CROP SCIENCES-III (SYLLABUS FOR ICAR’S JRF/SRF(PGS) )

SYLLABUS FOR THE ALL INDIA COMPETITIVE EXAMINATION FOR ADMISSION TO DOCTORAL DEGREE PROGRAMMES AND THE AWARD OF JRF/SRF(PGS) 

[NOTE: Section Bcomprising of 180 MCQs will contain questions fromeach of the Sub-subject listed under a Major Subject Group]

03. CROP SCIENCES-III

 ( 3.1 Plant Biochemistry/Biochemistry, 3.2 Plant Physiology/Crop Physiology, 3.3 Agricultural Biotechnology/Biotechnology/Molecular Biology & Biotechnology, 3.4 Agricultural Microbiology/Microbiology)

3.1 PLANT BIOCHEMISTRY

Unit 1: Basic Biochemistry and Biomolecules

Scope and importance of biochemistry and molecular biology in plants. Structural and functional organization of prokaryotic and eukaryotic cells, viruses and bacteriophages, cell organelles function and their fractionation.Chemical bonding in biological systems, pH and buffers. Thermodynamics and bioenergetics- concept of entropy,and free energy changes in biological reactions, Redox reactions, Role of high energy phosphates. Biomembranes. Classification structure, chemistry, properties and function of carbohydrates, proteins, lipids and nucleic acids.Components of immune system, Prostaglandins.

Unit 2: Intermediary Metabolism

Anabolism, catabolism and their regulation. Metabolism of carbohydrates – glycolytic pathway, HMP pathway,TCA cycle, glyoxylate pathway and gluconeogenesis. Biological oxidation- electron transfer and oxidative phosphorylation. Lipid metabolism, degradation and biosynthesis of fatty acids, ketogenesis and causes of ketosis.Biosynthesis of sterols and phospholipids. Amino acid metabolism – catabolism of amino acids, transamination and deamination, urea cycle, biosynthesis of amino acids. Conversion of amino acids into bioactive compounds.Metabolism of nucleic acids-degradation and biosynthesis of purines, pyrimidines and nucleotides. Integration of carbohydrate, lipid and amino acid metabolism. Signal transduction mechanisms. Role of G-proteins, cyclic nucleotides and calcium in transduction. Disorders of lipid, carbohydrate, nucleic acid, amino acid metabolism.

Inborn errors of metabolism. Secondary metabolites, biotransformation and over expression.

Unit 3: Enzymes, Vitamins and Hormones

Major classes of enzymes, general properties, kinetics, active site and its mapping, activation energy and transition state. Mechanisms of enzyme action, inhibition and activation. Coenzymes and cofactors. Isoenzymes and immobilized enzymes. Regulation of enzyme activity, allosteric regulation. Multi substrate reactions, kinetic experiments to determine the mechanism of multi substrate reactions. Isolation, purification and measurement of enzyme activity. Enzyme units. Enzyme engineering. Role of enzymes in agriculture, industry, and medicine. Structure, mode of action and metabolic functions of vitamins. Deficiency diseases associated with vitamins.General description of nature hormones and disorders associated with endocrine glands, viz. pituitary, thyroid,

adrenal, pancreas and gonads. Peptide and steroid hormones. Phytohormones – auxins, gibberellins, cytokinins, ethylene, abscisic acid and new plant bio-regulators like SA, Brassinosteroids.

Unit 4: Molecular Biology

Structure of DNA and RNA Replication, transcription and translation. Post-transcriptional and translational modifications. Transcriptional and translation control of prokaryotes and eukaryotes. Features of genetic code in prokaryotes and eukaryotes. Gene expression - operon model, induction and repression, control of gene expression in prokaryotes and eukaryotes. Chloroplast and Mitochondrial genomes. Replication of viruses.Mutagens, oncogenes and carcinogenesis. General principles of recombinant DNA technology, restriction enzymes. Methods of gene transfer-plasmid and viruses as vectors, DNA and protein sequence analysis, oligonucleotide synthesis, genomic and cDNA library construction, site-directed mutagenesis, transposon tagging, chromosome walking. Basics of genome organization and mapping, functional genomics. Gene silencing. Methods for the

development of transgenic organisms. Computer application in molecular biology, primer designing, sequence analysis and phylogenetic analysis. Benefits of gene manipulation in agriculture, nanobiotechnology, bio-chips.

Unit 5: Techniques in Biochemistry

Principles of optical, phase contrast, fluorescence and electron microscopy, spectrophotometry, UV and VIS, fluorimetry, turbidometry and atomic absorption spectrophotometry. Radioisotopic techniques – scintillation counters and autoradiography and their application in biological sciences. Electrophoresis - general principles and application, gel electrophoresis, isoelectric focusing, pulsed field gel electrophoresis, immunoelectrophoresis.Chromatographic techniques - paper, thin layer, column chromatography, GC and HPLC. Centrifugation -principles of sedimentation in various rotors, differential centrifugation, density gradient centrifugation and ultracentrifugation. Cell tissue and organ culture. Cryopreservation, PCR and application of RFLP, RAPD, AFLP, microsatellite and mitochondrial and ribotyping techniques. Southern, Northern and Western blotting, ELISA.

Microarray and DNA chips. Preliminary methods of statistical analysis as applied to agricultural data – standard deviation, standard error, ANOVA, correlation and regression.

Unit 6: Biochemistry of Food-grains, Fruits and Vegetables

Fundamentals of nutrition, concept of balanced diet. Nutritional quality of protein and its evaluation. Dietary fibre.Vitamins- biochemical functions and deficiency diseases. Fats and lipids-types of fatty acids and their significance in health. Biochemical composition and food value of various food grains (including cereals, pulses, oil seeds), fruits and vegetables. Biochemistry of fruit ripening, biochemical aspects of post-harvest technology, storage and preservation. Biochemical basis of quality improvement of food grains, vegetables and fruits. Antioxidants, nutraceuticals. Food toxins and anti-metabolites, food additives, storage proteins.

Unit 7: Photosynthesis

Photosynthesis – photosynthetic pigments, light reactions, photosystems. Photophosphorylation, dark reactions: C3, C4 and CAM pathways. Regulation of Rubisco. Chemisomotic coupling. Carbon cycle and its regulation, Ion fluxes and conformational changes during photosynthesis. Photorespiration. Relationship between photosynthesis, photorespiration and crop productivity. Chloroplasm morphology, structure and biochemical anatomy. Cytosolic and organelle interactions. Nature and exchange of metabolites through translocators. Seed reserve biosynthesis.

Unit 8: Plant Metabolic Processes

Uptake and metabolism of mineral nutrients in plants. Sulphur metabolism. Nitrogen cycle, nitrate and nitrite reduction, denitrification, symbiotic and non-symbiotic nitrogen fixation. Biochemical and physiological role of hydrogenase. Chemoautrotrophy in rhizobia and nitrifying bacteria. Cell cycle. Growth regulation in plants. Signal transduction and phytohormones. Molecular mechanisms of plant growth, hormone action. Role of oligosaccharides and polysaccharides in cellular metabolism. Metabolism of cyanogenic glycosides and glucosinolates.

Unit 9: Plant Molecular Biology

General organization of nuclear, mitochondrial and chloroplast genomes. Genomics and functional genomics.Tissue specific expression of genes. Molecular biology of various stresses – drought, salinity and temperature.Signal transduction and its molecular basis: molecular mechanism of plant hormone action. Structure,organization and regulation of nuclear genes. Genes involved in photosynthesis and nitrogen fixation. Regulation of chloroplast gene expression. Mitochondrial control of fertility. Molecular markers in plants and their uses.

Unit 10: Plant Biotechnology/Genetic Engineering

Totipotency, application of tissue culture for plant improvement, cryopreservation. Protoplasm fusion. General principles of gene cloning. Isolation and characterization of plant genes and promoters. Different methods of gene transfer –direct and vector mediated. Gene silencing. Site directed mutagenesis. Molecular analysis of transformants. Potential applications of plant genetic engineering for crop improvement – insect-pest resistance (insect, viral, fungal and bacterial diseases). Abiotic stress tolerance, herbicide resistance, storage protein quality improvement, increasing shelf- life, oil quality. Biosafety and IPR issues.

3.2 PLANT PHYSIOLOGY

Unit 1: Cell Organelles and Water Relations

Cell organelles and their physiological functions Structure and physiological functions of cell wall, cell inclusions.Cell membrane structure and functions. Water and its role in plants, properties and functions of water in the cell, water relations, water potential of plant cells. Mechanism of water uptake by roots transport in roots, movement of water in plants, water loss from plants, energy balance, solar energy, input energy dissipation at crop canopy level. Evapotranspiration, plant factors influencing transpiration rate. Stomata, structure function - Mechanism of stomatal movement, antitranspirants. Physiology of water high temperature and salinity stress in plants. Influence

of water stresses at cell, organ, plant and canopy levels. Indices for assessment of drought resistance.

Unit 2: Metabolic Processes and Growth Regulation

Energy and work, free energy and chemical potential, redox reactions and electrochemical potential. Enzyme classification and mechanism of action, factors affecting enzyme action. Gene expression and protein turnover.Photosynthesis, translocation and respiration as key processes regulating carbon metabolism and plant growth.Photosynthesis and bioproductivity. Photochemical process-Chloroplast, its structure, CAM plants and their significance. Rubisco structure and regulations, Photorespiration and its significance, CO2 fixation as a diffusive process, effect of environmental factors on photosynthetic rates. Synthesis of sucrose, starch, oligo and polysaccharides. Translocations of photosynthates and its importance in sink growth. Mitochondrial respiration,

growth and maintenance respiration, cyanide resistant respiration and its significance. Nitrogen metabolism. Inorganic nitrogen species (N2, N03, NH3) and their reduction, protein synthesis, nucleic acids. Sulphate uptake and reduction. Lipid metabolism- storage, protective and structural lipids. Secondary metabolites and their significance in plant defence mechanism. Growth and differentiation, hormonal concept of growth and differentiation, plant growth hormones (auxins, gibberellins, cytokinins, ABA, ethylene, etc.), biosynthesis of growth hormones and their metabolism, synthetic growth regulators, growth retardant, apical dominance, senescence, fruit growth, abscission, photo-morphogenesis, photo-receptors, phytochrome, physiology of

flowering, photoperiodism and vernalisation.

Unit 3: Crop Productivity and Modelling

Role of crop physiology in agriculture, crop growth and productivity, crop growth models describing yield (Duncan/Passioura), phenology-crop productivity, growth factors related to biomass - concept of growth ratescanopy photosynthesis (leaf area and net assimilation rates as determining factors). Light interception as a major function of leaf area-index, LAD canopy architecture- Light extinction coefficient relative growth rate. Net assimilation rate. Biomass and yield relations. Assimilate partitioning, yield and yield structure analysis. Concept of source and sink, factors influencing source and sink size and productivity. Environmental factors determining crop growth. Light, temperature and VPD, effect of photoperiod and thermoperiod on duration of growth stages.Ideotype concept-selection- indices for improving crop productivity.

Unit 4: Abiotic Stress Responses in Plants

Abiotic stresses affecting plant productivity. Basic principles of a crop improvement programme under stress, interactions between biotic and abiotic stresses. Drought 21 characteristic features, water potential in the soilplant-air continuum. Development of water deficits, energy balance concept, transpiration and it’s regulation –stomatal functions/VPD. Physiological process affected by drought. Drought resistance mechanisms: Escape,dehydration postponement (Drought avoidance), Dehydration tolerance, and characteristics of resurrection plants. Osmotic adjustment Osmoprotectants, stress proteins. Water use efficiency as a drought resistance trait.Molecular responses to water deficit stress perception, expression of regulatory and function genes and significance of gene products. Stress and hormones-ABA as a signaling molecule – Cytokinin as negative signal. Oxidative stress: reactive oxygen species (ROS) – role of scavenging systems (SOD, catalase etc.). High temperature stress: tolerance mechanisms- role of membrane lipids in high temperance tolerance. Functions of HSPs chilling stress; effects on physiological processes. Crucial role of membrane lipids. Salinity: species variation in salt tolerance. Salinity effects at cellular and whole plant level, tolerance mechanisms. Breeding for salt resistance. Heavy metal stress: aluminum and cadmium toxicity in acid soils. Role of phytochelatins (heavy, metal binding proteins).

Unit 5: Plant Growth Regulators and Plant Development

Plant growth regulators – Hormones, endogenous growth substances and synthetic chemicals. Endogenous growth regulating substances other than hormones. Brassinosteriods, triacontanol, phenols polyamines, jasmonates, concept of death hormone. Classification, site of synthesis, biosynthetic pathways and metabolism and influence on plant growth and development by auxins, gibberellins, cytokinins, abscisic acid and ethylene. Concept of hormone action - hormone receptors and signal transduction Hormone mutants. Hormonal regulation of gene expressions at various developmental stages of plant-flowering, seed maturity, seed dormancy. Action of hormones on cellular functions: Auxins- cell elongation, retardation of abscission of plant parts, gibberellins –

stem elongation, germination of dormant seeds, cytokinins-cell division, retardation of senescence. Abscisic acidstomatal closure and induction of drought resistance, ethylene- fruit ripening, acceleration of senescence of leaves. Interaction of hormones in regulation of plant growth and development processes. Synthetic growth regulators, growth retardants, apical dominance, senescence, fruit growth, abscission. Growth and differentiation, hormonal concept of growth and differentiations. Rooting of cuttings- flowering- physiological and molecular aspects of control of reproductive growth. Apical dominance, senescence and abscission. Fruit growth and development,

physiological and molecular aspects of ripening processes and improving post-harvest life of fruits. Induction and breaking dormancy in seeds and buds. Synthetic growth regulators. Practical utility in agriculture and horticulture. Herbicides, classification and their mode of action.

Unit 6: Mineral Nutrition

Importance of mineral nutrition in plant growth. Classification and essentiality criteria. General mechanisms - concept of apparent free space and nature of bio-membranes. Dual mechanism and other concepts of ion uptake.Short distance transport-pathway from external solution (Apoplasm) to sieve across the root cortical cells-factors contributing to xylem loading. Long distance transport in xylem and phloem, xylem unloading in leaf cells. Uptake and release of mineral nutrients by foliage. Rhizosphere and root biology, root growth, influence of microorganism in nutrient acquisition, release and uptake by plant roots. Yield and mineral nutrition-concept of nutrient use efficiency, Mineral nutrition under adverse soil situations-drought, salinity, acidity etc. Heavy metal toxicity and concept of phytoremediation. Interaction of phytohormones and nutrients. Molecular aspects- uptake

and transport, role of transporter genes, genetics of nutrient uptake, identification and transfer of genes for tolerance to nutrient deficiencies, etc. Soil less culture – Hydroponics - Role of Macro, Micro and beneficial nutrients- Identification of nutrient deficiencies and toxicities.

Unit 7: Climate and Climate Change

Climate- Analytical methods to determine long term changes in environment- Tree ring, cellulose, stable carbon isotope discrimination, stable 18O discrimination for hydrological changes. Likely changes in climate in future and its impact on crop and ecosystems. The greenhouse gases and global warning. CO2 as an important greenhouses gas, global carbon deposits, fluxes in the sinks and sources. Approaches to contain atmospheric CO2 level. Effect of elevated CO2 on plant growth and development. Methane as a greenhouse gas. Prediction on global warming, GCA models, effects on climate and biota. High temperature and CO2 interaction on plant growth and productivity,

ionising radiation UV-B chlorofluoro carbon (CFC)– their impact on ozone layer- ozone hole and alteration in UV-B radiation. Effects of UV-B radiation on plant ecosystem, repair and acclimation to UV-B damage. Carotenoids and their role in membrane stabilization. Air pollution, SO2, NO, methane, ozone, peroxy acetyl nitrate and their effect on ecosystem. Industrial and domestic effluent-their effect, on aquatic ecosystem, plant growth and development.

Unit 8: Seed Physiology

Structure of seeds and their storage. Seed development patterns and source of assimilates for seed development. Pathway of movement of assimilates in developing grains of monocots and dicots. Chemical composition of seeds. Storage of carbohydrates, proteins and fats in seeds. Hydration of seeds. Physiological processes. Seed respiration, mitochondrial activity Mobilization of stored resource in seeds. Chemistry of oxidation of starch, proteins and fats. Utilization of breakdown products by embryonic axis. Control processes in mobilization of stored reserves. Role of embryonic axes. Gibberellin and ?-amylase and other hydrolytic activity. Seed maturation phase and desiccation

damage, role of LEA proteins. Seed viability. Seed dormancy. Means to overcome seed dormancy.

Unit 9: Physiology of Flowering and Reproduction

Evolutionary history of flowering plants (angiosperms). Semelparous and iteroparous reproduction, monocarpic and perennial life etc. Flowering phenomenon, effect of plant age, juvenility- transition to flowering. Flowering nature and classification of plants. Photoperiodic responses and the mechanisms in short and long day plants. Theories related to flowering. Endogenous substances and flowering. Gene expression in flowering. Control of flowering. Thermoperiodism - photo and thermo-period interactions. Vernalization-mechanism. Photomorphogenesis, photoreceptors, phytochrome, cryptochrome, physiology of flowering, photoperiodism and vernalization. Optimization in flowering response-to environmental features (light, temperature, stress) etc. plant

reproductive physiology. Mating strategy in plants, molecular techniques to understand mating patterns, selfincompatibility responses, physiological processes mediating fertilization (pollen-stigma interactions), seed and fruit development, seed and fruit abortion and means to overcome it. Molecular biology of seed development, physiological basis of cytoplasmic male sterility and fertility restoration. Physiology of heterosis.

Unit 10: Physiology of Horticultural and Plantation Crop Species

Growth and development of horticultural and plantation crop species. Juvenility, shoot growth, types of shoots, patterns of shoot growth, cambial growth and its regulation. Physiological aspects of pruning and dwarfing. Growth measurements. Water relations of tree species. Water uptake and transport. Concepts of transpiration rate and water use efficiency. Sexual and asexual propagation. Rootstock and scion interactions. Physiology of flowering in perennial species, photoperiodism and thermoperiodism. Physiological aspects of fruit crops: mango, banana, grapes, citrus, papaya and pineapple etc. Physiological aspects of plantation crops: tea, coffee, cardamom, coconut, and black pepper. Physiological constraints and remedial measures of horticultural and plantation crops.

Unit 11: Post-Harvest Physiology

Senescence and ageing in plants. Ethylene – the senescence hormone, leaf senescence. Monocarpic plant senescence. Biochemistry and molecular biology of flower senescence. Gene expression during senescence. Concept of physiological maturity of seeds - post harvest changes in biochemical constituents in field crops - loss of viability, loss of nutritive value, environmental factors influencing post-harvest deterioration of seeds. Physiological and biochemical changes during fruit ripening and storage. Senescence and post-harvest life of cut flowers. Physical, physiological and chemical control of post - harvest deterioration of fruits, vegetables and cut flowers and its significance during storage and transport. Molecular approach in regulation of fruit ripening.Transgenic technology for improvement of shelf-life. Edible vaccine.

Unit 12: Morphogenesis, Tissue Culture and Plant Transformation

Morphogenesis; the cellular basis of growth and morphogenesis; polarity in tip growing cells and diffusive growing cells. Control of cell division and differentiation, phyto-chromes, different forms, physiological effects and gene regulation, and cellular totipotency, physiology and biochemistry of differentiation, in organ cell, tissue and cultures, micropropagation strategies, application of tissue culture in agriculture, horticulture, forestry and industry: plant transformation; transformation vectors, concept of selectable and scorable markers. Agrobacterium mediated transformation, binary vectors, biolistics. Electroporation, selection of putative transgenic plants, genetic analysis. PCR, Southern analysis evaluation of transgenic plants.

3.3 AGRICULTURAL BIOTECHNOLOGY

Unit 1: Cell Structure and Function

Prokaryotic and eukaryotic cell architecture, Cell wall, plasma membrane, Structure and function of cell organelles: vacuoles, mitochondria, plastids, golgi apparatus, ER, peroxisomes, glyoxisomes. Cell division, regulation of cell cycle, Protein secretion and targeting, Cell division, growth and differentiation. Transport across cell membrane, Cell signaling, Developmental biology of plants, programmed cell death (apoptosis).

Unit 2: Biomolecules and Metabolism

Structure and function of carbohydrates, lipids, proteins and nucleic acids, Synthesis of carbohydrate, glycolysis,HMP, Citric acid cycle and metabolic regulation, Oxidative phosphorylation and substrate level phosphorylation, Vitamins, plant and animal hormones. Functional molecules, antioxidants, nutrient precursor, HSPs, anti-viral compounds.

Unit 3: Enzymology

Enzymes, structure conformation, classification, assay, isolation, purification and characterization, catalytic specificity, mechanism of action, active site, regulation of enzyme activity, multienzyme complexes, immobilized enzymes and protein engineering, immobilized enzymes and their application.

Unit 4: Molecular Genetics

Concept of gene, Prokaryotes as genetic system, Prokaryotic and eukaryotic chromosomes, methods of gene isolation and identification, Split genes, overlapping genes and pseudo genes, Organization of prokaryotic and eukaryotic genes and genomes including operon, exon, intron, enhancer promoter sequences and other regulatory elements. Mutation – spontaneous, induced and site-directed, recombination in bacteria, fungi and viruses, transformation, transduction, conjugation, transposable elements and transposition.

Unit 5: Gene Expression

Expression of genetic information, operon concept, Transcription – mechanism of transcription in prokaryotes and eukaryotes, transcription unit, regulatory sequences and enhancers, activators, repressors, co-activators, Corepressors in prokaryotes and eukaryotes, inducible genes and promoters, Transcription factors post transcriptional modification and protein transport, DNA-protein interaction, Genetic code. Mechanism of translation and its control, post translational modifications.

Unit 6: Molecular Biology Techniques

Isolation and purification of nucleic acids. Nucleic acids hybridization: Southern, northern and western blotting hybridization. Immune response monoclonal and polyclonal antibodies and ELISA, DNA sequencing. Construction and screening of genomic and C-DNA libraries. Gel electrophoretic techniques. Polymerase chain reactor spectroscopy, RT-PCR ultracentrifugation, chromatography, FISH, RIA, etc. Next generation genome sequencing techniques. reaction, reverse transcription PCR, real time PCR, ultracentrifugation, spectroscopy, microarray, etc.

Unit 7: Gene Cloning

Restriction enzymes and their uses. Salient features and uses of most commonly used vectors i.e. plasmids, bacteriophages, phagemids, cosmids, BACs, PACs and YACs, binary vectors, expression vectors. Gateway cloning vectors. Gene cloning and sub-cloning strategies, chromosome walking, genetic transformation, Basis of animal cloning. Biology. Risk assessment and IPR.

Unit 8: Molecular Biology

Ribosome structure and function. Protein biosynthesis in prokaryotes and eukaryotes. Post-translational modification. Gene regulation, RNA processing and Post transcriptional modifications. Bioprospecting, biofortification, gene pyramiding and gene fusion, ribozyme technology. DNA chips and their use in transcriptome analysis; Mutants and RNAi in functional genomics; Proteomics, Metabolomics and ionomics.

Unit 9: Plant Molecular Biology

Photoregulation and phytochrome regulation of nuclear and chloroplastic gene expression. Molecular mechanism of nitrogen fixation. Molecular biology of various stresses, viz. abiotic stresses like drought, salt, heavy metals and temperature; and biotic stresses like bacterial, fungal and viral diseases. Signal transduction and its molecular basis, molecular mechanism of plant hormone action mitochondrial control of fertility, structure, organization and regulation of nuclear gene concerning storage proteins and starch synthesis. Crop genome sequencing projects.

Unit 10: Tissue Culture

Basic techniques in cell culture and somatic cell genetics. Regulation of cell cycle and cell division. Clonal propagation. Concept of cellular totipotency. Anther culture, somaclonal and gametoclonal variations. Hybrid embryo culture and embryo rescue, somatic hybridization and cybridization. Application of tissue culture in crop improvement. Secondary metabolite production. In vitro, mutagenesis, cryopreservation and plant tissue culture repository. Synthetic seeds, Virus indexing.

Unit 11: Plant Genetic Engineering

Isolation of genes of economic importance. Gene constructs for tissue-specific expression. Different methods of gene transfer to plants, viz. direct and vector-mediated. Molecular analysis of transformants. RNAi technology. molecular pharming, bioremediation. GM detection methods. Resistance management strategies for target traits. Potential applications of plant genetic engineering for crop improvement, i.e. insect-pest resistance (insect, viral, fungal and bacterial disease resistance), abiotic stress resistance, herbicide resistance, storage protein quality, increasing shelf-life, oil quality, Current status of transgenics, biosafety norms and controlled field trials and release of transgenics (GMOs).

Unit 12: Molecular Markers and Genomics

DNA molecular markers: Principles, type and applications; restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA sequences (RAPD), Simple sequence repeats (SSR), Single nucleotide polymorphism (SNP), Structural and functional genomics, gene  mapping, genome mapping, gene tagging and comparative genomics and application of genomics. Development of mapping population, linkage mapping. association mapping, Phylogeography, conservation genetics.

3.4 AGRICULTURAL MICROBIOLOGY

Unit 1: History of Microbial World

History, development and scope of microbiology, evolution of microbial life. Theory of spontaneous generation. Prokaryotes, archaebacteria and eukaryotes. Techniques used in identification and classification of bacteria. Important groups of prokaryotes – photosynthetic bacteria, blue green algae, chemoautotrophic bacteria, spore forming bacteria, mycoplasma, viruses, bacteriophages and actinomycetes. Heterotrophic bacteria nitrobacteria, nitrogen-fixing bacteria and cyanobacteria, lactic acid bacteria, halophiles, thermophiles acidophiles and methanogens. Structure and classification of viruses, growth of viruses, lytic and lysogenic cycles, plant viruses, viroids.

Unit 2: Microbial Ecology and Physiology

Principles of microbial ecology, Microbiology of ecosystems - soil, rhizosphere, phyllosphere, water - fresh and marine, and air. Microbial interactions - symbiosis, synergism, commensalism, parasitism, amensalism, antagonism and predation, adoption of micro-organisms to various ecosystems. Microbial growth curve. Mathematical expression of growth -continuous and batch cultures. Diauxic and synchronous growth. Microbial nutrition. Bacterial metabolism - aerobic and anaerobic respiration, electron transport chain, microbial photosynthesis, oxidative and substrate level photo-phosphorylation. Biosynthesis of cell wall, protein breakdown by microbes.

Unit 3: Soil Microbiology

Soil microorganisms: major groups, decomposition of organic matter, soil health. Root exudates and rhizosphere effects. Manipulation of rhizosphere microflora in plant productivity. Microbial biomass. Nitrogen cycle: ammonification, nitrification and denitrification. Biological nitrogen fixation–symbiotic and asymbiotic. Biochemistry and genetics of nitrogen fixation. Microbial transformations of phosphorus, sulphur and minor nutrients. Role of bio-fertilizers in agriculture and forestry. Bioremediation of problem soils, plant growth promoting rhizobacteria and their mode of action. Formation and composition of soil organic matter: fulvic acid and humic acid.

Unit 4: Environmental Microbiology and Basic Microbiological Techniques

Isolation and preservation of different types of microorganisms. Methods of sterilization and disinfection. Microscopy: Optical, phase contrast, fluorescent, dark field and electron. Microbial assay of vitamins, enzymes and antibiotics, Pollution of soil, water and air, Role of microorganisms in pollution, sources of pollution and their impact on environment, microbiology of sewage and industrial effluents and their safe disposal, management of solid and liquid organic wastes, composting, biogas, water purification, sewage treatment, water-borne diseases and effluent management.

Unit 5: Microbial Biotechnology

Industrial production of metabolites - organic acids, alcohols, antibiotics. Fermentor designs and types. Control of fermentation process - batch, feed batch and continuous. Downstream processing in fermentation industry. Production of single cell proteins and probiotics, hormones, biofertilizers, biopesticides. Phyto-remediation. Microbiology of raw and processed foods. Fermented food – vinegar, wine sauerkraut, pickles, cheese, yogurt. Food preservation, contamination and spoilage, food-borne illness and intoxication. Food as substrate for microorganism, microflora of meat, fish, egg, fruits, vegetables, juices, flour, canned foods; bio- degrading microbes, single cell protein for use as food and feed, bioactive food / probiotics