Recent evidence suggests it evolved from at least two autopolyploid events involving distinct populations of I. trifida or an extinct ancestor.
• Primary center of diversity: Central and South America.
• Secondary centers of diversity: Uganda in East Africa and the Papua New Guinea region.

🥔 Usage and importance

• Sixth most important food crop in 2013 based on total production in Sub-Saharan Africa (after cassava, maize, yams, rice, and sorghum).
• Grown for enlarged storage roots and leaves consumed as food, animal feed, starch source, and industrial purposes.
• A hardy, low-input crop that grows well without fertilizers and with limited water.
• Can be planted and harvested throughout the year in many locations; farmers can "store" roots in the ground and harvest as needed.
• Roots are boiled, baked, fried, or dried and pulverized to make flour.

🎨 Variability and nutrition

• Extremely variable in size, shape, color, moisture content, and carbohydrate content.
• White-fleshed types: Preferred by most consumers in SSA; high dry matter content.
• Orange-fleshed sweetpotato (OFSP): Being developed to be high in bioavailable beta-carotene and dry matter to alleviate vitamin A deficiency, especially in children.
• Purple-fleshed types: Usually high in dry matter with low sweetness.
• Leaves and petioles are good sources of protein, fiber, and minerals (K, P, Ca, Mg, Fe, Mn, Cu).

🦠 Major diseases and pests

🦟 Viral diseases

• Clonal propagation problem: Because sweetpotato is propagated via vines, root slips, or storage roots (not seed), it is often infected by several viruses; degeneration of clean material occurs rapidly (within weeks to a year).
• Most damaging viruses in humid, tropical, low- and mid-elevation regions of Eastern and Central Africa:
  • Sweet potato chlorotic stunt virus (SPCSV): Transmitted by whiteflies; more detrimental than SPFMV; causes permanent symptoms and yield losses.
  • Sweet potato virus disease (SPVD): Caused by co-infection of SPCSV + SPFMV; causes devastating yield losses in high-humidity regions.
  • Sweet potato feathery mottle virus (SPFMV): Transmitted by aphids; infection alone produces only transient symptoms and little yield loss.
• Resistance to SPCSV appears to be conferred by a recessive allele that occurs at low frequency in the gene pool.
• Some varieties (e.g., NAPSPOT 11 and Tanzania) possess some resistance to SPVD.

🍄 Other diseases and pests

• Alternaria stem blight: Dominant disease in humid, tropical highland regions of Eastern and Central Africa.
• Other diseases: scurf, foot rot, chlorotic leaf distortion, Rhizopus soft rot.
• Major pests: Plant-parasitic nematodes and weevils (Cylas spp.); weevils are a major problem in drought-prone regions of Southern and Eastern Africa.
• Currently no resistance to sweetpotato weevils exists.

🎯 Breeding goals and centers

🎯 Key breeding objectives

• Resistance to SPVD and Alternaria stem blight.
• Weevil resistance (currently unavailable).
• Improved yield, size, shape, and uniformity of roots; yield stability.
• High dry matter content.
• Orange-flesh varieties with high beta-carotene content for combating vitamin A deficiency.
• Improved chemical composition (starch, cellulose, sugars, protein, carotenes, anthocyanins).
• Improved micronutrient content (Zn, Fe).
• Extended harvest for subsistence cropping.
• Drought tolerance.
• Dense foliage with high protein content, improved palatability and digestibility.
• Vine survival and vigor after planting (especially during drought).
• Improved storage, resistance to skinning, lower acrylamide potential.

🏛️ Major breeding centers

• International Potato Center (CIP) in Peru.
• National programs in Ghana, Mozambique, Uganda, Kenya, Tanzania, Zambia, Malawi, Rwanda, Nigeria, Ethiopia, Burkina Faso, South Africa.
• Universities in the USA: North Carolina State University (NCSU), Louisiana State University (LSU).

📉 Constraints on yield in Africa

📊 Yield stagnation

• Although acreage planted with sweetpotatoes in Africa has steadily increased since the 1960s, average yield per hectare has remained basically unchanged.
• Average yield in Africa: 5.6 t/ha.
• Average yield in USA and China: 24.5 and 22.4 t/ha, respectively.
• Maximum achievable yield: 40-50 t/ha.

🚧 Five main constraints

1. Farmers' inability to acquire virus- and disease-free planting materials.
2. The lack of improved varieties.
3. Damage due to sweetpotato weevils.
4. Poor agronomic practices.
5. The lack of easily accessible markets.

💡 Potential for improvement

• Experiments in East Africa suggest yield could double if farmers had access to clean planting material of improved varieties.
• Addition of improved crop and soil fertility management practices could more than triple the yield potential.
• The lack of improved varieties results mostly from limited investment in sweetpotato breeding programs in Africa, though this trend is changing.

🧬 Genetic complexity of sweetpotato

🧬 Hexaploid nature

Sweetpotato is a hexaploid with 2 non-homologous genomes (B₁B₁B₂B₂B₂B₂) with tetradisomic inheritance.

• Cultivars are phenotypically homogeneous (clonally reproduced) and genetically heterozygous (self-incompatible outcrossers).
• Genetics of simple traits is more complex, with up to six alleles per locus.
• Heterozygous genotypes occur in much larger frequencies, making heterosis more important for quantitatively inherited traits (yield, yield stability, vigor).
• Major challenge: Extremely difficult to fix recessively inherited traits (e.g., resistance to certain viruses, orange flesh) even if the frequency of recessive alleles is greater than 70%.

🌿 Characteristics of clonally propagated crops

• Strong positive relationship between productivity/vigor and level of heterozygosity.
• Selfing reduces vigor due to inbreeding depression.
• Vigor/heterozygosity can be fixed and maintained for the life of the clone.
• Polyploids/aneuploids can be maintained via clonal propagation.
• Disadvantages: Often difficult to create large quantities of clones from one plant (unlike seed crops); clonal propagules are bulky and difficult to store.

🔄 Factors complicating genetic improvement

• Self- and cross-incompatibility.
• Highly heterozygous nature of individual clones.
• Large number of chromosomes (2n=6x=90).
• These factors contribute to low correlation between parent performance and offspring performance.
• Success relies mostly on the ability to grow and evaluate a large number of clones/hybrid progeny in selective environments that closely resemble the target environment.

🔬 Basic breeding procedures

📋 Five-step breeding procedure

1. Define breeding objectives: Yield stability, adaptation, taste, pest and disease resistance.
2. Assemble germplasm: Local varieties, wild species, cultivars from other parts of the world; establish a breeding nursery.
3. Develop segregating populations: Via hybridization (biparental cross, polycross nursery, or diallel crosses) and/or induced mutagenesis.
4. Evaluate and select superior clones:
   • Plot size, number of replications, and number of locations increase after each round of selection to reduce environmental variability.
   • Select early for traits with high heritability; select later for traits with low heritability.
5. Name and release a cultivar: Multiply and distribute clones.

🔁 Recurrent selection

Recurrent selection: a common method for improving a breeding population that captures additive variance; most effective for traits with moderate to high heritability.

Three phases:

1. Selection of genotypes and their hybridization in an insect-pollinated polycross nursery or using controlled crosses.
2. Evaluation of progeny.
3. Selection of superior progeny and creation of a new polycross nursery or controlled crosses with or without the best parents from the initial cycle.

• Proven method for increasing the frequency of desired alleles and creating a genetically broad-based population.
• New germplasm (new parents/genotypes and/or superior progeny from previous cycles) is added to the polycross nursery after each cycle.
• Allows for rapid increase in the percentage of minor and recessive alleles, but requires accurate screening techniques.

⚡ Accelerated Breeding Scheme (ABS)

⏱️ Time reduction

• Reduces total time to develop a new variety from 7-8 years to 4 years.
• Compresses early breeding stages into two years: 1 year of crosses/seedling multiplication + 1 year of evaluation in multiple locations (vs. traditional 1 year crosses + 3-4 years sequential evaluation in single locations).

🌍 Key principle: spatial vs. temporal variation

• In sweetpotato, genotype × year variation (temporal) is typically less than genotype × location variation (spatial).
• ABS shifts focus to making selections in more environments in fewer years.
• Evaluates as many genotypes as possible in the first season of Year 2 in 3-4 locations without replication.
• Allows simultaneous selection in multiple environments in a single year vs. sequential selection over several years.

📐 Design features

• Year 2, Season 1 (Observational Trial): 2000 clones evaluated in 3-4 locations with 1 replication each; focus on highly heritable traits.
• Year 2, Season 2 (Preliminary Trial): 150-300 clones in minimum of 3 locations with 2 replications; all traits evaluated.
• Year 3, Season 1 (Advanced Trial): 40 clones in minimum of 4 locations with 2 replications.
• Year 3, Season 2: 5-8 clones in advanced trials plus 10 on-farm locations.
• Year 4: Multiplication and distribution.

🎯 Independent culling

• Efficiency can be increased by using a low-input or high-stress (drought) environment during Season 1 of Year 2 in addition to 2-3 normal input locations.
• Genotypes that don't perform well in the low-input/high-stress location are eliminated from normal input locations before selections are made.
• Allows selection of only genotypes that perform well under both normal and stressful environments in a single season.

💰 Budget allocation

• Traditional programs allocate >60% of budget for replicated trials during later stages when few clones are evaluated.
• ABS shifts budget emphasis to Year 2 to maximize the number of clones evaluated in multiple environments.

📊 Variance components and GxE

• High yield and stability in different environments are not well correlated in sweetpotato, suggesting GxE interactions are important.
• For sweetpotato, GxE interactions are often larger than or equal to the genetic variation for some traits.
• Reducing replication to increase the number of locations can be beneficial.
• Inclusion of check varieties throughout the field (alpha lattice design) is suggested to account for microenvironments.

Example from Table 2:

• For yield (t²/ha): Genotype variance = 36.2, GxE variance = 39.4, Error = 64.2 (ratio 1:1.1:1.8).
• For dry matter (%²): Genotype variance = 14.8, GxE variance = 5.7, Error = 5.7 (ratio 1:0.4:0.4).
• This shows that for yield, environmental and GxE effects are as large or larger than genetic effects, justifying the ABS approach.

🌸 Crossing and seed production

🌺 Crossing block establishment

• Year 1, Season 1: Establish crossing block and/or make controlled crosses; harvest true (hybrid) seed.
• Major goal: Improvement of overall population mean from one cycle to the next.
• Creation of genetic variation is easy in sweetpotato due to high heterozygosity of individual clones/parents.
• Sweetpotato is generally self-incompatible, so seeds do not develop from self-fertilization.
• Minimum of 15 parents should be used; most programs use 20-30 parents; larger programs (e.g., CIP) use 150+ parents separated into different gene pools (heterotic groups).

🌱 Seedling nursery

• Year 1, Season 2: Hybrid seed planted in 0.5 × 0.5 m plots.
• Selection limited to natural selection for tolerance and resistance to pathogens and pests.
• Artificial selection by breeders typically avoided during "true seed plant stage" because seed plants often grow differently than plants from vegetative cuttings and because this stage is often in an artificial environment not representative of the field.
• Stem cuttings harvested after 10 weeks.

🌼 Flowering and pollination

• Flowering is best under short-day conditions; begins about 1.5 months after planting and continues for ~3-5 months.
• Each flower opens early in the day just after sunrise and lasts only a few hours before fading around noon.
• Each pistil contains 1 superior ovary with two carpels; each carpel has two locules containing 1-2 ovules, so a single capsule can produce 1-4 seeds.
• Hand-pollinated flowers usually produce 1-2 seeds; open-pollinated capsules produce 2-3 seeds.

🌾 Seed harvest and scarification

• Seeds mature 4-6 weeks after pollination.
• Capsule and pedicel turn brown and dry when seed is ready; must harvest before capsules dehisce (split open).
• Seeds can be hand-scarified (scratching seed coat with needle or file) or acid-scarified (concentrated sulfuric acid for 40 minutes, then 5-10 minute rinse).

🔀 Polycross nursery vs. controlled crosses

⚖️ Comparison table

Aspect	Polycross nursery	Controlled crosses
Advantages	Requires less labor; makes more seed/more cross combinations	Both parents known, so genetic advancement based on all genetic variation; superior combinations tracked and can be recreated
Disadvantages	Only female parent known, so genetic advancement based on ½ of genetic variation; unbalanced contribution from some clones (poor seed set, low pollen production, asynchronous flowering)	Requires more labor to make crosses by hand; less seed/fewer combinations created

📐 Theoretical efficiency

• Polycross nurseries are theoretically less efficient because genetic advancement is halved (parental control factor c = ½ vs. c = 1 for controlled crosses).
• Expected gain from selection: GS = (c)(i)VA / σP
  • GS = expected gain or predicted genetic advance from selection.
  • c = parental control factor (½ if only female parent known, 1 if both parents known).
  • i = selection intensity (constant based on percent selected).
  • VA = additive genetic variance.
  • σP = phenotypic standard deviation.

🧪 Case study: CIP experiment

• CIP compared three pollination designs using the same 22 clones:
  • (I) Open-pollinated polycross nursery.
  • (II) Partial diallel design: 4 best clones crossed to each other and to the rest (4 × 22).
  • (III) Factorial design: best 5 clones crossed to rest (5 × 17) ("best by the rest").
• Results showed method (II) produced highest average root yield (18.4 t/ha unselected, 23.5 t/ha after selection) and highest standardized response (R = 0.904).
• Method (I) had R = 1.35; method (III) had R = 0.715.
• Success of partial diallel may be attributed to successful performance of progeny from crossing the top 5 clones.
• Don't confuse: Despite gains from controlled crosses in this scenario, breeders must also consider staffing and resources; not all programs have enough staff for hand pollinations, so a polycross nursery may be a better option.

🌿 Polycross nursery design

• For ≤10 clones: Latin square design recommended (each genotype occurs exactly once in each row and column).
• For large number of clones: Randomized complete block design with replication recommended.
• Plant in isolation; use natural insect cross-pollination and artificial crosses to ensure random pollination.
• Plant extra reps of less vigorous clones or clones that don't flower well.
• Stagger planting times so all clones flower at the same time.

🧬 Cross-incompatibility and sterility

🚫 Self-incompatibility

Sweetpotato possesses a homomorphic, sporophytic type of self-incompatibility that is not affected by environment, chemical treatment, and cannot be overcome using bud pollination.

• Likely controlled by a single S-locus with multiple alleles with a dominant-recessive relationship.
• Self-fertilization is rare.
• Heterostyly also occurs but does not appear to affect fertility.

🔀 Cross-incompatibility types

Type	Expected outcome (A and B are different genotypes)
Reciprocal fertility	A × B and B × A both produce seed
Reciprocal incompatibility	A × B and B × A both do not produce seed
Unilateral fertility/incompatibility	A × B produces seed but B × A does not, OR B × A produces seed but A × B does not

• Cross incompatibility among varieties can limit recombination and seed production, hindering targeted breeding especially when parents with desirable traits are closely related and belong to the same incompatibility group.
• Breeders must maintain large populations containing non-related accessions with complementary traits.

⚠️ Incompatibility vs. sterility

• Don't confuse: Incompatibility and sterility are often used interchangeably but incorrectly.
• Sterility: Failure of reproduction due to failure of a plant to produce viable gametes.
• Incompatibility: Failure of viable gametes to fertilize one another.
• Sterility or reduced fertility in sweetpotato is not uncommon; aneuploidy due to multivalent formation among non-homologous chromosome pairs can lead to unbalanced chromosome numbers in gametes.

👥 Participatory plant breeding and parent selection

👩‍🌾 Participatory plant breeding (PPB)

• Women are responsible for most labor in growing sweetpotato; men are usually involved in land preparation, marketing, weeding, and harvesting (especially when intercropped).
• Traits important to farmers (piecemeal harvest for subsistence farming, resistance to regionally important stresses) are difficult to select for outside target environments.
• Cooperation with local farmers/growers provides access to additional testing locations and insight into farmer/grower preferences.
• PPB practices are beneficial especially during earlier steps when genetic diversity is high and most traits are visually evaluated.
• Less useful at later stages because highly heritable traits are already fixed.
• Involvement of farmers and consumers facilitates rapid adoption of new varieties and lessens chance of rejection.
• Regional and local preferences for flesh color, dry matter content, texture, and adaptability to local environment are critical and should be considered during early selection.

🌍 CIP's convergent-divergent scheme

• Designed to meet regional needs of growers by developing widely adapted cultivars and promoting collaboration among breeders and consumers.
• Starts with a diverse base population evaluated in a single centralized location; superior genotypes are intercrossed.
• Seed from this cycle is sent to collaborators in different regions where it is evaluated and intercrossed with elite germplasm adapted for each location.
• Introduces new germplasm while including elite germplasm carrying alleles for traits specific to a region (disease/pest resistance, taste profile, plant architecture).
• Selection in centralized location focuses on maintaining high genetic diversity while introducing desired traits.
• Selection at local level focuses on selecting varieties that grow well in specific environments.

🧬 Parent selection strategies

• Breeders often use morphological data, coancestry/pedigree information, and molecular marker data to choose parental combinations.
• Combination of analyses allows selection of parents that are phenotypically superior and genetically distant to limit inbreeding depression and cross-compatibility issues.
• Molecular markers useful for identifying duplicate clones or instances when genetically different clones are distributed under the same name.

Example: In one study, 15 clones were characterized using molecular markers (ISSR and RAPD) and 22 agronomic characters. Dendrograms based on morphological traits vs. molecular markers grouped clones differently. Breeders can use this information to select clones that are phenotypically similar (same phenotype group) but genetically different (different genotype group), reducing the number of parental clones from 15 to 8 without significantly reducing genetic variation.

📊 Combining ability

• Important to consider combining ability of individual clones when choosing parents.
• Combining ability can be estimated by comparing performance of a clone vs. average performance of open-pollinated progeny harvested from that clone when grown in a polycross nursery.
• If average performance of progeny is greater than performance of maternal clone, the clone has good combining ability (good GCA) when crossed with other clones.

💪 Exploiting heterosis

🧬 Creating heterotic gene pools

• Breeders are exploring exploiting heterosis in sweetpotato by creating two genetically distinct germplasm pools.
• Selection and recombination within each pool based on general combining ability (GCA) of clones crossed with the other germplasm pool.
• CIP work focused on creating high-yielding orange-fleshed sweetpotato varieties using this approach.

Example: Two populations created:

• Jewel population: Orange-fleshed clones released prior to 2004; mostly North American varieties including Jewel and Resisto.

• Zapallo population: Created using factorial crossing design with 8 male parents (Jonathan, Zapallo, Huambachero, Tanzania, Yurimaguas, Wagabolige, Xushu18, Ninshu1) and 200 orange-fleshed females.

• More than 200 families produced from cross combinations involving 49 clones from Jewel population crossed with 31 clones from Zapallo population.

• Mid-parent (MP) heterosis values for dry root yield were generally low to moderate, but some individual cross combinations/families had high MP heterosis values.

• Root yield of best clone within each family was typically double the average yield of parents; some clones produced 5 times the average yield of parents, indicating success of the approach.

🔧 Trial management and practical considerations

🌾 Trial conditions

• Strongly encouraged to plant check varieties, guard rows, and spreader/susceptible rows; use appropriate field design for each location.
• Best to harvest cuttings from plants that are 10 weeks old; helpful to plant a multiplication plot for each clone about 2.5 months before a trial is planted.
• Single vine cutting usually produces 5 vine cuttings; average-sized storage root yields about 20 vine cuttings.
• Use tip cuttings of same length and vigor when possible; if not available, divide cuttings by replication (best in rep 1, second-best in rep 2, etc.).
• All field management (weeding, fertilizer, irrigation) should be applied uniformly across all reps.
• If possible, each task should be divided so each worker completes an entire rep to partition out differences in technique as a rep effect.

🎯 Selection strategy

• Nearly impossible to simultaneously select top genotypes for every trait without growing an impracticably large population.
• Number of genotypes to screen increases exponentially as number of traits increases.
• Example: To select top 10 clones from 100 genotypes for 10 traits requires 100^10 genotypes to be grown and evaluated.
• Breeders usually compromise and select 3-5 quality traits at a time while maintaining sufficient genetic variation for yield, yield stability, and adaptability.

🔄 Multiple concurrent cycles

• Breeders usually have 3-5 different cycles of ABS at various stages (SN, HT/OT, PT, AT) running at the same time.
• Allows breeders to use advanced clones from later stages of one cycle to create new polycross nurseries/controlled crosses.

🌍 Sources of germplasm

• Institutions that maintain and distribute Ipomoea germplasm:
  • CIP (Centro Internacional de la Papa): >4,200 accessions.
  • USDA/ARS National Genetic Resources Information Network: >900 accessions.
  • NaCRRI National Crops Resources Research Namulonge/Uganda.
  • IITA (International Institute of Tropical Agriculture), Nigeria.
• Though some interspecific hybrid combinations can be made (especially using species within the Batatas section), wild species are typically not used in most breeding programs.

🧭 Overview

🧠 One-sentence thesis

Groundnut breeding aims to overcome low genetic diversity and multiple biotic and abiotic constraints by using conventional crosses, introgression from wild Arachis species, and accelerated breeding methods to develop high-yielding, disease-resistant cultivars suitable for diverse market types and environments.

📌 Key points (3–5)

• Genetic bottleneck: Cultivated groundnut (Arachis hypogaea) arose from a single hybridization event ~4000 years ago between two diploid wild species followed by chromosome doubling, creating low allelic diversity that limits breeding progress.
• Wild species as resistance sources: Wild Arachis species possess high levels of disease and pest resistance not found in cultivated groundnut, but introgression is challenging due to ploidy differences and reproductive barriers.
• Three introgression methods: Breeders use triploid-hexaploid-pentaploid pathways (Method 1), autotetraploid crosses (Method 2), or synthetic amphidiploid recreation (Method 3) to transfer traits from wild diploids into tetraploid cultivated groundnut.
• Common confusion—market types vs botanical varieties: Market types (Virginia, Runner, Spanish, Valencia) reflect seed size and end use, while botanical varieties (hypogaea, fastigiata, vulgaris, etc.) reflect taxonomic classification based on flowering pattern, branching, and pod traits; the two systems overlap but are not identical.
• Speed breeding innovation: Controlled-environment "speed breeding" can advance lines from F₂ to F₄ in one calendar year (3 generations/year vs. 1–2 traditionally), reducing cultivar development time from 10–15 years to 6–7 years.

🌱 Biology and origin of groundnut

🌱 Species characteristics and genome structure

Groundnut or peanut (Arachis hypogaea L. Millsp): a self-pollinated species belonging to the Fabaceae family, classified as a disomic allotetraploid (2n = 4x = 40).

• The two chromosome sets (A and B genomes) are highly diploidized, meaning recombination between A and B genomes is rare except when infrequent quadrivalents form during meiosis.
• Groundnut is found in the Arachis section along with A. monticola (also tetraploid) and ~25 diploid species.
• The genus Arachis contains 68 species subdivided into nine taxonomic sections; groundnut belongs to the Arachis section.
• Unique trait: flowers form above ground but seed pods develop below ground (geocarpy), distinguishing Arachis from closely related genera.

🌍 Geographic origin and evolutionary history

• The genus Arachis originated in South America with six centers of diversity: Paraguay-Paraná, upper Amazon, west coast of Peru, Brazil, and southwest Amazon (Bolivia), plus a secondary center in Africa.
• A. hypogaea is believed to have originated in the region from southern Bolivia to northern Argentina.
• Evolutionary bottleneck: Cultivated groundnut arose ~4000 years ago from a single hybridization between two diploid species (A. duranensis contributed the A genome, A. ipaensis contributed the B genome) followed by spontaneous chromosome doubling of the sterile hybrid to form a fertile allotetraploid (AABB).
• This single origin event plus reproductive isolation from progenitor species created a strong genetic bottleneck, partially responsible for the low allelic diversity in modern cultivated peanut.
• Example: Because all cultivated groundnut traces back to one ancient hybridization, breeders have limited variation to work with compared to crops with multiple domestication events.

🌸 Flower structure and subspecies classification

• Inflorescences occur in leaf axils on primary and secondary branches; typically one flower per inflorescence opens per day.
• Flowers have a standard petal (deep orange to light yellow, rarely white), wing and keel petals, and an elongated tubular hypanthium (calyx tube) that makes flowers appear stalked but they are actually sessile.
• A. hypogaea is divided into two subspecies (hypogaea and fastigiata) and six botanical varieties based on flowering pattern, branching, growth habit, and pod traits (see table below).

Botanical variety	Market type	Key traits
hypogaea	Virginia/Runner	No flowers on central stem, alternating floral/vegetative axes on lateral branches, spreading habit, large seeds (Virginia) or small seeds for peanut butter (Runner)
hirsuta	Peruvian runner	More hairy
fastigiata	Valencia	Flowers on mainstem, sequential/disorganized axes, erect to procumbent, shorter life cycle, 2+ seeds/pod, smooth pericarp, primary type in Uganda
peruviana	n/a	Less hairy, deep pod reticulation
aequatoriana	n/a	Very hairy, deep pod reticulation, purple stems, more branched, upright
vulgaris	Spanish	More branched, upright, shorter life cycle, flowers on central stem, disorganized axes, 2 seeds/pod

Don't confuse: Botanical varieties are taxonomic classifications; market types (Virginia, Runner, Spanish, Valencia) reflect commercial use and seed size preferences but map loosely onto botanical varieties.

🥜 Importance and uses

🥜 Nutritional composition and adaptability

• Seeds contain 35–56% oil, 25–30% protein, 9.5–19.0% carbohydrates, minerals (P, Ca, Mg, K), and vitamins (E, K, B).
• Groundnut is adapted to hot, semi-arid climates, survives under rainfed conditions, fixes atmospheric nitrogen, and requires few inputs—ideal for smallholder farms.
• Provides fat, protein, and phytonutrients (vitamin E, antioxidants) in low-input environments.

🏭 Industrial and agricultural uses

• Human consumption: edible oil, vegetable protein, confectionery products (in-shell, roasted, peanut butter).
• Animal feed: forage (haulms) for horses and cattle; low-quality lots (blemished seeds, aflatoxin-contaminated) are crushed for oil.
• Industrial products: paints, lubricants, insecticides.
• Crop rotation: Natural nitrogen fixation makes groundnut valuable in rotation and intercropping systems.

🔬 Oil quality and market preferences

• Oil quality is determined by the oleic (O) to linoleic (L) fatty acid ratio; higher O/L ratio → better storage, less oxidation, longer shelf life, fewer off-flavors.
• For oil extraction: high oil content and high O/L ratio are priorities; seed size matters less than total yield.
• For human consumption: larger seed size is desired; lower oil content and high O/L ratio preferred.
• Example: In the U.S., ~70% of production is Runner types (small seeds for peanut butter), 20% Virginia (large seeds for in-shell consumption), 10% Spanish, <1% Valencia.

⚠️ Limitations to use

• Allergenic properties in adults and children limit use in food and confectionery industries.
• Aflatoxin contamination caused by Aspergillus niger and A. flavus is carcinogenic and immunosuppressive in animals and humans, restricting marketability.

🐛 Biotic constraints and resistance sources

🦠 Major diseases

Pathogen type	Examples
Fungi	Rust (Puccinia arachidis), early leaf spot (ELS, Cercospora arachidicola), late leaf spot (LLS, Phaeoisariopsis personata)
Viruses	Groundnut rosette disease (GRD), peanut clump virus (PCV), peanut bud necrosis virus (PBNV), tomato spotted wilt virus (TSWV)
Bacteria	Bacterial wilt (Burkholderia solanacearum)
Nematodes	Meloidogyne, Scutellonema, Pratylenchus, Helicotylenchus, Aphelenchoides, Telotylenchus, Paralongidorus species

🐜 Major insect pests

Environment	Pests
Field	Aphids (Aphis craccivora), jassids (Amrasca devastans), leafminers (Aproarema modicella), termites (Isoptera), army worms (Spodoptera litura), thrips (Frankliniella spp.)
Storage	Bruchid (Caryedon serratus), red flour beetle (Tribolium castaneum), rice moth (Corcyra cephalonica), pod-sucking bug (Elasmolomus sordidus)

• Thrips and aphids are more harmful as virus vectors than through direct plant damage.
• Groundnut leaf miner (A. modicella) causes extensive defoliation in major producing regions (e.g., Uganda).
• Seed storage requires careful management due to sensitivity to heat and high moisture at all stages of the seed production chain.

🛡️ Wild Arachis species as resistance sources

• Wild Arachis species possess high levels of disease resistance and wide morphological variation not present in cultivated groundnut.
• Example: A. diogoi has virus resistance genes absent from the cultivated gene pool.
• The excerpt provides tables (Figures 2–7) showing which wild species are resistant to specific pests and diseases (rust, leaf spots, groundnut rosette virus, nematodes, aflatoxin, defoliators, etc.).
• Resistance traits reported in cultivated vs. wild species (from Table 4):

Trait	Cultivated accessions	Wild Arachis species
Rust	169	29
Late leaf spot	69	27
Early leaf spot	37	11
Groundnut rosette virus	116	12
Nematode	21	–
Aflatoxin resistance	21	4
Sclerotinia blight	51	–
Defoliator resistance	9	28
Aphid	2	Not evaluated
Drought	40	Not evaluated

Don't confuse: Wild species have resistance genes but are diploid (2n = 2x = 20) while cultivated groundnut is tetraploid (2n = 4x = 40), so direct crosses are not straightforward.

🧬 Germplasm resources and gene pools

🏛️ Major germplasm collections

• Largest collection: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India—~15,000 accessions of cultivated groundnut and ~500 accessions of 48 wild Arachis species representing all six botanical varieties.
  • Breakdown: var. hypogaea (45.8%), var. vulgaris (36.6%), var. fastigiata (15.7%), var. peruviana (1.7%), var. aequatoriana (0.10%), var. hirsuta (0.13%).
• Other major collections:
  • National Research Center for Groundnut, Junagadh, India (~8,000 accessions)
  • USDA NPGS, Griffin, GA, USA (~9,000 accessions)
  • Texas A&M and North Carolina State University, USA (large wild Arachis collections)
  • National Center of Genetic Resources (CENARGEN), Brazil (>1200 accessions of 81 species from 9 sections)
  • Oil Crops Research Institute (OCRI), China (8083 accessions); Guangdong Academy of Agricultural Sciences, China (4210 accessions)
  • Instituto Nacional de Technologia Agropecuaria (INTA) and Instituto de Botánica del Nordeste (IBONE), Argentina
• Two well-defined core and minicore collections represent the majority of variation in cultivated groundnut germplasm.

🧬 Gene pool classification

Primary gene pool: cultivated accessions (Arachis hypogaea) and the wild tetraploid species A. monticola.

Secondary gene pool: diploid species of the section Arachis that can be successfully crossed with cultivated groundnut.

Tertiary gene pool: species in sections other than Arachis that cannot be crossed with A. hypogaea using conventional crosses; limited by both pre- and postzygotic hybridization barriers.

• Example: A breeder wanting to introgress a trait from a diploid wild species in the secondary gene pool must use special techniques (see next section) because ploidy differences prevent direct crosses.

🔬 Introgression methods from wild species

🔬 Overview of introgression challenges

• Wild Arachis species have been successfully used as sources of resistance to pathogens (Sclerotinia blight, TSWV, early and late leaf blights) and pests (root knot nematodes).
• Challenge: Most wild species are diploid (2n = 2x = 20) while cultivated groundnut is tetraploid (2n = 4x = 40), so direct crosses produce sterile hybrids.
• Three main methods exist for strategic incorporation of diversity from wild species into cultivated groundnut.

🔬 Method 1: Triploid → Hexaploid → Pentaploid → Tetraploid

1. Cross a diploid wild species (2n = 2x = 20) with tetraploid cultivated groundnut (2n = 4x = 40) → produces a sterile triploid hybrid (2n = 3x = 30).
2. Treat the sterile F₁ hybrid with colchicine to double chromosomes → produces a hexaploid plant (2n = 6x = 60).
3. Backcross the hexaploid with cultivated groundnut → produces pentaploid progeny (2n = 5x = 50).
4. Self-pollinate pentaploid progeny for several generations → aneuploid progeny lose chromosomes due to meiotic problems (mispairing, lagging chromosomes) and eventually stabilize at 2n = 4x = 40 (tetraploid).
5. Select for useful agronomic traits from the cultivated parent and exotic traits from the wild species.

Why this method works: Chromosome doubling restores some fertility; repeated selfing and selection allow recovery of stable tetraploids carrying introgressed traits.

Most useful: Method 1 is the most useful for developing new varieties (reviewed by Dwivedi et al. 2003a and Holbrook and Stalker 2003).

🔬 Method 2: Autotetraploid crosses (less useful)

1. Use colchicine to double chromosomes in two wild diploid species (AA and BB) → produces autotetraploids (AAAA and BBBB).
2. Cross the two autotetraploids → produces an allotetraploid hybrid (AABB).
3. Cross and backcross the allotetraploid with cultivated groundnut for multiple generations, selecting for agronomic traits from the cultivated parent and exotic traits from the wild species.

Limitation: Less useful for developing varieties because of sterility problems in the autotetraploids (AAAA, BBBB).

🔬 Method 3: Synthetic amphidiploid (recreating evolution)

1. Cross two wild diploid species (AA and BB) → produces a sterile F₁ hybrid (AB).
2. Treat the sterile F₁ with colchicine to double chromosomes → produces a fertile allotetraploid (synthetic amphidiploid, AABB).
3. Backcross the synthetic allotetraploid with cultivated groundnut A. hypogaea → produces tetraploid hybrids carrying agronomic traits from the cultivated parent and exotic traits from the wild species.

Why this method works: Synthetic tetraploid varieties are relatively normal with normal meiosis, pollen fertility, and genetic recombination.

Design rationale: Method 3 recreates the evolutionary events that originally gave rise to cultivated groundnut (hybridization of two diploid species followed by chromosome doubling).

Example: Arachis cardenasii and A. diogoi were used as A genome donors, crossed with A. batizocoi (B genome donor) → resulting allotetraploid was then crossed with cultivated groundnut to introgress resistance genes.

🔬 Practical considerations for interspecific crosses

• Female parent choice: Crosses are usually more successful when the species with higher ploidy (usually A. hypogaea) is used as the female parent when crossed with diploid wild species.
• Annual vs. perennial: Greater success when the annual species is the female parent and the perennial species (smaller stigmas) is the pollen parent.
• Recombination barriers: Even when crosses produce hybrid progeny, genetic recombination during meiosis is often restricted; desired genes may not be incorporated due to lack of crossing over between different genomes.
• Multiple crosses needed: Because of these problems, breeders must make multiple crosses using different parents to increase the probability of success.

Don't confuse: Successful cross ≠ successful introgression; the hybrid must also undergo normal meiosis and recombination to transfer the desired trait.

🌾 Breeding methods and strategies

🌾 General breeding approaches

• Biparental or complex crosses are used to generate variability.
• Pedigree and bulk-pedigree selection methods are used to identify and select superior genotypes.
• Single seed descent (SSD) (with or without concurrent selection) is often used to increase homozygosity during early generations (F₂–F₅) prior to selection.
• Selection timing:
  • Early generations (F₂–F₅): select for qualitative traits (e.g., disease/pest resistance).
  • Late generations (F₅–F₆ onward): test for quantitative traits (yield, oil content, O/L ratio) and traits influenced by environment.
• Most programs begin preliminary yield trials in F₅ or F₆, by which time heterozygosity has been minimized through inbreeding.

🌾 Recurrent selection and backcross breeding

• Recurrent selection: Sometimes used to maintain genetic diversity in breeding populations, but limited by negative correlations between disease resistance and yield in some populations.
• Backcross breeding: Commonly used for introgressing 1 or 2 genes into a superior genotype.

🌾 Breeding strategies by trait (from Table 5)

Trait	Conventional breeding	Marker-assisted selection	Wide crosses + marker-assisted backcross	Genetic transformation	Genetic basis
Maturity, pod yield, pod size/shape, 100-seed weight, shelling outturn, sound mature seeds	X	–	–	–	Polygenic
Seed dormancy	X	–	–	–	Monogenic
Oleic/Linoleic fatty acid ratio	–	X	–	–	Oligogenic
Aflatoxin	–	–	–	X	Polygenic
Drought	–	X	–	X	Polygenic
Leaf miner, Spodoptera	–	–	X	–	Unknown
Rust, bacterial wilt	X	–	–	–	Oligogenic
Early leaf spot, late leaf spot	–	–	X	–	Polygenic
Groundnut rosette disease	X	–	–	X	Mono- and diagenic
Peanut bud necrosis disease	–	–	–	X	Unknown

Key insight: Strategy depends on genetic basis of the trait—monogenic and oligogenic traits are amenable to conventional breeding or marker-assisted selection, while polygenic traits with no cultivated sources require wide crosses or genetic transformation.

🌾 Breeding goals

• Yield improvement: Less vegetative biomass, shorter main stem, increased flower production.
• Quality: High oil content for extraction, large seeds for confectionery, high oleic/linoleic ratio.
• Resistance: Major pests and diseases (rosette, Cercospora leafspots, peanut bud necrosis, root rot), aflatoxin resistance.
• Adaptation: Short to medium-term maturity, drought tolerance.

⏱️ Speed breeding innovation

⏱️ Traditional timeline constraints

• In temperate regions, groundnut breeders can grow only 1 generation per year in the field → 10–15 years from first cross to cultivar release.
• Use of a winter nursery for single seed descent can increase to 2 generations per year, reducing time to develop a cultivar.

⏱️ Speed breeding concept

Speed breeding: use of a controlled environment with continuous light and optimal temperatures and humidity to advance lines from F₂ to F₄ in a single calendar year, increasing the number of generations per year to 3.

• Decreases growing period to maturity by ~30% relative to field time.
• Reduces cultivar development time from 10–15 years to 6–7 years.

⏱️ Three breeding strategies compared

Strategy	Description	Time to F₆
Strategy 1	Pedigree breeding with one summer generation per year	42 months
Strategy 2	Pedigree breeding with two generations per year (1 summer, 1 winter nursery)	23 months
Strategy 3	Speed breeding/SSD (F₂–F₄ in controlled environment with 24-hour lights, optimal conditions)	17 months

• In all strategies, F₅ is grown in the field to maximize F₅:₆ seed numbers for preliminary yield trials in F₆.

⏱️ Best applications of speed breeding

• Backcrossing programs: Best suited for incorporating simply inherited traits controlled by one or two genes into a new variety.
• RIL development: Appropriate for rapid development of recombinant inbred lines (RILs) useful for genetic studies and molecular marker discovery.

Don't confuse: Speed breeding accelerates generation advancement but does not change the need for field testing of quantitative traits like yield in later generations.

🌾 Breeding example: 'Bailey' cultivar

🌾 Breeding objective

Develop a large-seeded Virginia-type peanut (Arachis hypogaea L. subsp. hypogaea var. hypogaea) with partial resistance to five diseases common in the Virginia-Carolina production area:

• Early leaf spot (caused by Cercospora arachidicola)
• Late leaf spot (caused by Cercosporidium personatum)
• Cylindrocladium black rot (caused by Cylindrocladium parasiticum)
• Sclerotinia blight (caused by Sclerotinia minor)
• Tomato spotted wilt (caused by Tomato spotted wilt tospovirus)

The variety should possess characters suitable for the confectionary market (sold as in-shell groundnut or shelled kernel).

🌾 Breeding method

• Modified pedigree selection with several generations of single seed descent to develop a pureline cultivar named 'Bailey'.
• Initial cross: NC 12C (cultivar partially resistant to early leaf spot) × N96076L (breeding line resistant to early leaf spot, CBR, and TSWV).
• Backcross strategy: Multiple F₁ plants were backcrossed as males to NC 12C to increase chances of recovering an inbred line with suitable agronomic characteristics, because NC 12C possessed more desirable traits relative to N96076L.
• Selection approach: Simultaneous selection for resistance to multiple diseases using both early-generation testing for resistance combined with late-generation selection for improved pod and seed characteristics in superior families.

Why backcross to NC 12C? NC 12C was the superior parent for agronomic traits; backcrossing recovers more of the desirable background while retaining the resistance genes from N96076L.

🚧 Limitations and challenges

🚧 Genetic and breeding limitations

1. Unfavorable linkages: Useful disease resistance genes are often linked to loci conferring undesirable pod and seed characteristics.
2. Maturity and photoperiod sensitivity: Most disease-resistant accessions are later maturing types that are more sensitive to photoperiod and partition less to below-ground pod development.
3. Genotype × environment interactions: Large G×E interactions for economically important traits complicate selection.
4. Small progeny numbers: Artificial crosses produce only 1–2 seeds per pod, limiting the number of progeny per cross; breeders must make as many crosses as possible, especially for backcrosses introgressing traits from wild species.

🚧 Practical considerations for selection

• Photoperiod and temperature effects: Greatly affect how growth is partitioned between above- and below-ground structures; critical to make selections in an environment similar to the target environment, especially for genotypes with large seeds.
• Resistance testing environment: Important to select for pest and pathogen resistance in an environment with the same photoperiod conditions as the target environment, because late maturing types are often more affected by photoperiod variation.
• Outcrossing rates: Typically around 2%, though rates near 8% have been identified; low outcrossing supports the use of pureline breeding methods.

🚧 Crossing success factors

• Timing: Artificial crosses are most successful when made during early morning hours after sunrise when pollen is mature and viable and stigmas are receptive.
• Humidity: High humidity helps ensure pollen adhesion to the stigmatic surface; spraying greenhouse floors with water in the morning increases humidity, especially on dry days.
• Pod development timing: In cultivated groundnut, pod development begins 16–17 days after pollination; in other species, development is delayed until 23–25 days.
• Peg fragility: Pegs of cultivated groundnut are short and robust; pegs of wild Arachis species may be 1 m or more in length and are fragile, so it is preferable to use cultivated groundnut as the female parent whenever possible.

🚧 Recommended approach

Because of these limitations, a varied approach to breeding groundnut is recommended (combining conventional breeding, marker-assisted selection, wide crosses with marker-assisted backcross, and genetic transformation depending on the trait and its genetic basis).

📚 Summary of breeding system

📚 Core breeding cycle

• Biparental or complex crosses generate variability.
• Pedigree and bulk-pedigree selection identify superior genotypes.
• Single seed descent (with or without selection) increases homozygosity in early generations (F₂–F₅).
• Early-generation selection (F₂–F₅) targets qualitative traits (disease/pest resistance).
• Late-generation testing (F₅–F₆ onward) evaluates quantitative traits (yield, oil content, O/L ratio) influenced by environment.
• Preliminary yield trials begin in F₅ or F₆ when heterozygosity is minimized.

📚 Key constraints shaping breeding strategy

• Narrow genetic base: Single origin event ~4000 years ago created a genetic bottleneck; successful cultivars are often recycled as parents, further narrowing diversity.
• Introgression difficulty: Wild species have valuable resistance genes but ploidy differences, sterility, and restricted recombination make introgression challenging.
• Negative correlations: Disease resistance and yield are sometimes negatively correlated, limiting the use of recurrent selection.
• Environmental sensitivity: Photoperiod and temperature strongly affect trait expression, requiring selection in target environments.

Don't confuse: Groundnut's self-pollinating nature and low outcrossing rate (~2%) support pureline breeding methods, but the narrow genetic base means breeders must actively seek diversity from wild species and diverse germplasm collections to make progress.

🧭 Overview

🧠 One-sentence thesis

Cassava breeding aims to develop high-yielding, disease-resistant clonal cultivars through controlled crosses and multi-year selection trials, leveraging the crop's vegetative propagation and increasing genetic diversity through molecular tools and farmer participation.

📌 Key points (3–5)

• What cassava is: a perennial shrub with starch-rich tuberous roots, serving as a staple food for over 500 million people, primarily in developing countries.
• Why vegetative propagation matters: cassava is highly heterozygous, so seed propagation produces variable offspring; commercial cultivars are clones multiplied by stem cuttings to preserve desirable traits.
• Breeding pipeline: starts with large segregating populations (up to 100,000 seedlings), then progressively selects through five years of trials (seedling → clonal → preliminary → advanced → regional) to release 1–5 superior clones.
• Common confusion—roots vs. stems: cassava roots are true roots (not tubers) and cannot be used for propagation; only stem cuttings (stakes) can regenerate plants clonally.
• Key objectives: high root yield, improved root quality (low cyanide, high dry matter), resistance to devastating diseases (cassava mosaic disease, cassava brown streak disease), and extended post-harvest shelf life.

🌱 Cassava biology and production

🌿 Plant anatomy and growth

Cassava (Manihot esculenta Crantz): a dicot perennial shrub in the family Euphorbiaceae, reaching 1–4 m in height, with tuberous storage roots containing 20–40% starch.

• Growth habit: two types—erect (with or without branching at the top) and spreading (not cultivated). Branching occurs due to flower induction ("reproductive branchings").
• Roots: true roots, not tubers. Only 3–10 of the fibrous roots bulk into storage roots through secondary growth; the rest remain thin and absorb water and nutrients.
• Why growth habit matters: erect growth with intermediate branching height correlates with high root yield, a key breeding target.

🌍 Economic importance and production

• Global rank: sixth-most important crop worldwide (after wheat, rice, maize, potato, barley).
• Staple for 500 million people, mostly in developing countries where food security is critical.
• Adaptability: grows between 30°N and 30°S, tolerates drought (600 mm annual precipitation), thrives on marginally fertile soils (pH 3–8), and roots can remain unharvested in the ground as a food security reserve.
• Main production regions (2014): Africa (largest share), Asia, Caribbean, South America. Top producer: Nigeria.

🍽️ Uses of cassava

Use	Description
Food	Roots eaten raw, cooked, or baked; leaves consumed as vegetables; numerous culinary applications worldwide.
Animal feed	High energy content makes roots ideal carbohydrate ingredient; all plant parts usable; majority of South Asian production goes to animal feed (chips, pellets).
Industrial	Starch extraction for wide variety of uses; bioethanol production gaining attention due to fossil fuel concerns.

🌸 Reproductive biology and propagation

🌺 Flowering and pollination

• Monoecious: separate male and female flowers on the same plant.
• Timing variability: flowering is genotype- and environment-dependent; some genotypes flower one month after planting, others take 24 months. Synchronization is challenging. Rarely flowers during long dry periods (irrigation needed for crossing blocks).
• Inflorescence structure: female flowers (larger, fewer) at the base; male flowers (numerous) on the upper part.
• Protogyny: female flowers open 1–2 weeks earlier than male flowers on the same inflorescence, but flowers on different inflorescences can overlap, allowing selfing.

🐝 Pollination behavior

• Primarily cross-pollinated by insects, despite self-pollination occurrence.
• Pollen characteristics: large and heavy (122–148 μm), short longevity (no more than 2 days).
• Inbreeding depression: severe; selfed progeny show low vigor and lack competitiveness.

🌰 Seed formation and dormancy

• Fruit: trilocular capsule, each containing a single seed. Takes 75–90 days after pollination to mature.
• Explosive dehiscence: bagging required before maturity to collect seed in controlled crosses.
• Dormancy: freshly harvested seeds are dormant; 3–6 months of dry storage at ambient temperature breaks dormancy.
• Germination: physiologically active seed germinates in ~15 days at 30–35°C. Seed stored at 4–5°C and 60% relative humidity maintains >80% germination for a year.

✂️ Vegetative propagation methods

• Why stem cuttings: cassava plants are highly heterozygous; seed propagation produces heterogeneous offspring that lose desirable traits. Commercial propagation uses stem cuttings (stakes).
• Multiplication rates:
  • Standard: one mature plant (one year) produces 10–30 stakes (~25 cm each).
  • Enhanced: reducing stake size to 2-node or 1-node increases rate to 100 or 200 per plant per year.
  • High-density system: growing 2-node stakes in moist chambers, continuously removing and rooting shoots can achieve multiplication rate of 36,000.
• Tissue culture: plantlets regenerated from pre-existing meristem or somatic embryogenesis; virus-indexed plants obtained by culturing very small meristems.

🎯 Breeding objectives and constraints

📈 Yield improvement

• Highest priority for most cassava breeding programs.
• Complex trait: affected by genetics, environment, and their interactions.
• Correlated traits:
  • Intermediate branching height → highly correlated with high yield.
  • Good leaf retention (longer leaf life) → correlated with high root yield.

🥔 Root quality traits

• Cyanogenic glucosides: cultivars with highly reduced levels desired (lower hydrogen cyanide content).
• Dry matter content: increased dry matter preferred.
• Protein: naturally low in cassava roots; enhanced protein content desirable for animal feed.
• Starch: altered starch content and composition for specialty uses.
• Consumer acceptance: root quality affects adoption success.

🦠 Biotic stress resistance

• Devastating viral diseases:
  • Cassava mosaic disease (CMD): can cause significant yield loss.
  • Cassava brown streak disease (CBD): major constraint.
• Bacterial diseases: cassava bacterial blight, root rot.
• Insect pests: cassava mites, mealybugs, whiteflies (whiteflies transmit CMD).
• Wild relative contribution: M. glaziovii (ceara rubbertree) made significant contributions to CMD resistance.

⏱️ Abiotic stress: post-harvest deterioration

• Notoriously short shelf life: often within 2 days after harvest.
• Manifestation: internal discoloration causing immediate loss of marketability.
• Breeding goal: develop cultivars resistant to post-harvest physiological deterioration.

🔬 Breeding scheme and methods

🌾 Population development (three methods)

Method	Description	Advantages / Limitations
Controlled biparental crosses	Male flowers collected from male parent, used to pollinate chosen female parents.	Limited seed yield due to labor; but cassava pollination is easy (large flowers, large sticky pollen, no emasculation needed).
Crossing blocks	Set of cultivars grown in isolated block; male flowers removed from female parents; seed harvested from female parents are hybrids.	Commonly used in recurrent selection; physical separation of male/female flowers makes male removal easy.
Polycross	Elite parents replicated and randomly grown in polycross nursery; random pollination ensures fair representation.	More efficient in producing sufficient hybrid seed than biparental; does not prevent self-pollination.

📅 Five-year selection pipeline

🌱 Year 1: Seedling evaluation trial

• Starting population: up to 100,000 hybrid seeds sown directly in the field.
• Screening criteria: resistance to major diseases (CMD, CBD), ideal growth habit (medium branching height ~100 cm), low HCN in leaves.
• At harvest: compact roots with short necks.
• Selection philosophy: concentrate on eliminating poor genotypes rather than selecting good ones.
• Output: up to 3,000 individuals selected.

🌿 Year 2: Clonal evaluation trial

• Method: entries multiplied by stem cuttings, grown in single-row plots without replication.
• Evaluation: disease resistance, root yield, root dry matter content, HCN content in root.
• Check cultivar: locally-adapted leading cultivar grown to aid selection.
• Output: up to 100 individuals selected.

🌾 Year 3: Preliminary yield trial

• Method: larger plots, at least 2 replications, multiple locations, randomized within each location.
• Evaluation: root yield, root quality, disease/pest resistance, consumer acceptance.
• Output: 25 genotypes selected.

🌽 Year 4: Advanced yield trial

• Method: larger plot size, more replications (e.g., 4), more locations.
• Focus: root yield and root quality traits.
• Output: up to 5 genotypes selected.

🏆 Year 5: Regional yield trial

• Method: large-scale farms, multiple locations within target region, at least 4 replications per location.
• Final selection: based on yield, root quality, consumer acceptance.
• Outcome: planting materials rapidly multiplied and distributed to end-users.

Continuous improvement: "upgraded" base populations created by crossing elite entries from each step with additional germplasm; new selection cycles performed on upgraded populations.

🤝 Farmer Participatory Breeding (PPB)

• Traditional approach: farmers not involved until near commercial release; limited influence on cultivar development.
• PPB approach: farmers play active role early in breeding process.
• Example (Kenya): farmers invited after 1st clonal evaluation trial to evaluate root quality traits (appearance, size, taste/texture); inputs used alongside breeders' in final selection.
• Why it matters: subsistence farmers in Africa often grow multiple crops/cultivars to counter uncertain climatic conditions. PPB proven useful and increases adoption rate of new cultivars.

🧬 Genetics and molecular tools

🧪 Marker-assisted breeding

DNA markers: variations in DNA sequences detected using PCR or high-throughput sequencing; not affected by environment or developmental stage; can be assessed anytime from any tissue.

• Applications: cultivar fingerprinting, assessing genetic diversity, marker-assisted selection.
• Marker types developed: many simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers.
• High-resolution map: composite map covering 2,412 cM, organizing 22,403 genetic markers on 18 chromosomes (International Cassava Genetic Map Consortium).
• Practical use: linked DNA markers developed for cassava mosaic disease resistance; map facilitates marker-assisted selection.

🧬 Genome sequencing

• Genome size: ~770 Mbp (resequencing project reported 760 Mbp).
• Sequenced from: partially inbred line AM560-2 developed at CIAT.
• Availability: complete sequence available via Joint Genome Institute (JGI).
• Chromosome number: 36 chromosomes, forming 18 bivalents at meiosis. Cytological and sequence evidence supports paleotetraploidy nature.

🔬 Genetic transformation

• Advantages over traditional breeding:
  • Very long and imprecise traditional process (>10 years to release new cultivar).
  • Transformation introduces traits efficiently and rapidly.
  • Breaks reproductive barrier; transfers traits from unrelated species.
  • Vegetative propagation allows immediate "fixing" of traits in elite cultivars without inbreeding or backcrossing.
• Methods: Agrobacterium or particle bombardment; success relies on efficient plant regeneration protocol using friable embryogenic callus (FEC) from immature leaf explants.
• Demonstrated applications:
  • Insect and disease resistance.
  • Herbicide tolerance.
  • Altered starch content, increased protein.
  • Reduced cyanogenic content in storage roots.
  • BioCassava Plus (BC+): biofortified cassava with increased zinc, iron, proteins, vitamin A (supported by Bill and Melinda Gates Foundation).

🏛️ Germplasm conservation

🌍 Importance and erosion

• Why conserve: genetic diversity essential to plant breeding; modern agriculture and habitat destruction cause significant erosion of cassava genetic resources.
• Major collections: Centro Internacional de Agricultura Tropical (CIAT, Colombia) and International Institute for Tropical Agriculture (IITA, Nigeria) hold UN mandate for cassava; maintain large numbers of accessions freely available to the public.

📦 Three conservation methods

🌾 Field genebanks

• Method: cassava plants representing each accession grown and maintained in the field.
• IITA practice: 11 plants per accession on 2.5 m row plot, 25 cm between plants, 50 cm between rows.
• Limitations: requires large field space; germplasm may be lost due to biotic and abiotic stresses.

🌰 Seed genebanks

• Method: seed maintained in controlled environment with low temperature and humidity.
• Viability: cassava seeds remain viable after 14 years of hermetic storage at -20°C with 6% moisture content.
• IITA practice: seeds harvested in bulk from all plants of an accession (therefore heterogeneous).

🧪 In vitro genebanks

• Method: cultures established from apical buds or nodes with axillary buds, maintained on media/conditions that slow growth.
• Maintenance: cultures can be kept 8–12 months without subculture.
• Advantage: following disease and virus indexing, suitable for exchange among collaborators across countries.

📊 Major collections (FAOSTAT 2010)

• CIAT: 5,436 accessions (87% landraces/old cultivars, 11% research materials, 1% wild species).
• Brazil: 2,889 accessions (100% others/mixture).
• IITA: 2,756 accessions (28% landraces, 47% research materials, 25% others/mixture).
• Other significant collections: India (1,327), Nigeria (1,174), Uganda (1,136), Malawi (978), Indonesia (954), Thailand (609).

🌏 Origin and diversity

🗺️ Geographic origin

• Origin: widely believed to be from the southern rim of Amazonia.
• Domestication: ~5,000–7,000 years BC.
• Introduction to Africa: by Portuguese and Spanish explorers, likely in the sixteenth century.
• Asia: did not become popular until the 1960s.

🌿 Genus Manihot

• Species diversity: contains more than 100 species, all naturally occurring between 33°N (southwest USA) and 33°S (Argentina).
• Wild relatives used in hybridization: M. catingae, M. dichotama, M. glaziovii, M. melanobasis, M. saxicola.
• Don't confuse: only M. glaziovii has made significant contributions to developing CMD-resistant germplasm; other wild relatives have been used but with less impact.

🎓 Hybridization techniques

🌸 Preparing female flowers

• Readiness test (Kawano 1980): peel back a petal of unopened female flower; if a drop of nectar is observed at the base of the pistil, the flower will open that afternoon.
• Protection: ready flowers covered with large cloth bag (20 × 25 cm) to avoid stray pollen.
• Emasculation: generally not necessary because male flowers on same inflorescence open 1–2 weeks later.

🌼 Preparing male flowers

• Collection time: between noon and 2 pm; freshly open male flowers collected by glass bottle or suitable device.
• Pollination: can be performed immediately; single male flower can pollinate up to 3 female flowers.
• Timing: pollination after 5 pm less effective.
• Post-pollination: pollinated flowers can be left uncovered (minimal risk of stray pollen hybridization); covering with small cloth bag needed 1–2 weeks later to collect seeds.

🧭 Overview

🧠 One-sentence thesis

Viable seed supply system strategies—spanning formal, informal, and integrated approaches—are essential to ensure farmers have timely, affordable access to high-quality seed, which drives crop productivity, household incomes, and agricultural sustainability in sub-Saharan Africa.

📌 Key points (3–5)

• Three seed system types: formal (commercial, highly regulated), informal (farmer-based, flexible), and integrated (semi-formal, community-based).
• Formal vs informal contribution: formal systems produce only 10–20% of seed demand in Africa; informal systems supply 80–100% but lack regulation and quality assurance.
• Variety release requirements: new cultivars must demonstrate distinctness, uniformity, stability (DUS) and value for cultivation and use (VCU) through multi-year, multi-location trials.
• Common confusion: seed classes (breeder → foundation → registered → certified) represent successive multiplication stages with decreasing genetic purity standards, not different varieties.
• Plant breeder's rights: intellectual property protection (via UPOV or regional bodies like ARIPO) grants breeders exclusive control over seed production, sale, and import/export of their new varieties for 20–25 years.

🌾 Seed system categories in sub-Saharan Africa

🏢 Formal (commercial) seed system

The formal seed supply system is highly regulated and covers seed production and supply mechanisms involving a chain of activities leading to clearly defined products, i.e., certified seed of verified cultivars.

• Who participates: public and private sectors (seed companies, research institutions).
• What it covers: formal plant breeding → multiplication following established procedures (processing, bagging, labeling, marketing).
• Quality standards: maintains distinctness, uniformity, and stability (DUS) of varieties; assures cultivar identity and purity through all multiplication levels (breeder/prebasic → foundation/basic → registered → certified).
• Crop focus: mainly economically viable crops with recurrent seed demand (e.g., hybrid maize).
• Contribution: produces only 10–20% of seed demand in Africa; dominant in developed countries but more complex than informal systems.

🌱 Informal seed system

Also called 'farmer seed system' or 'traditional seed system'; a chain of seed multiplication and marketing steps involving farmers who produce, disseminate, or access seed through farmer-to-farmer exchange based on barter system and local grain/seed markets.

• Who participates: farmers, small private companies, farmer cooperatives.
• Characteristics:
  • Flexible, operates under non-law regulated conditions.
  • Cultivars may be landraces, local varieties, mixtures, or heterogeneous populations.
  • Seed quality (purity, physical, physiological) is variable.
• Contribution: covers 80–100% of seed supply to farmers in most of sub-Saharan Africa.
• Benefits to farmers:
  • Retain seed on-farm from previous harvest (farm-saved seeds).
  • Farmer-to-farmer exchange networks.
  • No certification process → less expensive.
• Limitations: little is known about production and marketing chains due to lack of regulation; enhances wide diffusion but quality is inconsistent.

🤝 Integrated (semi-formal) seed supply system

A mix of informal and formal seed supply systems where small farmers and community-based organizations (e.g., small farmers' cooperatives) multiply and sell small amounts of good quality seed of improved cultivars to other farmers within a restricted production area with minimal quality control.

• Combines elements: community-based production with some quality oversight.
• Scale: small-scale, localized distribution.

🔬 Variety development and release regulations

📋 Cultivar regulation system

• Purpose: controls the release of cultivars by private seed companies and government research institutions.
• Requirements for registration: new cultivars must show:
  • Distinctness, uniformity, and stability (DUS).
  • Value for cultivation and use (VCU): better performance than existing commercial cultivars in target environments.
• Testing duration: DUS and VCU tests typically take 1–3 years (three seasons) before sufficient data are available for registration.
• Challenge: seed laws and implementation differ and are inconsistent among sub-Saharan African countries, making it costly and discouraging for private seed companies to release and market new cultivars across borders.

🧪 Variety performance testing

• Focus: selection of new cultivars with desirable traits meeting farmer/consumer requirements.
• Process: multi-environment, multi-year trials (2–3 years) across different agro-ecological zones (at least 3–4 locations) to select better-performing cultivars.
• Standard: new cultivar must show better performance in an acceptable number of tests compared to existing/commercial cultivar(s).
• Decision-making: National Variety Releasing Committee (NVRC) makes the release decision.
• Exception: in countries with few released varieties, NVRC may release varieties even if not better than existing ones, provided they have unique quality.

✅ Common features of release regulations

• Developed guidelines and standard procedures for testing cultivars proposed for release.
• Independent National Varietal Releasing Committee (NVRC) formed with mandate to recommend release or reject based on test results.
• Officially released cultivars must be registered and made available to the public with clear information: morphological description, year of release, variety name, releasing institution.

📄 Conditions for release

• Appropriate documents: clear morphological description, distinguishing characters, vegetative description, quality tests (palatability, taste, etc.).
• Sufficient season data from multiple sites (check country guidelines); wide adaptation (national level) or specific adaptation (regional level).
• New cultivar shows better performance compared to existing commercial cultivars in intended environments.
• Cultivar demonstrates DUS and VCU.

🌍 Regional harmonization example

• Drought Tolerant Maize for Africa (DTMA) under CIMMYT has proposed regional harmonization of seed laws in eastern, southern, and western Africa.
• Benefit: a maize cultivar released in one country can be considered for automatic release in neighboring countries with similar environments.
• Impact: helps release varieties in mega-environments covering large adaptation zones across country boundaries; creates larger seed markets and faster variety release across regions.

🛡️ Intellectual property and breeder's rights

🌐 International Union for the Protection of New Varieties of Plants (UPOV)

An intergovernmental organization with a goal of providing and promoting plant variety protection.

• Objective: strengthen development of new cultivars that benefit farmers; recognize rights of plant breeders for varieties they develop.
• Mechanism: UPOV convention provides intellectual property rights to the breeder, enabling full authority on seed multiplication of their cultivar.
• Eligibility: breeder's right is implemented if the variety is new, distinct, uniform, and stable.
• Sub-Saharan African members: South Africa, Kenya, Morocco, Tunisia (as of 2017).

🌍 African Regional Intellectual Property Organization (ARIPO)

• Purpose: pooling resources of member countries to solve intellectual property (IP) issues through harmonizing IP laws and facilitating IP activities.
• Members (19 countries): Botswana, The Gambia, Ghana, Kenya, Lesotho, Malawi, Mozambique, Namibia, Sierra Leone, Liberia, Rwanda, São Tomé and Príncipe, Somalia, Sudan, Swaziland, Tanzania, Uganda, Zambia, Zimbabwe.

🔐 Plant breeder's right

An intellectual property right granted to a crop breeder in respect to new plant varieties developed by him/her against exploitation without his/her permission.

• Scope: exclusive control over new plant materials (seed, cuttings, tissue culture, harvested materials including fruit and foliage) for a number of years.
• Duration (South Africa's Plant Breeders' Rights Act, Act 15 of 1976):
  • 25 years for vines and trees.
  • 20 years for annual crops.
  • Starts from the date a certificate of registration is given.
• Benefits: provides recognition and economic reward for breeder's effort; energizes breeders to continue developing new and better high-yield, good-quality varieties.

✅ Eligibility for protection

The cultivar must be:

• New: not previously commercialized.
• Distinct: distinguishable from any other existing cultivars of common knowledge at the time of application.
• Uniform: adequately uniform in its unique characteristics.
• Stable (DUS): essential characteristics remain unchanged after repeated propagation or multiplication.
• Acceptable variety name.

👤 Who can apply

• The breeder who bred the cultivars.
• The employer of the breeder who bred the varieties.

🔑 Rights of plant breeders

According to South Africa breeder's right, the following must be authorized by the breeder:

• Seed production and reproduction.
• Permission for sale.
• Exporting and importing.

The breeder has:

• The right to sell their new varieties, including the right to delegate other persons to sell or multiply their varieties.
• Full right to multiply their new cultivars, including the right to authorize other persons to multiply or propagate their varieties for sale.

Example: A breeder develops a new drought-tolerant maize variety. With plant breeder's rights, they control who can produce seed of that variety, who can sell it, and whether it can be exported—ensuring they receive economic benefit from their innovation.

🌾 Seed quality, certification, and production

🏅 Seed certification

A tool to produce genetically pure and good quality standard seed of improved varieties for farmers.

• What it assures: true-to-type physical purity, germination, seed health, moisture content, true labeling, backed with appropriate laws and regulation, and DUS.
• Importance: newly released variety must have excellent seed quality attributes, which is critical to crop production; poor quality seed lowers the potential yield of the variety.

📊 Seed quality attributes

Attribute	Description	Standards (example)
Genetic purity	Seeds are genetically pure, true-to-type of the specific seed lot	Breeder seed: 100%; Foundation seed: 99.5%; Certified seed: 98%
Physical purity	Minimal damaged seed (broken, cracked, shriveled), minimal noxious weed seed or other crop seeds, minimal inert matter, minimal diseased seed (discolored, stained)	Clean, uniform seed lot
Physiological attributes	High germination and vigor of the seed	High germination percentage
Seed health	Free from diseases and insect pests	No seedborne diseases that impact health and productivity

Don't confuse: genetic purity (true-to-type of the variety) with physical purity (absence of foreign material, weed seeds, damaged seeds).

🏭 Seed production systems

• Formal: involves public institutions and private seed companies.
• Informal: includes small-scale informal village and community-level seed production.
• Crop differences:
  • Hybrid maize seed production is mainly run by both public and private seed companies.
  • Legume crop seeds are not extensively produced by public and private seed companies; mostly produced by informal village and community-level production (legumes are not widely commercial crops in most African countries, so market demand for good quality and uniform seeds is low).
• Quality control: advanced/formal seed production systems follow international protocols (e.g., International Seed Testing Association (ISTA), OECD seed schemes, UPOV).
• Example: seed laboratories of Zimbabwe and Zambia are accredited to ISTA for seed quality control.

🔢 Different classes of seed

Four major classes of seeds are currently produced by public institutions and private companies in sub-Saharan Africa:

1. Breeder seed

   The highest purity of the new cultivar, maintained and multiplied by breeder, and provided to seed companies for multiplication by breeder's institutions.

   • Used to increase foundation seed.
   • Genetic purity: 100%.

2. Foundation seed

   Produced from breeder seed; breeder and research institutions keep genetic purity and identity.

   • Depending on seed regulation, may be produced by public or private seed companies.
   • Genetic purity: 99.5%.

3. Registered seed

   Produced from foundation seed by selected farmers and seed companies under seed regulation agency to keep varietal identity and purity.

   • Production undergoes field and seed (lab) inspection by representative seed inspectors to ensure fulfillment of standards.

4. Certified seed

   Produced from foundation, registered, or sometimes certified seed; available to farmers for general production.

   • Grown by selected farmers with experience and capacity to produce certified seed.
   • Maintains varietal purity.
   • Subjected to field and seed (lab) inspection prior to approval by certifying agency.
   • Genetic purity: 98%.

Don't confuse: seed classes are successive multiplication stages from the original breeder seed, not different varieties. Each class has progressively lower genetic purity standards but still maintains varietal identity.

🌍 Comparing international seed class systems

US Seed Class	Label color	Equivalent OECD Seed Classes	OECD Label color
Breeder	n/a	Prebasic	White with diagonal violet stripe
Foundation	White	Basic	White
Registered	Purple	Basic	White
Certified	Blue	1st Generation Certified Seed	Blue
Certified produced from certified	Blue	2nd Generation Certified Seed	Red

Note: Some sub-Saharan African countries (South Africa, Kenya, Zimbabwe) have accredited seed certification by OECD and AOSCA (Association of Official Seed Certifying Agency).

🔄 Formal vs informal seed sector comparison

Component	Formal seed system	Informal seed system
Varietal development	Plant breeders employed by public institution or private company select for specific traits and produce varietal pure "breeder seed"	Farmers select seed from plants with desirable traits, but seed is not necessarily varietally pure
Seed production	State or private seed companies multiply seed under strict conditions to avoid mixture of varieties; sometimes contract farmers	Farmers produce seed along with crops; in some cases the portion destined for seed is given special management
Processing	Seed is dried using mechanical dryers; processing machinery removes dirt, rocks, and seeds of other plants; may be treated to extend shelf-life	Seed may be cleaned by hand, dried in the sun, and sometimes treated to extend shelf-life
Certification	Seed is subjected to formal quality control procedure based on tests of purity and germination of random samples	Seed is generally not tested, certified, or labeled
Distribution	Seed is bagged and labeled, distributed by stockists, extension agents, NGOs, and cooperatives	Farmers use seed they save from previous harvest, acquired from other farmers through barter, gift, or sales, or acquired in local grain markets

Example: A farmer in the formal system receives certified hybrid maize seed in a labeled bag with guaranteed germination rate; a farmer in the informal system saves seed from their best plants and exchanges it with neighbors, with no formal quality testing.