Plant breeding

In short

Plant breeding is the deliberate genetic improvement of crop plants — assembling variability, selecting superior genotypes and multiplying them into stable varieties or hybrids with higher yield, better quality and resistance to stresses. It rests on Mendelian genetics, quantitative genetics and, now, molecular markers and recombinant DNA. For a B.Sc Botany student it is a core scoring unit in the Genetics and Biotechnology paper and a standing topic in ICAR-JRF/SRF, CSIR-UGC NET (Life Sciences), GATE Biotechnology and IARI entrance papers. Employers who test it include ICAR institutes and State Agricultural Universities, and seed companies such as Nuziveedu, Kaveri, Rasi, Mahyco, Bayer-Monsanto, Syngenta, Advanta and Namdhari.

Explained

Objectives, scope and genetic base

• Definition: the art and science of changing the genetic constitution of plants for human benefit; "art" because selection needs a trained eye, "science" because it applies genetics and statistics.
• Objectives: higher yield; better quality (protein, oil, fibre length, milling recovery); resistance to diseases, insects and abiotic stress (drought, salinity, heat); early maturity and photo-insensitivity for multiple cropping; synchronous maturity and lodging resistance for machine harvest; wider adaptation; non-shattering, determinate habit.
• Prerequisite — variability. Sources: existing land races and local cultivars, germplasm collections, wild and weedy relatives, introduction from abroad, recombination by hybridization, induced mutation, polyploidy, somatic variation and genetic engineering.
• Centres of origin (Vavilov, 1926) and centres of diversity tell the breeder where to look for genes; the Hindustani/Indian centre is the origin of rice, sugarcane, pigeonpea, brinjal, cucumber, mango, black pepper.
• Germplasm classes: land races, obsolete cultivars, modern cultivars, breeding lines, wild relatives. Conserved ex situ (seed gene banks at −18 to −20 °C, field gene banks, in vitro and cryobanks at −196 °C) and in situ (biosphere reserves). India's National Gene Bank at NBPGR, New Delhi holds over four lakh accessions (figure grows yearly).
• Modes of reproduction decide the method: self-pollinated (wheat, rice, barley, chickpea, pea, groundnut, tomato — natural outcrossing under 5%), cross-pollinated (maize, bajra, sunflower, cucurbits, alfalfa — above 50%), often cross-pollinated (sorghum, cotton, pigeonpea), and asexually propagated (sugarcane, potato, banana, mango).

Breeding self-pollinated crops

• Plant introduction: importing genotypes, then quarantine and acclimatization. Primary introduction — released as such (e.g. Sonora-64, Lerma Rojo wheats of the Green Revolution); secondary introduction — used as a parent. In India all import/export of germplasm is routed through NBPGR under the Destructive Insects and Pests Act, 1914 and the Plant Quarantine (Regulation of Import into India) Order, 2003.
• Mass selection: many similar plants are selected on phenotype and their seed bulked. Improves a mixed land race, keeps adaptability, but gives no new recombination and the variety stays heterogeneous.
• Pure line selection: single plants are selected and their progenies evaluated separately; the best progeny becomes the variety. The variety is a pure line — homozygous and homogeneous, so very uniform but genetically narrow and vulnerable.
• Pedigree method after hybridization: F1 → F2 single-plant selection → records of ancestry maintained each generation to F5/F6 → yield trials. Needs careful record-keeping; allows selection for heritable traits early; effective for disease resistance.
• Bulk method: F2 to about F6 are harvested and sown in bulk under natural selection, then single-plant selection is done late. Cheap, little labour, lets natural selection act; slow.
• Single seed descent (SSD): one seed per plant per generation; rapid homozygosity in 4–5 generations, often off-season or in a glasshouse; retains maximum variability but no selection for yield en route.
• Backcross method: transfer of one or a few genes from a donor to an adapted recurrent parent. Six to eight backcrosses recover about the recurrent genome; used for disease and insect resistance, and for converting a line to male sterility or to a cytoplasm.
• Multiline and varietal blends: a mixture of near-isogenic lines differing in resistance genes, used to buy durability against rusts.

Breeding cross-pollinated crops, heterosis and hybrids

• Hardy-Weinberg population: cross-pollinated crops are heterozygous populations; breeding manipulates gene frequency, not single genotypes.
• Inbreeding depression: loss of vigour on selfing, due to fixation of deleterious recessives and loss of heterozygosity; severe in maize and alfalfa, mild in sorghum, nil in self-pollinated crops.
• Heterosis (hybrid vigour, Shull 1914): superiority of F1 over the mean of parents (relative/average heterosis), over the better parent (heterobeltiosis) or over the best check (economic/standard heterosis). Explained by dominance (masking of deleterious recessives) and over-dominance (heterozygote per se superior); epistasis contributes.
• Population improvement: mass selection; progeny selection (ear-to-row); recurrent selection — simple, for general combining ability (GCA), for specific combining ability (SCA), and reciprocal recurrent selection (improves both GCA and SCA); synthetic variety (from lines of known good GCA, Syn-1 onwards) and composite (from phenotypically good lines) — both can be re-sown by the farmer, unlike hybrids.
• Hybrid development steps: (1) develop inbreds by 6–7 generations of selfing; (2) evaluate for combining ability by top cross, polycross or diallel; (3) make single (A × B), three-way ((A × B) × C), double ((A × B) × (C × D)) or multiple crosses; (4) multiply parental seed and produce certified hybrid seed each season.
• Pollination control for hybrid seed: hand emasculation and bagging (cotton, tomato); detasselling (maize); cytoplasmic male sterility (CMS), needing the A-line (CMS), B-line (maintainer) and R-line (restorer) — the standard three-line system in bajra, sorghum, sunflower and rice; genic male sterility (GMS); TGMS/PGMS (temperature- and photoperiod-sensitive) two-line system in rice; self-incompatibility in cole crops; chemical hybridizing agents (gametocides).
• Hybridization technique (examination step list): choose parents → selfing/purification → emasculation (hand, hot water at about 45–48 °C for 10 min in sorghum/rice, suction, cold treatment, gametocide) → bagging → pollination (dust fresh pollen on receptive stigma) → tagging with date and cross number → harvest F1 seed separately.

Special and non-conventional methods

• Mutation breeding: physical mutagens — X-rays, gamma rays (Co-60), fast and thermal neutrons, UV; chemical mutagens — EMS (most used alkylating agent), MMS, nitroso compounds, sodium azide, base analogues (5-BU), acridine dyes. Steps: fix objective → choose material and mutagen → determine LD-50/optimum dose by a kill curve → treat M1 seed → grow M1 (selfed, chimeric) → screen M2, confirm in M3. Mutations are mostly recessive, random and deleterious, so large populations are screened. Indian examples: groundnut TG-series and *Trombay* varieties from BARC, blackgram TAU-1, mustard TM-series, basmati PNR-102; India has released several hundred mutant varieties, among the highest in the world (exact count is updated in the IAEA/BARC mutant variety database).
• Polyploidy breeding: autopolyploids (triploid banana and watermelon — seedlessness; tetraploid rye and berseem), allopolyploids (Triticale = wheat × rye; *Raphanobrassica*; the natural allohexaploid bread wheat AABBDD). Colchicine (0.1–0.5%) doubles chromosomes by blocking spindle formation. Limits: reduced fertility, slower growth, poor seed set.
• Distant hybridization and wide crosses: introgression of genes from wild relatives; barriers are pre-fertilization (pollen–pistil incompatibility) and post-fertilization (embryo abortion) and are overcome by bridge crosses, reciprocal crosses, embryo rescue, ovule and ovary culture and protoplast fusion. Example: *Oryza nivara* gave grassy stunt resistance to rice; *Solanum* wild species gave late blight genes.
• Haploid and DH breeding: anther culture and chromosome elimination routes give doubled haploids — instant homozygosity in one step.
• Marker-assisted selection (MAS): RFLP, RAPD, AFLP, SSR and SNP markers linked to a gene or QTL allow selection in the seedling stage, in any season, without phenotyping. Marker-assisted backcrossing with foreground, recombinant and background selection; gene pyramiding of several resistance genes; genomic selection using genome-wide marker effects. Indian successes: Improved Pusa Basmati 1 (*xa13* + *Xa21* for bacterial blight), Improved Samba Mahsuri, and *Sub1* submergence-tolerant Swarna-Sub1.
• Transgenic breeding: *Agrobacterium*-mediated or biolistic transfer of a gene with promoter, coding sequence, terminator and a selectable marker. Commercial examples — Bt cotton (*cry1Ac*, *cry2Ab* from *Bacillus thuringiensis*), herbicide tolerance (*bar*, *CP4-EPSPS*), virus resistance (coat-protein genes), Golden Rice (*psy* + *crtI* for β-carotene), Flavr Savr tomato. In India Bt cotton is the only transgenic crop approved for commercial cultivation; Bt brinjal is under moratorium and GM mustard DMH-11 received an environmental-release recommendation that remains under Supreme Court consideration — confirm current status before quoting.
• Genome editing: CRISPR-Cas9 site-directed nuclease. India's 2022 guidelines exempt SDN-1 and SDN-2 edited plants (no foreign DNA) from Rules, 1989 GMO clearance; SDN-3 is regulated as a GMO. Two genome-edited rice lines (DRR Dhan 100 Kamala, Pusa DST Rice 1) were announced in 2025.

Evaluation, release, seed chain and Indian regulation

• Trials: breeder's own trials → station trials → multilocation/All India Coordinated Research Project (AICRP) trials for 2–3 years → Initial Varietal Trial, Advanced Varietal Trial → identification by the AICRP workshop.
• Release: by the Central Sub-Committee on Crop Standards, Notification and Release of Varieties (CVRC) for central release, or a State Varietal Release Committee; notification under the Seeds Act, 1966 makes the variety's seed legally regulable.
• Seed chain: nucleus seed → breeder seed (golden yellow tag) → foundation seed (white tag) → certified seed (azure blue tag); truthfully labelled seed carries an opal green tag. Certification by State Seed Certification Agencies under the Seeds Act, 1966 and Seeds Rules, 1968; field and seed standards in the Indian Minimum Seed Certification Standards. Genetic purity is maintained by isolation distance, roguing and generation-system control.
• PPV&FR Act, 2001 (Protection of Plant Varieties and Farmers' Rights): registers new, extant, farmers' and essentially derived varieties on DUS (distinctiveness, uniformity, stability) testing; protection generally 15 years for crops and 18 years for trees and vines; uniquely, it retains Farmers' Rights to save, use, sow, exchange and sell farm-saved seed of a protected variety (not as branded seed). Administered by the PPV&FR Authority, New Delhi. India is not a UPOV member.
• Other instruments: Biological Diversity Act, 2002 (as amended 2023) and NBA approval for access to Indian genetic resources; Rules, 1989 under the Environment (Protection) Act, 1986 with GEAC as the apex GMO regulator; National Seeds Policy, 2002.
• Indian milestones: the Green Revolution (1966 onward) with Norin-10 *Rht* dwarfing genes in wheat (Kalyan Sona, Sonalika — M. S. Swaminathan) and *sd1* in rice (IR8, Jaya, Padma); hybrid bajra HB-1 (1965); Pusa Basmati 1121; Bt cotton from 2002, which took India to the world's largest cotton area.

Quantitative genetics tools the breeder uses

• Phenotype = genotype + environment + G×E; variance partitioning VP = VG + VE + VGE, with VG = VA (additive) + VD (dominance) + VI (epistatic).
• Heritability: broad sense H² = VG/VP; narrow sense h² = VA/VP — only the additive part is transmitted, so h² predicts response to selection. High h² traits (plant height, maturity) respond to simple selection; low h² traits (yield) need progeny testing and replicated trials.
• Selection methods for quantitative traits: tandem selection, independent culling levels, and selection index (simultaneous, weighted — most efficient).
• Combining ability: GCA reflects additive effects and is estimated from line means; SCA reflects non-additive effects and is estimated from specific cross deviations — diallel (Griffing) and line × tester analyses.
• Correlated response and genetic advance guide how hard and on what to select; genotype × environment interaction is why multilocation testing exists.

Key points

• Plant breeding - genetic improvement of crops by creating variability and selecting superior genotypes.
• Vavilov's centres of origin - regions of maximum diversity where a crop and its wild relatives evolved; the hunting ground for new genes.
• Mass selection - bulking seed of many selected plants; keeps a heterogeneous, adapted variety.
• Pure line selection - progeny testing of single plants; gives a homozygous, uniform but narrow variety.
• Pedigree method - single-plant selection with ancestry records from F2 to F6.
• Bulk method - bulk harvest for several generations, selection late; cheap and lets natural selection operate.
• SSD - one seed per plant per generation; fastest route to homozygosity with maximum variability retained.
• Backcross - repeated crossing to the recurrent parent to add one gene while retaining the adapted background.
• Inbreeding depression - vigour lost on selfing because deleterious recessives become homozygous.
• Heterosis - F1 superiority over parents; explained by dominance and over-dominance; the basis of hybrid seed.
• CMS three-line system - A (sterile) × R (restorer) gives hybrid seed; B maintains the A-line.
• Emasculation - removal or inactivation of anthers before dehiscence to force cross-pollination.
• Synthetic vs hybrid - a synthetic can be re-sown with little loss; a hybrid must be bought fresh each season.
• Mutation breeding - EMS or gamma rays create new alleles; M2 is the screening generation.
• Allopolyploid - hybrid followed by chromosome doubling (Triticale); autopolyploid - doubling within a species.
• MAS and gene pyramiding - SSR/SNP markers select genes directly, early and season-independently.
• Transgenic status in India - Bt cotton alone is commercially approved; GEAC regulates under Rules, 1989.
• PPV&FR Act, 2001 - DUS-based variety registration (15 years for crops, 18 for trees/vines) with Farmers' Rights preserved.
• Seed chain - nucleus → breeder (golden yellow) → foundation (white) → certified (azure blue) seed.

Formulas and examples

Example 1 — Heterosis in maize. Parent P1 yields 42 q/ha, P2 yields 38 q/ha, F1 yields 60 q/ha; best check 54 q/ha.

• MP = (42 + 38)/2 = 40 q/ha.
• Relative heterosis = (60 − 40)/40 × 100 = 50.0%.
• Heterobeltiosis = (60 − 42)/42 × 100 = 18/42 × 100 = 42.86%.
• Economic heterosis = (60 − 54)/54 × 100 = 6/54 × 100 = 11.11% — the figure that decides commercial release.

Example 2 — Homozygosity on selfing. An F1 heterozygous at 8 independent loci is selfed.

• After n = 5 selfings (F6), F = 1 − (1/2)⁵ = 1 − 0.03125 = 0.96875 per locus.
• All 8 loci homozygous = (0.96875)^8. ln = 8 × (−0.031749) = −0.253995 → 0.7758 ≈ 77.6% of plants.
• After n = 7 (F8): per locus 0.99219; (0.99219)⁸ = 0.9393 ≈ 93.9% — why pedigree selection is usually stopped around F6–F8.

Example 3 — Backcross genome recovery. A donor gene for bacterial blight is moved into a popular rice variety.

• After m = 1 backcross (BC1F1): recurrent genome = 1 − (1/2)² = 75%.
• BC2 = 1 − (1/2)³ = 87.5%; BC3 = 93.75%; BC4 = 96.875%; BC6 = 1 − (1/2)⁷ = 99.22%.
• Each generation halves the residual donor genome; with background SSR markers the same recovery is reached in 2–3 backcrosses instead of 6.

Example 4 — Heritability and genetic advance. In a wheat F3 population for grain yield: VG = 18, VE = 30, VA = 12 (units (q/ha)²); mean yield x̄ = 36 q/ha; selection intensity 5% (k = 2.06).

• VP = 18 + 30 = 48; H² = 18/48 = 0.375 (37.5%); h² = 12/48 = 0.25 (25%).
• σP = √48 = 6.928 q/ha.
• GA = 2.06 × 0.25 × 6.928 = 3.568 q/ha.
• GA as % of mean = 3.568/36 × 100 = 9.91% — moderate heritability with moderate advance indicates additive control and worthwhile selection.

Example 5 — F2 segregation in a two-gene resistance cross. 320 F2 plants from a cross between two lines differing at *Xa21* and *xa13*.

• Dominant *Xa21* segregates 3:1; recessive *xa13* needs the homozygote, 1:4.
• Plants with *Xa21* present and *xa13* homozygous = 3/4 × 1/4 = 3/16 → 320 × 3/16 = 60 plants.
• Only these 60 carry both genes; marker screening of 320 seedlings replaces three seasons of inoculation tests.

Where it is used

• Public breeding programmes: ICAR institutes (IARI, IIRR, IIWBR, CICR), the CGIAR centre ICRISAT at Patancheru, and State Agricultural Universities — scientist and senior research fellow posts filled through ICAR-NET/ARS and university recruitment.
• Private seed industry: Nuziveedu, Kaveri, Rasi, Mahyco, Advanta, Namdhari, Bayer, Syngenta and Corteva employ breeders, research associates, trial managers and seed-production officers for cotton, maize, bajra, rice, vegetables.
• Seed certification and regulation: State Seed Certification Agencies, National Seeds Corporation, state seed corporations, PPV&FR Authority DUS centres, NBPGR germplasm and quarantine units.
• Biotech and marker labs: genotyping services, SNP arrays and marker-assisted backcross pipelines; agri-biotech firms and CGIAR-linked platforms hire molecular breeders and bioinformatics staff.
• Products in Indian fields: Bt cotton hybrids, HD-series and DBW-series wheats, Pusa Basmati 1121 and 1509, Swarna-Sub1 for flood-prone eastern India, pearl millet and sorghum CMS hybrids, biofortified varieties (iron-rich bajra, zinc-rich wheat and rice).
• Allied roles: agri-input and seed marketing, FPO and extension advisory work, intellectual-property and regulatory affairs for variety registration and GMO dossiers.

Interview questions

• Q: Why is mass selection unsuitable for creating genuinely new variability? A: It only sorts genotypes already present in the population; without hybridization, mutation or polyploidy no new gene combinations are generated.
• Q: What makes the bulk method cheaper than the pedigree method? A: No individual plant records or separate progeny rows are kept for several generations; the bulk is simply harvested and re-sown, letting natural selection cull the weak.
• Q: Why does a farmer have to buy hybrid seed every season but not synthetic seed? A: A hybrid's vigour comes from heterozygosity, which segregates and falls in F2; a synthetic is a broad-based random-mating population, so its performance declines only slightly on re-sowing.
• Q: What are the three lines in CMS hybrid seed production and what does each do? A: The A-line is male sterile and receives pollen, the B-line is its isogenic fertile maintainer used to multiply the A-line, and the R-line carries restorer genes so the commercial F1 sets seed.
• Q: Why is M2 and not M1 the screening generation in mutation breeding? A: Most induced mutations are recessive and M1 plants are heterozygous and chimeric; selfing exposes the mutants as homozygotes in M2.
• Q: How does marker-assisted backcrossing shorten a resistance-breeding programme? A: Foreground markers confirm the target gene without inoculation, recombinant markers trim linked donor segments, and background markers pick plants with the most recurrent genome — cutting six backcrosses to two or three.
• Q: Which is more useful to a breeder, broad-sense or narrow-sense heritability, and why? A: Narrow-sense, because only additive variance is reliably transmitted from parent to offspring and therefore predicts the response to selection.
• Q: Differentiate GCA and SCA. A: GCA is a line's average performance across crosses and reflects additive gene action; SCA is a particular cross's deviation from that expectation and reflects dominance and epistasis — GCA guides parent choice, SCA guides hybrid choice.
• Q: Why is Triticale an allopolyploid and seedless banana a triploid? A: Triticale combines whole wheat and rye genomes followed by doubling; the banana's three homologous sets cannot pair evenly at meiosis, so viable seeds are not formed.
• Q: What does DUS testing establish under the PPV&FR Act, 2001? A: That a candidate variety is distinct from known varieties, uniform within itself and stable over generations — the precondition for registration.
• Q: Which transgenic crop is commercially cultivated in India and which gene does it carry? A: Bt cotton, carrying *cry1Ac* (and *cry2Ab* in Bollgard II) from *Bacillus thuringiensis* for lepidopteran resistance.
• Q: Why do multilocation trials run for two to three years before release? A: To estimate genotype × environment interaction and confirm that superiority is stable across sites and seasons, not an artefact of one favourable environment.

Common mistakes

• Treating heterosis as always measured over the mid-parent; examiners usually want heterobeltiosis or economic heterosis, so state which base is used.
• Using F = 1 − (1/2)ⁿ with n as the generation number instead of the number of selfings — F2 corresponds to one selfing, not two.
• Writing the recurrent-parent recovery as 1 − (1/2)^m; the correct exponent is (m + 1) because the F1 itself already carries 50%.
• Confusing broad- and narrow-sense heritability, or quoting heritability without the population and environment it was estimated in.
• Calling a synthetic, composite and hybrid the same thing, or claiming hybrids can be re-sown without yield loss.
• Mixing up mutagen types and generations — applying chemical-mutagen doses as "Gy", or selecting in M1.
• Saying several GM crops are grown in India; only Bt cotton is approved for commercial cultivation, and genome-edited SDN-1/SDN-2 plants follow a separate exempted route.

Related topics

• Genetics · Plant tissue culture · Recombinant DNA technology and transgenics · Biostatistics and quantitative genetics · Economic botany and crop plants · Plant pathology and host resistance