M.Sc. Genetics & Plant Breeding Syllabus & Important Instruction

Quick summary 

• Total credits: 70 (Major 20, Minor 8, Supporting 6, Common 5, Seminar 1, Thesis 30)
• Duration: Minimum 2 academic years (4 semesters); maximum 5 years
• Mandatory common courses: 5 one-credit courses (library, writing, IPR, lab techniques, research & rural development)
• Seminar: 1 credit (mandatory)
• Optional IDEA internship: Internship in lieu of thesis (30 credits) with industry co-guidance

Syllabus

Principles of Genetics

Content: Beginning of genetics, early concepts of inheritance, Mendel’s laws; Discussion on Mendel’s paper, Chromosomal theory of inheritance; Multiple alleles, Gene interactions, Sex determination, differentiation and sex-linkage, Sex-influenced and sex-limited traits; Linkage-detection, estimation; Recombination and genetic mapping in eukaryotes, Somatic cell genetics, Extra chromosomal inheritance. Mendelian population, Random mating population, Frequencies of genes and genotypes, Causes of change: Hardy-Weinberg equilibrium. Nature, structure and replication of the genetic material; Organization of DNA in chromosomes, Genetic code; Protein biosynthesis, Genetic fine structure analysis, Allelic complementation, Split genes, overlapping genes, Pseudogenes, Oncogenes, Gene families and clusters; Regulation of gene activity in prokaryotes and eukaryotes; Molecular mechanisms of mutation, repair and suppression; Bacterial plasmids, insertion (IS) and transposable (Tn) elements; Molecular chaperones and gene expression, RNA editing. Gene isolation, synthesis and cloning, genomic and cDNA libraries, PCR based cloning, positional cloning; Nucleic acid hybridization and immunochemical detection; DNA sequencing; DNA restriction and modification, Anti-sense RNA and ribozymes; Micro-RNAs (miRNAs). Genomics and proteomics; metagenomics; Transgenic bacteria and bioethics; Gene silencing; genetics of mitochondria and chloroplasts. Concepts of Eugenics, Epigenetics, Genetic disorders. Practical: Laboratory exercises in probability and chi-square; Demonstration of genetic principles using laboratory organisms; Chromosome mapping using three-point test cross; Tetrad analysis; Induction and detection of mutations through genetic tests; DNA extraction and PCR amplification; Electrophoresis: basic principles and running of amplified DNA; Extraction of proteins and isozymes; Use of Agrobacterium mediated method and Biolistic gun; Detection of transgenes in the exposed plant material; Visit to transgenic glasshouse and learning the practical considerations.

Principles of Plant Breeding

Content: Early Plant Breeding; Accomplishments through plant breeding; Objectives of plant breeding; Patterns of Evolution in Crop Plants: Centre of Origin, Agro-biodiversity and its significance. Pre-breeding and plant introduction and role of plant genetic resources in plant breeding. Genetic basis of breeding: self and cross pollinated crops including mating systems and response to selection; Nature of variability, components of variation; Heritability and genetic advance, genotype environment interaction; General and specific combining ability; Types of gene actions and implications in plant breeding. Pure line theory, pure line and mass selection methods; pedigree, bulk, backcross, single seed descent and multiline breeding; Population breeding in self-pollinated crops with special reference to diallel selective mating; Transgressive breeding. Breeding methods in cross pollinated crops; Population breeding: mass selection and ear-to-row methods; S1 and S2 progeny testing, progeny selection schemes, recurrent selection schemes for intra and inter-population improvement and development of synthetics and composites. Hybrid breeding: genetical and physiological basis of heterosis and inbreeding, production of inbreeds, breeding approaches for improvement of inbreeds, predicting hybrid performance; seed production of hybrid and their parent varieties/ inbreeds. Self-incompatibility, male sterility and apomixes in crop plants and their commercial exploitation. Breeding methods in asexually/ clonally propagated crops, clonal selection. Special breeding techniques: Mutation breeding, Breeding for abiotic and biotic stresses; Concept of plant ideotype and its role in crop improvement, concept of MAS, concept of polyploidy and wide hybridization, doubled haploidy. Cultivar development: testing, release and notification, maintenance breeding, Participatory Plant Breeding, Plant breeders’ rights and regulations for plant variety protection and farmers rights. Practical: Laboratory exercises in probability and chi-square; Demonstration of genetic principles using laboratory organisms; Chromosome mapping using three-point test cross; Tetrad analysis; Induction and detection of mutations through genetic tests; DNA extraction and PCR amplification; Electrophoresis: basic principles and running of amplified DNA; Extraction of proteins and isozymes; Use of Agrobacterium mediated method and Biolistic gun; Detection of transgenes in the exposed plant material; Visit to transgenic glasshouse and learning the practical considerations. Learning techniques in hybrid seed production using male-sterility in field crops; Prediction of performance of double cross hybrid.

Fundamentals of Quantitative Genetics

Content: Introduction and historical background of quantitative genetics, Multiple factor hypothesis, Qualitative and quantitative characters, Analysis of continuous variation mean, range, SD, CV; Components of variation- Phenotypic, Genotypic, Nature of gene action- additive, dominance and epistatic, linkage effect. Principles of analysis of variance and linear model, Expected variance components, Random and fixed effect model, Comparison of means and variances for significance. Designs for plant breeding experiments- principles and applications; Variability parameters, concept of selection, simultaneous selection modes and selection of parents, MANOVA. Association analysis- Genotypic and phenotypic correlation, Path analysis Discriminate function and principal component analysis, Genetic divergence analysis- Metroglyph and D2, Generation mean analysis, Parent progeny regression analysis. Mating designs- classification, Diallel, partial diallel, L × T, NCDs, and TTC; Concept of combining ability and gene action, G × E interaction-Adaptability and stability; Methods and models for stability analysis; Basic models- principles and interpretation, Bi-plot analysis. QTL mapping, Strategies for QTL mapping- Desired population and statistical methods, QTL mapping in genetic analysis; Markers, Marker assisted selection and factors influencing the MAS, Simultaneous selection based on marker and phenotype. Practical: Analysis and interpretation of variability parameters; Analysis and interpretation of Index score and Metroglyph; Clustering and interpretation of D2 analysis; Genotypic and phenotypic correlation analysis and interpretation; Path coefficient analysis and interpretation, Estimation of different types of heterosis, inbreeding depression and interpretation; A, B and C Scaling test; L × T analysis and interpretation, QTL analysis; Use of computer packages; Diallel analysis; G × E interaction and stability analysis.

Varietal Development and Maintenance Breeding

Content: Variety Development systemsand Maintenance; Definition- variety, cultivar, extant variety, essentially derived variety, independently derived variety, reference variety, farmers’ variety, landraces, hybrid, and population; Variety testing, release and notification systems and norms in India and abroad. DUS testing- DUS Descriptors for major crops; Genetic purity concept and maintenance breeding. Factors responsible for genetic deterioration of varieties - safeguards during seed production. Maintenance of varieties in self and cross pollinated crops, isolation distance; Principles of seed production; Methods of nucleus and breeder seed production; Generation system of seed multiplication -nucleus, breeders, foundation, certified. Quality seed production technology of self and cross-pollinated crop varieties, viz., cereals and millets (wheat, barley, paddy, pearlmillet, sorghum, maize and ragi, etc.); Pulses (greengram, blackgram, cowpea, pigeonpea, chickpea, fieldpea, lentil); Oilseeds (groundnut, soybean, sesame, castor, sunflower, safflower, linseed, rapeseed and mustard); fibres (cotton/ jute) and forages (guar, forage sorghum, teosinte, oats, berseem, lucerne). Seed certification procedures; Seed laws and acts, plant variety protection regulations in India and international systems. Practical: Identification of suitable areas/ locations for seed production; Ear-to-row method and nucleus seed production; Main characteristics of released and notified varieties, hybrids and parental lines; PGMS and TGMS; Identification of important weeds/ objectionable weeds; Determination of isolation distance and planting ratios in different crops; Seed production techniques of varieties in different crops; Hybrid seed production technology of important crops; DUS testing and descriptors in major crops; Variety release proposal formats in different crops.

Principles of Cytogenetics

Content: Cell cycle and architecture of chromosome in prokaryotes and eukaryotes; Chromonemata, chromosome matrix, chromomeres, centromere, secondary constriction and telomere; artificial chromosome construction and its uses; Special types of chromosomes.Variation in chromosome structure: Evolutionary significance; Introduction to techniques for karyotyping; Chromosome banding and painting –In situ hybridization and various applications. Structural and numerical variations of chromosomes and their implications; Symbols and terminologies for chromosome numbers, euploidy, haploids, diploids and polyploids; Utilization of aneuploids in gene location; Variation in chromosome behaviour, somatic segregation and chimeras, endomitosis and somatic reduction; Evolutionary significance of chromosomal aberrations, balanced lethal and chromosome complexes; Inter-varietal chromosome substitutions. Fertilization barriers in crop plants at pre-and postfertilization levels; In-vitro techniques to overcome the fertilization barriers in crops; Polyploidy. Genetic consequences of polyploidization and role of polyploids in crop breeding; Evolutionary advantages of autopolyploid vs allopolyploids; Role of aneuploids in basic and applied aspects of crop breeding, their maintenance and utilization in gene mapping and gene blocks transfer; Alien addition and substitution lines, creation and utilization; Apomixis, evolutionary and genetic problems in crops with apomixes. Reversion of autopolyploid to diploids; Genome mapping in polyploids; Interspecific hybridization and allopolyploids; Synthesis of new crops (wheat, Triticale, Brassica, and cotton); Hybrids between species with same chromosome number, alien translocations; Hybrids between species with different chromosome number; Gene transfer using amphidiploids, bridge species. Chromosome manipulations in wide hybridization; case studies; Production and use of haploids, dihaploids and doubled haploids in genetics and breeding. Practical: Learning the cytogenetical laboratory techniques, various chemicals to be used for fixation, dehydration, embedding, staining, cleaning, etc.; Microscopy: various types of microscopes; Preparing specimen for observation; Fixative preparation and fixing specimen for light microscopy studies in cereals; Studies on mitosis and meiosis in crop plants; Using micrometres and studying the pollen grain size in various crops. Pollen germination in vivo and in-vitro; Demonstration of polyploidy.

Molecular Breeding and Bioinformatics

Content: Genotyping; Biochemical and Molecular markers; Morphological, biochemical and DNA-based markers (RFLP, RAPD, AFLP, SSR, SNPs, ESTs, etc.), Functional markers; Mapping populations (F2s, back crosses, RILs, NILs and DH); Molecular mapping and tagging of agronomically important traits; Statistical tools in marker analysis. Allele mining; Marker-assisted selection for qualitative and quantitative traits; QTLs analysis in crop plants; Marker-assisted backcross breeding for rapid introgression; Genomics- assisted breeding; Generation of EDVs; Gene pyramiding. Introduction to Comparative Genomics; Large scale genome sequencing strategies; Human genome project; Arabidopsis genome project; Rice genome project; Comparative genomics tools; Introduction to proteomics; 2D gel electrophoresis; chromatography and sequencing by Edman degradation and mass spectrometry; Endopeptidases; Nanotechnology and its applications in crop improvement. Recombinant DNA technology, transgenes, method of transformation, selectable markers and clean transformation techniques, vector-mediated gene transfer, physical methods of gene transfer; Production of transgenic plants in various field crops: cotton, wheat, maize, rice, soybean, oilseeds, sugarcane, etc. and commercial releases; Biotechnology applications in male sterility/ hybrid breeding, molecular farming; Application of Tissue culture in molecular breeding; MOs and relatedissues (risk and regulations); GMO; International regulations, biosafety issues of GMOs; Regulatory procedures in major countries including India, ethical, legal and social issues; Intellectual property rights; Introduction to bioinformatics: bioinformatics tools, biological data bases (primary and secondary), implications in crop improvement. Practical: Requirements for plant tissue culture laboratory; Techniques in plant tissue culture; Media components and media preparation; Aseptic manipulation of various explants, observations on the contaminants occurring in media, interpretations; Inoculation of explants, callus induction and plant regeneration; Standardizing the protocols for regeneration; Hardening of regenerated plants; stablishing a greenhouse and hardening procedures; Visit to commercial micropropagation unit; Transformation using Agrobacterium strains; GUS assay in transformed cells/ tissues; DNA isolation, DNA purity and quantification tests; Gel electrophoresis of proteins and isozymes, PCR-based DNA markers, gel scoring and data analysis for tagging and phylogenetic relationship; Construction of genetic linkage maps using computer software; NCBI Genomic Resources, GBFF, Swiss Prot, Blast n/ Blast p, Gene Prediction Tool, Expasy Resources, PUBMED and PMC, OMIM and OMIA, ORF finder; Comparative Genomic Resources: - Map Viewer (UCSC Browser and Ensembl); Primer designing- Primer 3/ Primer BLAST.

Breeding for Quality and Special Traits

Content: Developmental biochemistry and genetics of carbohydrates, proteins, fats, vitamins, amino acids and anti-nutritional factors; Nutritional improvement - A human perspective. Breeding for grain quality parameters in rice and its analysis; Golden rice and aromatic rice: Breeding strategies, achievements and application in Indian context; Molecular basis of quality traits and their manipulation in rice; Post harvest manipulation for quality improvement; Breeding for baking qualities in wheat, characters to be considered and breeding strategies, molecular and cytogenetic manipulation for quality improvement in wheat. Breeding for quality improvement in Sorghum, pearl millet, barley and oats; Quality protein maize, specialty corns, concept and breeding strategies; Breeding for quality improvement in important forage crops for stay green traits; Genetic resource management for sustaining nutritive quality in crops. Breeding for quality improvement in pulses – Chickpea, pigeonpea, green gram and black gram cooking quality; Breeding for quality in oilseeds -groundnut, mustard, soybean, sesame, sunflower and minor oilseeds; Molecular basis of fat formation and manipulation to achieve more PUFA in oil crops; Genetic manipulation for quality improvement in cotton. Breeding for quality improvement in Sugarcane, potato. Genetic engineering protocols for quality improvement: Achievements made; Biofortification in crops; Classification and importance, Nutritional genomics and Second generation transgenics. Practical: Grain quality evaluation in rice; Correlating ageing and quality improvement in rice; Quality analysis in millets; Estimation of anti-nutritional factors like tannins in different varieties/ hybrids: A comparison; Quality parameters evaluation in wheat, pulses and oilseeds; Evaluation of quality parameters in cotton, sugarcane and potato; Value addition in crop plants; Post-harvest processing of major field crops; Quality improvement in crops through tissue culture techniques; Evaluating the available populations like RIL, NIL, etc. for quality improvement using MAS procedures; Successful example of application of MAS for quality trait in rice, mustard, maize, etc.

Mutagenesis and Mutation Breeding

Content: Mutation and its history, nature and classification of mutations: spontaneous and induced mutations, micro and macro mutations, pre and post adaptive mutations; Detection of mutations. Paramutations in crops plants. Mutagenic agents: physical – radiation types and sources: Ionizing and non-ionizing radiations. Radiobiology: mechanism of action of various radiations (photoelectric absorption, Compton scattering and pair production) and their biological effects – RBE and LET relationships; Effect of mutations on DNA – repair mechanisms operating at DNA, chromosome, cell and organism level to counteract the mutation effects; Dosimetry -Objects and methods of treatment; Factors influencing mutation: dose rate, acute vs chronic irradiation, recurrent irradiation, enhancement of thermal neutron effects; Radiation sensitivity and modifying factors: External and internal sources – Oxygen, water content, temperature and nuclear volume. Chemical mutagens: Classification – base analogues, antibiotics, alkylating agents, acridine dyes and other mutagens: their properties and mode of action; Dose determination and factors influencing chemical mutagenesis; Treatment methods using physical and chemical mutagens, Combination treatments; other causes of mutation – direct and indirect action, comparative evaluation of physical and chemical mutagens. Observing mutagen effects in M1 generation: plant injury, lethality, sterility, chimeras, etc.; Observing mutagen effects in M2 generation; Estimation of mutagenic efficiency and effectiveness – spectrum of chlorophyll and viable mutations; Mutations in traits with continuous variation; Factors influencing the mutant spectrum: genotype, type of mutagen and dose, pleiotropy and linkage, etc.; Individual plant based mutation analysis and working out effectiveness and efficiency in M3 generation; Comparative evaluation of physical and chemical mutagens for creation of variability in the some species- Case studies. Use of mutagens in creating oligogenic and polygenic variations – Case studies; In-vitro mutagenesis – Callus and pollen irradiation; Handling of segregating M2 generations and selection procedures; Validation of mutants; Mutation breeding for various traits (disease resistance, insect resistance, quality improvement, etc.) in different crops; Procedures for micromutations breeding/ polygenic mutations; Achievements of mutation breeding- varieties released across the world, problems associated with mutation breeding. Use of mutagens in genomics, allele mining, TILLING. Practical: Precautions on handling of mutagens; Dosimetry-Studies of different mutagenic agents:Physical mutagens and Chemical mutagens; Learning on Radioactivity- Production source and isotopes at BRIT, Trombay, Learning about gamma chamber; Radiation hazards: Monitoring – safety regulations and safe transportation of radioisotopes, visit to radio isotope laboratory; learning on safe disposal of radioisotopes; Hazards due to chemical mutagens – Treating the plant propagules at different doses of physical and chemical mutagens; Procedures in combined mutagenic treatments; Raising the crop for observation; Mutagenic effectiveness and efficiency, calculating the same from earlier literature; Study of M1 generation – Parameters; Study of M2 generation – Parameters; Mutation breeding in cereals and pulses-achievements made and an analysis; Mutation breeding in oilseeds and cotton- achievements and opportunities; Mutation breeding in forage crops and vegetatively propagated crops; Procedure for detection of mutations for polygenic traits in M2 and M3 generations

Hybrid Breeding

Content: Historical aspect of heterosis, nomenclature and definitions of heterosis; Heterosis in natural population and inbred population; Evolutionary aspects – Genetic consequences of selfing, sibbing and crossing in self-and cross-pollinated and asexually propagated crops; Pre-Mendelian and Post-Mendelian ideas – Evolutionary concepts of heterosis; Genetic theories of heterosis – Physiological, Biochemical and molecular factors underlining heterosis; theories and their estimation; Biometrical basis of heterosis. Prediction of heterosis from various crosses, inbreeding depression, coefficient of inbreeding and its estimation, residual heterosis in F2 and segregating populations, importance of inbreeding in exploitation of heterosis – case studies.; Relationship between genetic distance and expression of heterosis, case studies; Divergence and genetic distance analyses, morphological and molecular genetic distance in predicting heterosis; Development of heterotic pools in germplasm/ genetic stocks and inbreeds, their improvement for increasing heterosis. Male sterility and use in heterosis breeding; Male sterile line creation and diversification in self-pollinated, cross pollinated and asexually propagated crops; Creation of male sterility through genetic engineering and its exploitation in heterosis; Maintenance, transfer and restoration of different types of male sterility; Use of self-incompatibility in development of hybrids. Hybrid seed production system: 3-line, 2-line and 1-line system; Development of inbreeds and parental lines- A, B and R lines – functional male sterility; Commercial exploitation of heterosis, maintenance breeding of parental lines in hybrids; Fixation of heterosis in self, cross and often cross pollinated crops, asexually/ clonally propagated crops, problems and prospects; Apomixis in fixing heterosis-concept of single line hybrid; Organellar heterosis and complementation. Hybrid breeding in wheat, rice, cotton, maize, pearl millet, sorghum and rapeseedmustard, sunflower, safflower and castor oilseed crops and pigeonpea. Practical: Characterization of male sterile lines using morphological descriptors; Restorer line identification and diversification of male sterile sources; Male sterile line creation in crop plants, problems in creation of CGMS system, ways of overcoming them; Diversification and restoration; Success stories of hybrid breeding in Maize, Rice, Pearl millet, Sorghum and Pigeon pea; Understanding the difficulties in breeding apomicts; Estimation of heterotic parameters in self, cross and asexually propagated crops; Estimation from the various models for heterosis parameters; Hybrid seed production in field crops—an account on the released hybrids, their potential, problems and ways of overcoming it; Hybrid breeding at National and International level, opportunities ahead.

Seed Production and Certification

Content: Importance of seed as basic input in agriculture; Seed quality concept and importance; Generation system of seed multiplication -Varietal replacement rate, Seed multiplication ratios, Seed replacement rate, Seed renewal period and seed demand and supply; Various factors influencing seed production –Physical and Genetic purity in seed production; Factors responsible for varietal and genetic deterioration. Nucleus seed production and its maintenance - Maintenance of parental lines of hybrids, Production of breeder, foundation and certified seed and their quality maintenance; Principles of seed production in self- and cross-pollinated crops; Hybrid seed production - system and techniques involved in Seed village concept; Organic seed production and certification. Principles of seed production in field crops; Floral structure, pollination mechanism and seed production techniques in self- and cross-pollinated cereals and millets. Floral structure, pollination mechanism and methods and techniques of seed production in major pulses and oilseed crops; Varietal and hybrid seed production techniques in Pigeon pea, Mustard, Castor and Sunflower. Floral structure, pollination mechanism and methods and techniques of seed production in major commercial fibres. Hybrid-seed production techniques in major vegetatively propagated crops. Seed certification - history, concept, objectives;Central seed certification board Seed certification agency/ organization and staff requirement; Legal status - Phases of seed certification, formulation, revision and publication of seed certification standards; Minimum Seed Certification Standards (MSCS) for different crops - General and specific crop standards, Field and seed standards; Planning and management of seed certification programs; Eligibility of a variety for certification, area assessment, cropping history of the seed field. Practical: Planting design for variety- hybrid seed production techniques, planting ratio of male and female lines, synchronization of parental lines and methods to achieve synchrony; Identification of rogues and pollen shedders, supplementary pollination, detasseling, hand emasculation and pollination; Pollen collection and storage methods, pollen viability and stigma receptivity; Pre-harvest sanitation, maturity symptoms, harvesting techniques; Visits to seed production plots - visit to seed industries; Planning for seed production: cost benefit ratio, seed multiplication ratio and seed replacement rate; General procedure of seed certification, identification of weed and other crop seeds as per specific crops, field inspection at different stages of a crop and observations recorded on contaminants and reporting of results, inspection and sampling, harvesting/ threshing, processing and after processing for seed law enforcement; Specifications for tags and labels to be used for certification purpose.

Crop Breeding I (Kharif Crops)

Content: Rice: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement, Aerobic rice, its implications and drought resistance breeding. Maize: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, releasedvarieties, examples of MAS used for improvement- QPM and Bt maize – strategies and implications. Small millets: Evolution and distribution of species and forms - wild relatives and germplasm; Cytogenetics and genome relationship - breeding objectives yield, quality characters, biotic and abiotic stress resistance, etc. Pigeon pea: evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement - Hybrid technology; maintenance of male sterile, fertile and restorer lines, progress made at National and International institutes. Groundnut: Origin, evolution mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship, breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, released varieties, examples of MAS used for improvement. Other pulses: Urdbean, mungbean, cowpea,: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship, breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), released varieties, examples of MAS used for improvement. Interspecific crosses attempted and its implications, reasons for failure, ways of overcoming them. Soybean: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement. Castor and Sesame: Origin, evolution mode of reproduction, chromosome number; Genetics –cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), released varieties, examples of MAS used for improvement; Hybrid breeding in castor – opportunities, constraints and achievements. Cotton: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement, Development and maintenance of male sterile lines – Hybrid development and seed production – Scenario of Bt cottons, evaluation procedures for Bt cotton. Jute: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement. Sugarcane: Evolution and distribution of species and forms, wild relatives and germplasm; Cytogenetics and genome relationship – Breeding objectives- yield, quality characters, biotic and abiotic stress resistance, etc. Forage crops: Evolution and distribution of species and forms – Wild relatives and germplasm; Cytogenetics and genome relationship; Breeding objectives- yield, quality characters and palatability studies; Biotic and abiotic stress resistance, etc. Seed spices: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc.; Breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement; Achievements of important spice crops. Practical: Floral biology, emasculation, pollination techniques in rice, maize, pigeon pea, soybean, sesame, cotton; Study of range of variation for yield and yield components; Study of segregating populations in cereal, pulses and oilseed crops; Learning on the crosses between different species; attempting crosses between black gram and green gram; Evaluating the germplasm of cotton for yield, quality and resistance parameters, learning the procedures on development of Bt cotton; Visit to Cotton Technology Laboratory and Spinning Mills; Learning on the Standard Evaluation System (SES) and descriptors; Use of software for database management and retrieval; Practical learning on the cultivation of fodder crop species on sewage water, analysing them for yield components and palatability; Laboratory analysis of forage crops for crude protein, digestibility percent and other quality attributes; Visit to animal feed producing factories; Learning the practice of value addition; Visiting the animal husbandry unit and learning the animal experiments related with palatability and digestibility of fodder.

Crop Breeding-II (Rabi Crops)

Content: Wheat: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement. Oats: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, released varieties, examples of MAS used for improvement. Barley: Origin, evolution, center of origin, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, released varieties, examples of MAS used for improvement. Chickpea: Origin, evolution mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, released varieties, examples of MAS used for improvement. Other pulses: Lentil, field pea, Rajma, Horse gram: Origin, evolution, mode of reproduction, chromosome number; Genetics. cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement. Interspecific crosses attempted and its implications, reasons for failure, ways of overcoming them. Rapeseed and Mustard: Origin, evolution, mode of reproduction, chromosome number; Genetics – cytogenetics and genome relationship; Breeding objectives; yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement, Oil quality, Improvement for oil quality. Sunflower, Safflower: Origin, mode of reproduction, chromosome number; Genetics, cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, heterosis breeding, released varieties, examples of MAS used for improvement. Mesta and minor fibre crops: Origin, mode of reproduction, chromosome number; Genetics–cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, released varieties, examples of MAS used for improvement. Forage crops: Origin, evolution mode of reproduction, chromosome number; Genetics–cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance. Seed spices: Origin, evolution, mode of reproduction, chromosome number; Genetics– cytogenetics and genome relationship; Breeding objectives: yield, quality characters, biotic and abiotic stress resistance, etc., breeding approaches, introgression of alien gene(s) (if required), biotic and abiotic stress resistance, scope of heterosis breeding, released varieties, examples of MAS used for crop improvement. Practical: Floral biology, emasculation and pollination techniques in wheat, oats, barley, chickpea, rajma, rapeseed mustard, sunflower; Study of range of variation for yield and yield components; Study of segregating populations in cereal, pulses and oilseed crops; Use of descriptors for cataloguing; Learning on the crosses between different species; Trait based screening for stress resistance; Learning on the Standard Evaluation System (SES) and descriptors; Use of software for database management and retrieval.

Breeding Vegetable Crops

Content: Breeding for Leafy vegetables: Amaranth, chenopods and lettuce. Breeding for Cucurbits: Gourds, melons, pumpkins and squashes. Breeding for Solanaceae: Potato and tomato, eggplant, hot pepper, sweet pepper. Breeding for Cole crops: Cabbage, cauliflower, broccoli and knolkhol. Breeding for Root vegetables: Carrot, beetroot, radish, sweet potato and tapioca. Breeding for other vegetable crops: Peas, beans, onion, garlic and okra. Practical: Selection of desirable plants from breeding population, observations and analysis of various qualitative and quantitative traits in germplasm; Hybridization and handling segregating generations; Induction of flowering, palanological studies, selfing and crossing techniques in vegetable crops; Hybrid seed production of vegetable crops in bulk; Screening techniques for insect-pests, disease and environmental stress resistance in vegetable crops; Demonstration of sib-mating and mixed population; Molecular marker techniques to identify useful traits in the vegetable crops and special breeding techniques; Visit to breeding blocks, MAS for incorporating traits governed by major and polygenes.

Breeding Fruit Crops

Content: Fruit crop breeding: History, importance of fruit breeding, centers of diversity, distribution, domestication and adaptation of commercially important fruits. Issues in fruit crop breeding – heterozygosity, polyploidy, polyembryony, parthenocarpy and seed lessness, incompatibility and sterility systems. Apomixis - merits and demerits, types, variability for economic traits, role of genetic engineering and biotechnology in improvement of fruit crops. Crop improvement in Mango, Banana, Citrus, Grapes, Papaya, Sapota and Pomegranate, Pineapple and Guava, Apple and other Rosaceous crops andregion specific fruit crops. Practical: Germplasm documentation; Floral biology of mango, guava, citrus, grape, pomegranate, pollen viability in major fruit crops; Pollen germination to study time of anthesis and stigma receptivity; Hybridization technique in important fruit crops, hybrid seed collection and raising; Colchicine treatment for induction of polyploidy; Exposure to resistance breeding and screening techniques; Mutation breeding practices raising and evaluation of segregating populations; Use of mutagens to induce mutations and polyploidy; Visit to Biotechnology Lab and study of in-vitro breeding techniques.

Breeding Ornamental Crops

Content: History of improvement of ornamental plants; Centre of origin of ornamental crop; Objectives and techniques in ornamental plant breeding. Introduction, selection, hybridization, mutation and biotechnological techniques for improvement of ornamental and flower crops, viz., Rose, Jasmine, Chrysanthemum, Tuberose, Gerbera, Gladiolus, Dahlia, Lilium, Gaillardia, Petunia, Bouganvillea, Pansy, Marigold, Geranium, Antirrhinum, China aster, Orchids, Carnation, Hibiscus, etc. Development of promising cultivars of important ornamental and flower crops; Role of Heterosis and its exploitation, production of F1 hybrids and utilization of male sterility. Production of open pollinated seeds, harvesting, processing and storage of seeds; Seed certification. Practical: Study of floral biology and pollination in important species and cultivars of ornamental crops; Techniques of inducing polyploidy and mutation; Production of pure and hybrid seed; Methods of breeding suited to seed propagated plants; Polyploidy and mutations to evolve new varieties; Breeding methods for biotic and abiotic stresses; Visit to research institutes involved in ornamental crop breeding.

Breeding for Stress Resistance and Climate Change

Content: Concept and impact of climatic change; Importance of plant breeding with special reference to biotic and abiotic stress resistance; Classification of biotic stresses – major pests and diseases of economically important crops. Concepts of resistance to insect and pathogen resistance; Analysis and inheritance of resistance variation; Host defence responses to pathogen invasions- Biochemical and molecular mechanisms; Acquired and induced immunity and systemic acquired resistance (SAR); Host-pathogen interaction, gene-for-gene hypothesis, molecular evidence for its operation and exceptions; Concept of signal transduction and other host-defence mechanisms against viruses and bacteria. Types and genetic mechanisms of resistance to biotic stresses –Horizontal and vertical resistance in crop plants; Quantitative resistance/ adult plant resistance and slow rusting resistance; Classical and molecular breeding methods – Measuring plant resistance using plant fitness; Behavioural, physiological and insect gain studies; Phenotypic screening methods for major pests and diseases; Recording of observations; Correlating the observations using marker data – Gene pyramiding methods and their implications. Classification of abiotic stresses - Stress inducing factors, moisture stress/ drought and water logging and submergence; Acidity, salinity/ alkalinity/ sodicity; High/ low temperature, wind, etc.; Stress due to soil factors and mineral toxicity; Physiological and Phenological responses; Emphasis of abiotic stresses in developing breeding methodologies. Genetics of abiotic stress resistance; Genes and genomics in breeding cultivars suitable to low water regimes and water logging and submergence, high and low/ freezing temperatures; Utilizing MAS procedures for identifying resistant types in important crops like rice, sorghum, wheat, cotton, etc.; Breeding for resistance to stresses caused by toxicity, deficiency and pollutants/ contaminants in soil, water and environment. Use of crop wild relatives as a source of resistance to biotic and abiotic factors in major field crops; Transgenics in management of biotic and abiotic stresses, use of toxins, protease inhibitors, lectins, chitinases and Bt for diseases and insect pest management. Practical: Understanding the climatological parameters and predisposal of biotic and abiotic stress factors- ways of combating them for diseases caused by fungi and bacteria; Symptoms and data recording; use of MAS procedures; Phenotypic screening techniques for sucking pests and chewing pests – Traits to be observed at plant and insect level; Phenotypic screening techniques for nematodes and borers; Ways of combating them; Evaluating the available populations like RIL, NIL, etc. for pest resistance; Use of standard MAS procedures. Breeding strategies - Weeds – ecological, environmental impacts on the crops; Breeding for herbicide resistance; Screening crops for drought and flood resistance; factors to be considered and breeding strategies; Screening varieties of major crops for acidity and alkalinity- their effects and breeding strategies; Screening forage crops for resistance to sewage water and tannery effluents; Quality parameters evaluation.

Germplasm Characterization and Evaluation

Content: Understanding genetic diversity in crop plants; Crop descriptors, descriptor states; germplasm characterization/ evaluation procedures; evaluation of germplasm for specific traits; Measuring diversity using agro-morphological data, statistical procedures to measure population genetic variation, markers and their use in PGR, evaluation of biotic and abiotic stresses, Principles and methods for formulating core and mini core collections and their validation, Web based tools for management of data. Principles and practices of germplasm regeneration and maintenance, breeding systems and mode of reproduction; maintaining sufficiently large populations for effective conservation of farmer landraces, evaluation and maintenance of wild relatives of crop plants. Genetic enhancement, Use of CWRs genetic resources for crop improvement. High throughput phenotyping systems- imaging and image processing concepts for automated germplasm characterization (phenotyping) – evaluation for nutritional traits, resistance traits -Biochemical and molecular markers for characterization. Practical: Field layout and experimental designs; Recording field data on germplasm evaluation in different agri-horticultural crops, post-harvest handling; Evaluating quality traits, biochemical and phyto-chemical evaluation of crop germplasm, data processing; Documentation, analysis of diversity and cataloguing, data analysis, viability equations, sampling strategies, data documentation, cataloguing, biochemical analyses of samples.

Genetic enhancement for PGR Utilization

Content: Concepts of gene pools; Introduction, potential of pre-breeding. Role of crop wild relatives, semi exotics, creating and managing variation, basic concepts to set up a successful pre-breeding programme. Understanding crop adaptation, handling and maintenance of CWRs, synchronization of flowering, overcoming impediments to flowering through photoperiodic adjustments, role of other barriers to flowering, role of amphidiploids, semi exotics and other unadapted germplasm, identifying desirable traits in natural populations, screening for biotic and abiotic stress resistance traits; screening of nutritionally important traits, genetic analysis to understand the inheritance of novel traits. Parental selection for prebreeding, search for superior genotypes, breeding methods for trait transfer; moving the genes - unadapted to adapted, wide hybridization, Incongruity and its management, modern tools for incongruity management, cytogenetical approaches for gene transfer such as alien addition and substitution, segregating populations and their management in wide crosses, purging the undesirable traits, testing and improving the adaptability of wide cross derivatives, cytological studies, florescence microscopy, embryo rescue methods, pollen physiology and storage, pollen storage methods to facilitate wide hybridization, pre- and postzygotic barriers. Practical: Characterization of CWRs by visiting the fields; Screening methods for special traits-biotic and abiotic resistance; Screening for nutritional traits; Crossability studies in CWRs of cereals, legumes, oilseeds, vegetables. Assessment of pre and post-zygotic barriers in wide hybridization crosses; Pollen storage studies; Special requirements for growing CWRs, inducing flowering by manipulating day length, temperature, chemical spraying, etc.

Full instructions & regulations

Academic year, registration & orientation

The academic year normally runs from July to June and is divided into two semesters. Students must register at the start of each semester. An orientation programme is arranged for newly admitted students at the start of the semester.

Credit structure (M.Sc.)

The M.Sc. programme follows a 70-credit structure as shown below:

• Major courses: Minimum 20 credits (core GPB courses)
• Minor courses: 8 credits (from closely related subjects)
• Supporting courses: 6 credits (e.g., statistics, computing)
• Common courses: 5 credits (one-credit each; compulsory)
• Seminar: 1 credit
• Thesis / Research: 30 credits

Common courses include:
1) Library and Information Services
2) Technical Writing & Communication Skills
3) Intellectual Property & its Management in Agriculture
4) Basic Concepts in Laboratory Techniques
5) Agricultural Research, Research Ethics & Rural Development Programmes

Residential requirement & completion timeline

Minimum: 2 academic years (4 semesters).
Maximum: 5 academic years (10 semesters).
Students who fail to finish within the maximum period will have their admission cancelled. Thesis submission can occur any time after the 4th semester.

Evaluation & examinations

Assessment for M.Sc. typically includes multiple levels—first test, midterm and final semester exams. Continuous assessment (assignments, seminars) is encouraged. The comprehensive (pre‑PhD) examination is considered redundant for M.Sc. students and is not mandatory.

Advisory committee & academic mentoring

Each student must have an Advisory Committee (minimum three members) chaired by the Advisor. The committee should represent the major and minor fields. The Advisor must convene the committee at least once per semester to review progress and offer guidance on course selection and research.

Notes on membership: A PG teacher should not chair advisory committees for more than five students. Changes in committee membership are allowed only under exceptional circumstances with proper approvals.

Research evaluation & plagiarism

Regular (annual) reviews of research progress by the Advisory Committee are strongly recommended. Institutions must have mechanisms to detect and prevent plagiarism. Academic misconduct and data manipulation carry serious penalties.

Online learning & MOOCs

Students may take up to 20% of semester credits through approved online courses (SWAYAM/MOOCs). The host institute conducts evaluation; the Board of Studies sets a conversion method for GPA/grades and may require additional checks.

IDEA — Internship for Development of Entrepreneurship (optional)

Internship (IDEA) is an optional pathway replacing thesis (30 credits). It is intended to develop entrepreneurship and industry linkages. Key points:

• Maximum 50% of students can choose IDEA in a batch.
• Credits split: 20 (industry training) + 10 (report & viva‑voce).
• Major advisor must be from academia; co‑advisor from industry.
• IPR terms follow the university policy and any MoU with the industry partner.

Teaching Assistantship (mostly Ph.D. students)

Teaching assistantships are encouraged for doctoral students after course completion; they provide practical teaching experience. Ph.D. students may take a maximum of 16 classes per month. Remuneration rules depend on university policy and fellowships.

Registration of project personnel (SRF/RA) for Ph.D.

Project personnel may register for Ph.D. after a selection process; PI approval is mandatory. Course credit load for such candidates should generally be limited (not more than 8 credits per semester) to avoid compromising project work.

Compliance with NEP 2020

Programme design is aligned with NEP‑2020 principles: flexibility, multidisciplinary opportunities, internships, emphasis on research and innovation, ethics, communication, and holistic student development.

Definitions & grading

Important definitions:

• Credit: 1 theory hour/week or 2 practical hours/week.
• GP (Grade Point): percent marks / 10 (rounded to two decimals).
• GPA: weighted average of grade points for a semester.
• CGPA: cumulative GPA across semesters.
• OGPA: overall GPA across the entire programme.

M.Sc. (Ag) in Genetics and Plant Breeding (GPB)

Course List with Credit Hours

Course Code	Course Title	Credit Hours
GPB 501	Principles of Genetics	3 (2+1)
GPB 502	Principles of Plant Breeding	3 (2+1)
GPB 503	Fundamentals of Quantitative Genetics	3 (2+1)
GPB 504	Varietal Development and Maintenance Breeding	2 (1+1)
GPB 505	Principles of Cytogenetics	3 (2+1)
GPB 506	Molecular Breeding and Bioinformatics	3 (2+1)
GPB 507	Breeding for Quality and Special Traits	3 (2+1)
GPB 508	Mutagenesis and Mutation Breeding	3 (2+1)
GPB 509	Hybrid Breeding	3 (2+1)
GPB 510	Seed Production and Certification	2 (1+1)
GPB 511	Crop Breeding-I (Kharif Crops)	3 (2+1)
GPB 512	Crop Breeding-II (Rabi Crops)	3 (2+1)
GPB 513	Breeding Vegetable Crops	3 (2+1)
GPB 514	Breeding Fruit Crops	3 (2+1)
GPB 515	Breeding Ornamental Crops	3 (2+1)
GPB 516	Breeding for Stress Resistance and Climate Change	3 (2+1)
GPB 517	Germplasm Characterization and Evaluation	2 (1+1)
GPB 518	Genetic enhancement for PGR Utilization	2 (1+1)

Program Structure

Major courses

Minimum 20 credits from above courses including *marked Courses

Minor courses

To be selected from related disciplines

Supporting courses

To complement the major and minor courses

Common compulsory courses

Required for all M.Sc. (Ag) programs

Seminar

GPB 591

Thesis/Research

GPB 599

Prepared from: ICAR - Restructured & Revised Syllabi of Postgraduate Programmes – Volume I (Plant Sciences), 2021.