University of Kerala Courses

M.Sc. (Genetics and Plant Breeding)

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Duration: 2 Years

Eligibility: Graduate or Equivalent

Course Structure

Course Code	Course Title
Semester - I
BOT. 511	Mendelian Genetics
BOT. 512	Techniques in Cell Biology
BOT. 513	Cytology
Semester - II
BOT. 521	Molecular Genetics
BOT. 522	Cytogenetics
BOT. 523	Plant Breeding
BOT. 524	Plant Biochemistry
Semester - III
BOT. 531	Genetic Engineering
BOT. 532	Plant Biotechnology
BOT. 533	Environmental Genetics
BOT. 534	Modern Methods in Crop Breeding
Semester - IV
BOT. 541	Population Genetics
BOT. 542	Developmental Genetics
BOT. 543	Biosystematics
Elective papers
BOT. 501	Biophysics
BOT.505	Applied Palynology
BOT.51A	Plant tissue culture
BOT.507	Transgenic plants
BOT.508	Biotechnology
BOT.53A	Phytochemicals
BOT.52A	Plant Cell Culture Technology

 

Course Syllabus

 BOT 511. Mendelian Genetics

Unit I. Gregor Mendel's Discoveries

• Mendel’s Experimental approach to study the pattern of inheritance, Monohybrid cross, Dihybrid cross, Trihybrid cross, Mendel's analytical approach, Punnet square, Forkline method, Relations among pairs of independent alleles, Test cross.
• Laws of probability, Binomial Theorem, Chi-Square analysis, Pedigree analysis. Human disorders follow Mendelian patterns of inheritance

Extending Mendelian Genetics

• Codominance, Multiple alleles. Lethal alleles. Epistasis, Complementation analysis, X linkage in Drosophila, X-linkage in humans, Sex limited and sex influenced inheritance, Hollandric genes, penetrance and expressivity, pleiotropy, position effects, temperature and nutrition effects, genomic imprinting.
• Quantitative traits, Additive alleles, Statistical analysis of polygenic traits, mapping of quantitative trait loci.

Unit II. Linkage maps and sex determination mechanisms

Relating Mendelism to Chromosomes

• Chromosome theory of heredity, coupling and repulsion theory,  Morgan and crossing over, Sturtvant and mapping, single cross overs, linkage ratio.
• Three point Mapping in Drosophila, crossing over involves physical exchange between chromatids. Works of Stern, Creighton and McClintock, determination of gene sequences, interference.

Sex determination and Sex Chromosomes

• Sex determination in Drosophila, humans and plants, Klinefelter and Turner’s syndrome, Barr bodies, Lyon’s hypothesis. The mechanism of inactivation, dosage compensation in Drosophila.

Unit III. Errors and Exceptions to Chromosomal Inheritance

• Extranuclear inheritance, Chloroplast variation in Four O'clock plant, Mitochondrial mutations, Mutations in mitochondrial DNA cause human disorders. kappa in Paramoecium, maternal effect.

Practicals

• Problems related to Mendel’s laws, Probability, Pedigree analysis
• Problems related to codominance, multiple alleles, lethal alleles, epistasis, complementation analysis, X linkage, sex-limited and sex influenced inheritance.
• Statistical analysis of polygenic traits. Mapping of quantitative trait loci.
• Problems related to two-point test cross, three point mapping in Drosophila, Determination of gene sequences, Interference
• Sex determination in Drosophila humans, and plants
• Chloroplast variation in Four O'clock plant, Mitochondrial mutations, Inheritance of Kappa in paramecium, Inheritance of Maternal effect.

 

BOT 512. Techniques In Cell Biology

Unit I. Microscopy

• Principles, Light, Phase contrast, Interference , Fluorescent, Electron Scanning, Transmission, Scanning, EDX, Scanning, Voltage

Unit II. Processing of tissues

• Killing and fixing: Principles and Techniques, Properties of chemical reagents used, Constituents and properties of killing and fixing fluids-different types, Flemming’s fluid, FAA, Carnoy’s fluid, Nawaschins fluid, Zircles fluid, Killing and fixing methods  for electron microscopy.
• Dehydration: Principles, Important dehydrating and clearing agents, their properties and uses, Alcohol, xylol, glycerol, chloroform, dioxan, Types of micro-slide preparation, temporarysemi- permanent and permanent – smears and squashes, Methods of dehydration preparation of serial section Tertiary- Butyl Alcohol method (TBA), Ethyl alcohol method, Method of embedding of  dehydrated material in paraffin wax.
• Sectioning: Free hand sections, significance and problems. Types of Microtome: Rotary, Sledge, Sliding microtome, Freezing microtome (Cryotome, cryostat), Sectioning by Rotary microtome, Sledge microtome.
• Stains and Staining: Principles of staining, classification of stains, Protocol for preparation of the following stains:-
  • Natural Stains: Haematoxylin, carmine, orcein.
  • Synthetic Dyes: Fast green, Orange G, Safranin, Crystal Violet, Basic fuchsin, Eosin, Cotton blue.
  • Technique of staining: Single staining, Double staining, Triple staining, Significance.
  • Mounting media: Properties and techniques. Common mounting media used, Principles and techniques of maceration.
• Histochemistry.
  • Cytochemical Localization of Cell Components. Carbohydrates (Periodic acid –Schiff’s [PAS] method), Fats, Oils, Suberin, Cutin, Sudan Dyes, Lignin- Phlroglucinol, Mucopolysaccharides- Alcian Blue, Nucleic acids -Fuelgen Reaction, Pectin-Ruthenium red method, Hydroxylamine, Phospholipids -Orange G and Aniline Blue, Proteins- Coomassie brilliant blue stain, Lipids Sudan Blue method, Starch iodine – Potassium iodide (IKI).
  • Cytochemical localization of enzymes: Acid phosphatases, Alkaline phosphatase, Cytochrome oxidase, Dehydrogenase, Esterases, Lipases, Pectinase.

Unit III. Chromosome Banding Techniques

• Quinacrine banding, Giemsa banding (G-banding), Reverse  fluorescent banding, C- banding, Fuelgen banding, Silver banding (AG- NOR banding), N- banding, Orcein banding.

Practicals

• Preparation of double stained freehand sections of plant tissue.
• Freehand sections showing localization of primary metabolites- Proteins, Carbohydrates and Lipids.
• Dehydration of plant tissue using TBA method, embedding and Preparation of Paraffin blocks and preparation of serial sections.
• Histochemical localization of starch, protein, nucleic acid and fat
• Histochemical localization of estrase, acid phoshatase and pectinase
• Sectioning by using cryotome (demonstration only)
• Photo-documentation of micro-preparation by using image analyzer
• Chromosome banding techniques.

 

BOT-513. Cytology

Unit I. Cell Structure & Function

Ultrastructure, chemistry, functions, interrelationships and origin of cell organelles:

• Cell-wall
• Cytoplasm: Plasma membrane, endoplasmic reticulum, ribosomes, golgi-bodies, plastids, mitochondria, centrioles, cytoskeletal structures- microtubules, microfilaments, intermediate filaments, lysosomes, peroxisomes, spherosomes, ribozymes
• Nucleus: Nuclear envelope, Nucleoplasm, Nucleolus and Chromatin reticulum

Unit II. Chromosomes:

• Structure & Chemistry: DNA, histones, non-histones and other  associated proteins.
• Molecular structure and functions of centromeres: Nucleolar organizing region, telomere, euchromatin and heterochromatin, unique and repetitive sequences.

Unit III. Cell division:

• Mitosis.
  • Interphase stages;-G0, G1,S,G2. Discovery of regulatory proteins and their role, checkpoints. Concepts of DNA replication in prokaryotes and eukaryotes during S-phase, chromosome replication in eukaryotes, structure and function of centrioles.
  •  Prometaphase, metaphase, anaphase, telophase. Nuclear and cytoplasmic changes,spindle structure and mechanism, microtubule organizing centers, motor proteins and other regulatory proteins.
  • Cytokinesis: Mechanism of cytokinesis and proteins involved, variations in plants, animals and bacteria.
  • Significance of mitosis: A brief review of cell division and life cycle of bacteria, fungi, algae, bryophytes and pteridophytes.
  • Variations from the normal mitotic plan-endoreduplication and endomitosis, C-mitosis, somatic reduction and genetic consequences of the above variations.
• Meiosis:
  • Details of the prophase, metaphase, anaphase telophase. Role of spindle and regulatory proteins.
  • Molecular structure of the synaptonemal complex and its functions in pairing and synapsis. Variations in the pairing mechanism such as –asynapsis, desynapsis, exchange pairing, non-homologous pairing, distributive pairing, secondary pairing and somatic pairing.
  • Chiasma formation and genetic recombination. Models to explain molecular mechanism of genetic recombination.
  • Proteins (cohesins, securins, separase) involved in sister chromatid separation and terminalization.
  • Genetic significance of meiosis.

Unit IV. Karyotype & Pachytene analysis:

• Karyotype.
  • Standard parameters for karyotype analysis.Morphological classification and categorization of chromosomes. Natural karyotype. Current modifications in the system. Karyogram and Idiogram.
  • Karyotype differentiation and evolution. Factors affecting karyotype variations such as changes in chromosome number, structural alterations, centromere position, degree and distribution of heterochromatin. Unimodal and Bimodal karyotype. Banding techniques.
• Pachytene analysis.
  • Chromosomal parameters utilized for analysis, Idiogram.
  • Chromosomal behaviour such as pairing and synapsis in pachytene and factors affecting the pairing. Cytogenetic significance.

Practicals

The given list of plants may be used to study the mitosis and meiosis in cells. Observations should be recorded for all the division stages in the materials provided. Ten permanent slides of the countable metaphase spreads to be prepared and submitted at the end of semester I.

 

BOT- 521. Molecular Genetics

Unit I. Genetic organization:

• Genetics of Viruses, Bacteria, Neurospora and Yeast: - Types, Fine structure of genomes, life-cycle, genetic recombination and gene mapping.
• DNA structure: Chemistry of nucleotides , organization of the poly nucleotide strand, double helical structure of DNA as proposed by Watson and Crick, Importance of Watson-Crick model, exception to Watson Crick organization of DNA, X-ray diffraction studies, Conformational changes in DNA structure, Single stranded DNA, Organization of the Eukaryotic DNA, Repetitive DNA, DNA variation in organisms.
• DNA replication: Watson- Crick concept, electron microscopic autoradiograhy in E. coli DNA and in eukaryotic DNA, semidiscontinuous replication DNA polymerase I, II, III DNA gyrases, topoisomerases, ligases, initiation of replication, roles of RNA polymerase (primase) and replisome complex, current concept of DNA replication in prokaryotes and eukaryotes.

Unit II. Gene expression:

• Evolution of the Gene Concept, Functional definition: One geneone metabolic block, one gene-one enzyme, one gene-one polypeptide. Structural definition: Mutations and Recombinations within a gene. Operational definition: Intergenic and intragenic complementation
• Molecular Biology of gene expression: Brief overview of the Central Dogma and Teminism. Transcription in prokaryotes and eukaryotes. Types and structure of RNA polymerase, Different types of RNA : mRNA, tRNA, rRNA, snRNA, snoRNA, miRNA, Xist, RNA, siRNA, shRNA, antisense RNA. Regulatory sequences and transcription factors involved. Mechanism: Initiation, elongation and termination. Split genes and RNA splicing in eukaryotes. Translation in prokaryotes and eukaryotes. Basic structure of proteins, ribosomes, tRNA. Genetic code Experiments conducted to decipher the genetic code, salient features, exceptions, Wobble-hypothesis, tRNA-suppressor mutations. Mechanism of translation: Chain initiation, elongation and termination, proteins involved, factors affecting translation accuracy

Unit III. Molecular mechanism of Gene Regulation:

• Regulation in prokaryotes: Constitutive, Inducible and Repressible expression, positive and negative control. Induction and catebolite repression in lac operon, repression and attenuation in trp operon, lysogenic and lytic switches in lambda phage, Translational and post translational regulation.
• Regulation in Eukaryotes: Transcriptional activator proteins, enhancers, silencers, eukaryotic transcription complex, chromatin remodeling during gene expression, alternative promoters, Epigenetic mechanisms: methylation and transcriptional inactivation, cosuppression through transcriptional silencing, genome imprinting. RNA processing->alternative splicing, RNA stability, RNA interference. Translational regulation: Gene amplification, mating type interconversion.
• Transposons: Historical background, works of Rhoades and McClintock. Structure of typical transposons and types of transposons. Transposons in bacteria (IS elements, Composite elements), Transposons in maize (Ac/ Ds elements, Spm / Ex elements), Transposons in Drosophila (P elements ), Types of transposition, Genetic and evolutionary significance. Retro transposons Life cycle of retroviruses, Reverse transcription, LTRs. Retroposons in yeast (Ty elements), Retroposons in Drosophila (Copia elements), Retroposons in mammals (LINES,  SINES), Application of transposons and retroposons in breedingprogrammes.

Unit IV. Genomics and Bioinformatics:

• Genomics: Structural genomics, Genetic and physical mapping (RFLP), microsatellite maps,  cyotogenetic maps, physical maps, positional cloning, chromosome walks and jumps, Genome sequencing, genome databases, human genome sequencing project. Functional genomics. transcriptome, proteome and metabolome, Microarrays and gene-chips. Comparative genomics. Functional and evolutionary relationships prokaryotes, organelles and eukaryotes, orthologues and paralogues. Metabolomics: Identification and quantification of cellular metabolites in biological samples. Pharmacogenomics and drug designing.
• Bioinformatics: Detecting open reading frames, gene prediction, programs for finding genes, secondary databases of functional  domains, molecular phylogenetic programmes, comparing nucleotide and amino acid sequences using BLAST. Programmes for determination of protein structure

Practicals

• Raising pure cultures of specific strains of bacteria by plate streaking method.
• Plasmid DNA isolation using the alkaline lysis method
• Genomic DNA isolation from plant tissues by CTAB method.
• Electrophoresis: Separation of DNA and proteins.
• DNA quantification and Southern blotting.
• Problems relevant to concerned units

 

BOT- 522. Cytogenetics

Unit I. Chromosomal aberrations-numerical

• Haploidy: Types of haploids: Euhaploids, monohaploids, polyhaploids, amphihaploids, pseudohaploids, aneuhaploids, disomic haploids, addition haploids.
• Polyploidy: Types of euploids, autopolyploids, allo-polyploids– segmental allopolyploids – autopolyploids – agmatoploids – origin of different types of polyploids – meiosis in polyploids, morphological, physiological and genetical characters of polyploids.
• Aneuploidy: Hyperploids – trisomics, tetrasomics, double tetrasomics – Trisomics, types of trisomics, primary trisomics, secondary trisomics, tertiary trisomic, acrocentric trisomics, fragment trisomics, compensating trisomics – meiosis in trisomics, Hypoploids: monosomic, nullisomics. Meiosis in aneuploids, Role of aneuploids in the evolution.
• Genetics of Polyploids: Genetic consequences of autopolyploids, tetrasomy. Allopolyploids – genetic regulation of chromosome pairing, allopolyploidization of autopolyploids, genome analysis – genetic consequences – deviation segregation, aneuploids in allopolyploids- identification of homologous chromosomes. Segmental allopolyploids, fertility – Higher polyploids, diplodization, Agmatoploids. Complications with polyploids – primarytrisomics, transmission and genetic consequences – Teritary trisomics, transmission and genetic consequences – transmission of the extra chromosome through the female and male – morphology, physiology, anatomy and biochemistry of trisomics, Hypoploids. Aneuploidy of sex chromosome.

Unit II. Chromosomal aberrations-structural

• Structural aberrations: Deficiency – origin, cytological behaviour, genetic effects, pseudodominance: Duplication – origin, types of duplications – tandem, reverse tandem, displaced, cytological behaviour, position effect. Inversion origin, types of inversion: paracentric, pericentric, meiotic behaviour: Translocations, types of translocations – shift, simple reciprocal, aneucentric and pseudo-isochromosome, meiotic behaviour, Translocation complex in Rhoeo, Oenothera, Renner effect.
• Identification of chromosome segments and their alterations – Chromosome banding - Q band, G-band, R-band, C-band, Ebands, CT- bands, N-band and Q-bands – Physical localization of DNA sequences on chromosomes using in situ hybridization – GISH, FISH, Fiber FISH, Molecular maps etc.
• Transposable elements and their molecular properties: Transposons, Retrotransposons – S-SAP (Sequence Specific – Amplified Polymorphism, IRA P (Inter-retrotransposon – Amplified polymorphism), REMAP (Retrotransposon – Microsatellite Ampli) RBIP (Retrotransposon – Based insertional polymorphism) – Retroelements and C-value paradox. Evolutionary implications of Transposable Elements – Regulation of Transposon and Retrotransposon activity.

Unit III. Sex determination mechanisms and Human Cytogenetics

• Cytogenetics of sex determination:
  • Sex chromosomes; types of sex chromosomes – undifferentiated, structurally heteromorphic and multiple sex chromosomes, sex chromosomes in plants and animals, Evolution of sex chromosomes, origin of the sex chromosome mechanisms;
  • Sex chromatin: morphology and types: late replicating X chromosome and single X, origin of sex chromatin, Lyon’s hypothesis and dosage compensation; chromosomal and genetic mechanisms of sex determination in dioecious plants and animals, role of ‘sry’ and ‘tim’ genes in mammalian sex determination, inter sexes, gynandromorphic, sex reversal, environmental influence in sexual dimorphism, evolution of dioecism.
• Special types of chromosomes – polytene, lampbrush and Bchromosomes.
• Human cytogenetics: Human chromosome culture technique, Normal karyotype in man; chromosome aberrations associated with congenital defects in man. Sex chromosomal: Turner’s syndrome, Klinefelter’s syndrome, triple X syndrome, hermaphroditism Autosomal: Down’s syndrome, trisomy D1 and trisomy 18 syndromes. Chromosomes in malignant diseases in man. Molecular Tools for screening and diagnosis of human diseases – Prenatal Diagnosis of Genetic Disorders and Congenital Defects.

Practicals

• Haploid – Anther Culture
• Polyploid :Cytology of polyploid series of Chlorophytum - Allamanda Cytology of allopolyploid – wheat
• Aneuploidy eg. Datura
• Structural aberrations: Deletion, Duplication, Inversion – Eleuthrine bulbosa, Translocation - Rhoeo
• Sex chromosomes in plants
• Human cytogenetics
  • Human chromosome culture technique
  • Normal human karyotype
  • Chromosomal aberrations.

 

BOT-523. Plant Breeding

Unit I. Introduction, objectives, activities of plant breeding and Centers of origin

• Introduction : History of Plant Breeding, the disciplines to be known by a breeder – Botany of the crop, cytogenetics – agronomy – physiology – pathology – entomology – biochemistry – bacteriology – statistics – plant biotechnology.
• Objectives of plant breeding : High yield, improved quality, disease and pest resistance, early maturity, photosensitivity, varieties for new seasons, resistant varieties
• Activities in plant breeding : Creation of new varieties, selection, evaluation, multiplication and distribution
• Centres of origin: Different centres and their significance. Germplasm conservation- in situ seed banks, plant banks, shoot tip banks, cell and organ banks, DNA banks, germplasm evaluation- cataloguing- multiplication and distribution

Unit II. Plant introduction, reproduction, incompatibility, sterility and selection

• Plant introduction: History of plant introduction- primary and secondary, plant introduction agencies. Procedure of plant introduction –quarantine- cataloguing- evaluation – multiplicationdistribution – acclimatization, purpose of plant introduction , achievements, merits and demerits
• Mode of reproduction: Vegetative reproduction – different methods- grafting, layering, apomixis- classification with examples
• Incompatibility : different types – self incompatibilityhomomorphic and heteromorphic incompatibility – gametophytic and sporophytic incompatibility, mechanism of self incompatibility, pollen- stigma interaction, pollen tube -style interaction, pollen tube -ovary interaction –significance of self incompatibility, methods to overcome self incompatibility- bud pollination, surgical methods and off season pollination, high temperature, irradiation
• Sterility : male sterility – genetic male sterility - cytoplasmic male sterility – cytoplasmic genetic male sterility, application in crop improvement

Unit III. Selection, back cross method of selection, hybridization:

• Selection : History of selection, pureline selection , mass selection, pedigree selection, bulk method of selection, merits and demerits, achievements of each type
• Backcross method of selection : Introduction, requirements, applications of back cross methods, genetic consequences of repeated back crossing, procedure of back cross method - transfer of a dominant gene, transfer of a recessive gene, number of plants necessary in backcross generation, selection of the characters being transferred, transfer of quantitative characters, modification of back cross method, production of F2 and F3, use of different recurrent parents, application of back cross method in cross pollinated crops, merits and demerits, achievements
• Hybridization: History , techniques and consequences, objectives , types of hybridization –interspecific, intergeneric, distant hybridization, procedure of hybridization, choice of parents, evaluation of parents, emasculation – different methods, bagging, tagging, pollination , harvesting and storing of the F1 seeds and selfing, consequences of hybridization

Practicals

• Germplasm collection
  • Cereals - Paddy
  • Vegetables - Capsicum
  • Pulses - Green gram, Black gram, Red gram
• II Plant propagation
  • Vegetative
    • Layering:
      
      • Air layering
      • Mound layering
    • Grafting
    • Budding – T – budding (wild rose and Hibiscus)
  • Apomixis
    • Polyembryony – Mango seedlings
    • Vivipary - Alpinia and grass
• Hybridization Emasculation – different types Solitary flower
  • ‘V’ cut method
  • Slit method
  • Round cut method
  • Bagging
• Incompatibility – Pollen viability test In vitro
  
  • Brewbaker’s medium preparation
  • Staining test in acetocarmine
• In vivo – Pollen Germination on stigma ,, through style ,, through ovule

 

BOT-524.   Plant Biochemistry

1. Unit I: Chemistry of Biological Molecules

• Carbohydrates: General composition and properties: solubility, reducing and non-reducing optical isomerism, stereoisomerisms, mutarotation, Classification.
  • Monosaccharides, their structure, occurrence, role, their derivatives by oxidation, reduction and substitution.
  • Oligosaccharides: Disaccharides, tetrasaccharides their structure, occurrence and role in glycosidic bond formation.
  • Polysaccharides: Homo and heterosaccharides, structural and storage polysaccharides – starch, glycogen, cellulose, hemicellulose, pectic substances, chitin, agar, gum tc synthesis and breakdown of glycosidic bonds, Amylase, invertase and phosphorylase action.
  • Synthesis and degradation of Carbohydrates – Starch and Sucrose synthesis, Metabolism of Carbohydrates: Glycolysis, Fermentation, pentose phosphate pathway and gluconeogenesis.
• Aminoacids and Proteins: Classification of Amino acids, structure  of common amino acids, physio-chemical properties of amino acids, Synthesis and breakdown of peptide bonds, oxidation, reductive amination, transamination, deamination and deamination.
  • Proteins: Classification, General accounts, Functions of protein, Classification of protein according to solubility characteristics and chemical nature. Structure – primary, secondary, quarternary structure, Ramachandran plot, Protein sequencing, proteotype enzymes.
  • Nitrogen availability to plants, Nitrogen – compounds in soil – biological nitrogen fixation – non-synthetic and symbiotic nitrogen fixation. Structure of nodule, mechanism of nitrogen  fixation, Regulation of N2 fixation.
• Nucleic acids: Structure and forms: Types of DNA, Types of RNA their structure and functions, The structure of important purine and pyrimidine bases. General account of biosynthesis of purines and pyrimidines.

Unit II: Lipids and lipid like substances

• Lipids: Classification and structure, Functions: Lipids in biological system, fatty acids, essential fatty acids, try-glycerides, fats and oils.
• Lipid metabolism: Synthesis of fatty acids, oxidation of fatty acids a and b oxidation. Chemistry, structure and occurrence and physioliogical role of terpenes, (eg. hemi-mono, sequin, delta and poly-terpenes) alkaloids (eg. pyridine, pyrolidine, quinoline, iso quinoline, indole and purine derivatives) and phenols.
• Secondary Metabolism in plants : A general account of the types of secondary metabolites in plants (eg phenolics, phenolic acids,  alkaloids, steroids, terpenoids etc), Function of secondary metabolites to the producer plant. Importance of study of secondary metabolites.
• Vitamins: Water soluble and lipid soluble structure and role of vitamin A, D2, Tocopherol , thiamin, riboflavin, nicotinic acid, panthothenic acid, folic acid, Ascorbic acid, lipoic acid, PABA.
• Plant hormones: Chemical structure and synthesis of hormones in plants, transport, mode of action and physiological effects of Auxin, Gibberellin, Cytokinins and Ethylene in plants.
• Plant Pigments: Chemistry of photosynthesis and plant product, chemistry, structure and role of chlorophyll, carotenoids and anthocyanin, light absorption and energy transfer, light and dark reaction, Hill reaction O2 evolution, photosynthetic unit and reaction centre. Emerson enhancement effect, photosystems, electron transport system, mechanism of photophosphorylation, quantum requirements of quantum yield, CO2 fixation, Calvin cycle, Hatch and Slack pathway, CAM pathway, Bacterial photosynthesis, photorespiration.

Unit III. Enzymes and their function

• Enzymes: General account: Importance of enzymes in biological sciences, the classification and nomenclature of enzymes with examples, Mechanism of enzyme action role of enzyme in chemical action, various factors affecting the enzyme activity, Properties of enzymes, Competitive and non-competitive enzyme inhibition and types.
• Biochemical oxidation: Substrate of respiration, respiratory quotient, aerobic and anaerobic oxidation and mechanism of ATP synthesis in mitochondria after oxidative phosphorylations.

Practicals

• Quantitative tests for Carbohydrates
  • Molisch’s Test
  • Benedict’s Test
  • Fehling’s Test
  • Seliwanoff’s Test
  • Iodine Test for starch
• Acid hydrolysis of starch
• Qualitative and quantitative tests for proteins
  • Million’s Reaction
  • Xanthoproteic Reaction
  • Ninhydrin Test
  • Biuret Test
  • Precipitation Test
  • Estimation of protein using Lowry’s method.
• Qualitative Test for fats
  • Sudan IV Test
  • Formation of Acrolein from fat
• Qualitative Tests for Biological Compounds
  • Test for biological compounds in plant tissues
  • Tests for the chemical nature of milk.
• Calorimetric estimation of carbohydrates and proteins.
• Enzymes
  • Demonstration of polyphenoloxidase in plant tissue.
  • Action of invertase on sucrose.
  • Effect of temperature on enzyme activity.
  • Action of salivary enzyme on starch.
• Photosynthesis Pigments
  • Separation of the green and yellow pigments.

 

BOT- 531. Genetic Engineering

Unit I. Gene Cloning -Tools and Techniques

• Purification and Separation of Nucleic acids:
  
  • Extraction and Purification of Nucleic acids: Isolation of plasmid DNA, chromosomal DNA and plant cell DNA, total cellular RNA.
  • Separation and Purification of DNA using gel electrophoresis: Agarose, Polyacrylamide, DISC electrophoresis, Analytical and Preparative Gel Electrophoresis.
  • Elution of DNA from gels, Density and Ultra centrifugation.
• Vectors:
  • Plasmids, phages, cosmids, animal viruses such as SV40, Adenoviruses, retroviruses.
  • Special vectors such as shuttle vectors, expression vectors, dominant selectable vectors, amplifiable vectors, integrating vectors, single-stranded plasmid vectors, artificial mini chromosomes, broad host range vectors, P-elements, Retrotransposons.
• Recombinant DNA technology:
  • Cutting and joining DNA: Restriction enzymes, nomenclature, specificity, sticky and blunt ends.
  • Ligation: Enzymes involved and optimization conditions.
  • Modification of restriction fragments: Linkers, Adaptors.
• Gene transfer technology:
  • Introducing genes into prokaryotes: Transformation, transduction, conjugation transposition, cell transformation with plasmids, transfection with phage vectors.
  • Introducing genes into eukaryotes: Recombinant viral technique, DNA mediated gene transfer method, protoplast fusion, microcell fusion technique, metaphase chromosome transfer, liposomes, microinjection technique, electrophoration.
• Identifying the right clone:
  • Direct screening: Insertional inactivation of marker genes, visual screening methods, plaque phenotype.
  • Direct selection: Complementation or suppression of a mutation, selection of recombinant deficient phages, Spiphenotype recombinant efficiency, TK/HAT system, dhfr as a selectable marker, CAT system, Alu markers for human genes.
  • Indirect screening techniques: Immunological techniques,  Hybrid-arrested translation, Hybrid-selected translation, Rescue techniques, nucleic acid hybridization, colony and dotblot hybridization.
  • Probes and Tests: RNA, cDNA DNA, nick-translated probes,  antigen and antibody probes. Hybridisation and blotting techniques, immunological tests such as precipitin test, immuno-diffusion technique, immuno-electrophoretic technique, radioimmunoassay, enzyme linked immunoabsorbent assay, immuno-affinity chromatography.
• DNA Engineering techniques and applications:
  
  • Isolation of important crop genes: Plasmid and marker rescue techniques, transposon tagging.
  • Genomic and cDNA libraries.
  • Site directed mutagenesis: oligonucleotide directed, insertional mutagenesis, directed single base mutations.
  • Mapping of DNA: restriction mapping, DNA foot-printing, chromosome walking and jumping, DNA fingerprinting, RAPD, RFLP, AFLP, SSR, ISSR
  • DNA sequencing: Maxam-Gilbert method, Sanger-Caulson method, Messey’s shot gun method, DNA sequencer.
  • Applications: Agriculture, Biotechnology, Protein engineering, clinical, Environmental pollution, biosensors and biochips.

Unit II. Genetically modified organisms

• Methods of gene transfer to plants:
  • Protoplast fusion, organelle engineering. Recombinant vector techniques: Non-integrative DNA transfer- Caulimoviruses, Geminiviruses, plant RNA viruses, Cornybacterial plasmids. Integrative DNA transfer- Agrobacterium Ti and Ri plasmids, Agroinfection, homologous DNA and transposons as vector. Genetic transformation of Monocotyledonous plants: Factors and problems involved.
  • Procedure and protocols of producing transgenic plants., first  commercial transgenic plants- transgenic tomatoes, control of ripening by antisense technology, insect resistance (Bt. protein), golden rice, herbicide resistance, commercializing insect resistant cotton, next generation commercial transgenic plants, designer oils and biodiesel, plant secondary products, designer flowers, plants as bioreactors, vaccines, plantibodies, and bioplastics. Using molecular biology to probe plant physiological processes- prospects of engineering RUBISCO and nitrogen fixation. Production of male sterile lines.
• Gene transfer to animals:
  • Methods-DNA microinjection, stem cell mediated gene transfer, retroviral-mediated gene transfer .
  • Applications in medical research to identify the functions of specific factors in complex homeostatic systems through over- or under-expression of a modified gene (the inserted transgene); in toxicology: as responsive test animals (detection of toxicants); in mammalian developmental genetics; in molecular biology, the analysis of the regulation of gene expression makes use of the evaluation of a specific genetic change at the level of the whole animal; in the pharmaceutical industry, targeted production of pharmaceutical proteins, drug production and product efficacy testing; in biotechnology: as producers of specific proteins; genetically engineered hormones to increase milk yield, meat production; genetic engineering of livestock and in aquaculture affecting modification of animal physiology and/or anatomy; cloning procedures to reproduce specific blood lines; and developing animals specially created for use in xenografting.
  • Animal welfare and ethics.
• Transgenic microbes:
  • Genetic manipulation of microorganisms: Natural genetic engineering-forced evolution and adaptive mutations; specific environmental stresses used to force microorganism to mutate and adapt creating microorganism with new biological capabilities. Preservation of microorganisms-strain stability methods that provide this stability are lyophilization (freeze-drying) and storage in liquid nitrogen. Site- directed mutagenesis, Protoplast fusion, Transfer of genetic information between different organisms, Modification of gene expression.
  • Major Products of Industrial Microbiology: Antibiotics, Amino  acids, Organic acids, Specialty compounds for use in medicine and health-include sex hormones, ionophores, and compounds that influence bacteria, fungi, amoebae, insects, and plants, Biopolymers-microbially produced polymers, Biosurfactants, Bioconversion processes-microbial transformations or biotransformations, biodegradation,  bioremediation, bioleaching. Biotechnological Applications: Biosensors, Microarrays, Biopesticides.
  • Impacts of Microbial Biotechnology

Unit III. Hazards and Impact of GMOs.

•  Biosafety Considerations: Biological risks, ethical issues, economic issues, legal issues.

Practicals

• Raising pure cultures of specific strains of bacteria by plate streaking method.
• Plasmid DNA isolation using the alkaline lysis method
• Genomic DNA isolation from plant tissues by CTAB method.
• Electrophoresis: Separation of DNA and proteins.
• Demonstration of Plant transformation techniques, DNA quantification and Southern blotting
• Problems related to above topics.

 

BOT. 532 Plant Biotechnology

Unit I. Plant Tissue Culture Techniques

• Historical aspects and significance: Plant cell and tissue culture-Introduction, history, and scope. Development of organ, tissue and cell culture, exploitation of totipotency.
• Laboratory requirements for plant tissue culture: Designing of plant tissue culture laboratory. Lab maintenance and fumigation.
• Basic aspects of plant tissue culture: Sterilization techniques, different culture media components, growth regulators, undefined supplements, surface sterilization of explants, inoculation, subculturing etc.
• Types of Cultures: Cyto differentiation, organogenic differentiation, callus culture, callus mediated organogenisis, cell suspension culture- different types, measurements of growth pattern of cells in suspension, culture methods of single cells, testing viability of cells. Application of cell suspension and callus culture with special reference to medicinal and aromatic plants
• In vitro Techniques for Micropropagation: Axillary bud proliferation approach, meristem and shoot tip culture. Production of virus free plants, phases of micropropagation, Micropropagation of tree species, medicinal and aromatic plants. Organogenesis via callus formation.

Unit II. Plant Tissue Culture - Applications

• Somaclonal variation: Somoclonal and gametoclonal variations and importance. Technique for detection and isolation of somaclonal variants. Factors controlling somoclonal variation and its application in plant breeding.
• Cell Suspension Culture: Types of suspension culture Batch culture, Continuous culture, Open continuous, Closed continuous, Semi continuous, Growth measurements, Techniques for single cell culture Production of Secondary metabolites, Secondary products found in plants, Method of production – factors affecting yield. Immobilized cell systems, Bioreactors. Secondary metabolites detected in plant tissue culture. Root and hairy root culture. Methods of enhancement of secondary metabolite production in culture. Problem associated with secondary metabolite production.
• Somatic Embryogenesis: Principle and concept, Ontogeny and development of somatic embryos. Factors affecting embryo formation. Application of somatic embryogenesis.
• Artificial- Synthetic Seeds: Introduction to synseed, Production of  synthetic seed encapsulation, Steps of commercial artificial seed production, Artificial seed propagation, Application.
• In vitro Production of Haploids: In vitro production of haploids and uses of haploids, Androgenic methods, anther culture, microspore (pollen) culture, factors governing the success of androgenesis, Genotype, Physiological status of the donor plants, Stages of pollen, Pretreatment of anthers, Culture media, Process of androgenesis. The ploidy level and chromosome doubling, Diplodisation, Uses of haploids in plant breeding, Gynogenic  haploids, Factors affecting gynogenesis. Embryo rescue techniques, Ovary, ovule, endosperm and embryo culture In vitro pollination and test tube fertilization, methodology, factors affecting seed set application. Green pod culture of orchids. Application.

Unit III. Protoplast Isolation and Culture

• Protoplast Isolation: Isolation- different methods-Mechanical  method, Enzymatic method, Production of protoplasts, osmoticum, Protoplast viability and density, Protoplast purification,
• Culture of Protoplast: Culture techniques, Culture medium and environmental factors, Protoplast culture, cell wall formation, Growth, division and regeneration of plants, Protoplast fusion, somatic hybridization, different types, fusion methods, Spontaneous fusion, Induced fusion, Different types of Fusagen, Mechanism of fusion, Identification and selection of hybrid cells, Verification and characterization of somatic hybrids, Chromosome status of fused protoplasts, Cybrids, achievements and limitations, Significance of protoplast culture and somatic hybridization, Somatic hybridization for crop improvement, Problems and limitations of somatic hybridization, Genetic modification of protoplasts, Direct genetic transformation of DNA into protoplasts, Particle bombardment, transformation of protoplast by electroporation, microinjection and microprojectiles.
• Secondary metabolites: Secondary products found in plants, method of production – factors affecting yield. Bioreactors. Secondary metabolites detected in plant tissue culture. Root and hairy root culture, Methods of enhancement of secondary metabolite production in culture, Problem associated with secondary metabolite production.

Unit IV Transgenic Plants

• Transgenic plants for crop improvement (dicots and monocots), Insect resistance, insecticide, Resistance to virus, Resistance to other diseases, Recombinant DNA techniques for the production of transgenic plants, Procedure and protocols of producing transgenic plants. Transgenics for quality, Transgenics for improved storage, Transgenics for male sterility, Transgenics for flower color and shape, Transgenics for terminator seed, Transgenics plants as bioreactors, Transgenics plants to study  regulated gene expression, Commercial transgenics crops,
• Uses and applications of transgenic plants, new products, pharmaceuticals. Bioremediation, edible vaccines, antiviral proteins

Unit V. Germplasm Storage and Cryopreservation

• Conservation of germplasm, In vitro strategies, Short, medium and long term (cryopreservation) preservation application, Techniques of cryopreservation, Determination of survival and viability, Plant growth and regeneration, Application of cryopreservation.

Practicals

• Preparation of culture media (MS)
• Stock solution preparation
• Sterilization of culture media
• Techniques of isolation, surface sterilization and inoculation of different explants.
• Direct and indirect organogenesis (Medicinal plant)
• Preparation of artificial seeds
• Green pod (embryo culture) culture of orchid (Spathoglotis plicata).
• Protoplast isolation by enzymatic method
• Submit a record on the above work done.

 

BOT- 533. Environmental Genetics

Unit I. Environmental factors affecting genes and their expression

• Heritable changes: Spontaneous and induced mutations Luria Delbruck fluctuation Test, Somatic mutation and germinal mutation, genetic mosaics.
• Environmental Mutagens:
  • Physical- Corpuscular radiations-Alpha particles, Beta particles, and Neutrons.
  • Electromagnetic radiations - Gamma rays, X rays and ultra violet radiations, Interaction of radiations with matterionization and excitation, Photoelectric effect, Compton effect, Pair production, Properties of radio nucleotides, Radiation units.
  • Chemical- Alkylating agents, Base analogues, Acridines, deaminating agents and miscellaneous.
  • Environmental impact on genetic organization of organisms.
• Chromosomal mutations:
  •  Variation in chromosome number -Monosomy, Cri-du-Chat syndrome, Trisomy, Down syndrome, Patau Syndrome, Edward syndrome.
  • Chromosome structure mutations- Deletion, Duplication- Bar eye in Dropsophila, Inversion-Consequences of inversions, Translocation- Familial Down syndrome, Fragile sites in Humans

Unit II Molecular basis of mutations

• Molecular Mutations : Tautomeric shifts, transitions and trasversions, back mutations, suppression mutations, Silent mutations, Neutral mutation, Missense mutations, Nonsense mutations and Frame shift mutations
• Mutation detection systems: Specific locus test, Ames test, CIB method, Muller-5 method, Attached X-Chromosomes, mutation detection in humans, mutation frequency, SuperMutagens
• DNA repair mechanisms: Photoreactivation, Excision repair, Post replication recombination, Mismatch repair, SOS repair.

Unit 3. Human mutations

• Understanding of mutations in Humans, ABO blood types, Muscular Dystrophy, Fragile X syndrome, Huntigton's disease, Xeroderma pigmentosum, Site-directed Mutagenesis, Knock out mutations and transgenes, Transposable genetic elements in maize, in Drosophila and in humans.

Practicals:

• Problems related to radiation dose and mutation frequency.
• Problems related to chromosome variations in number and structure.
• Problems related to variation in genetic code and protein synthesis
• Problems related with point mutations and frame shift mutations
• Problems with mutation detection systems in plants, Drosophila and humans.
• Problems related with DNA repair mechanisms.
• Problems with mutations in humans
•  Chromosomal aberrations due to the effects of mutagens eg. EMS, 2,4-D or acridine orange in Allium cepa or Vicia faba

 

BOT- 534. Modern Methods in Crop Breeding

Unit I. Heterosis and Inbreeding, Hybrids and synthetic varieties:

• Heterosis and Inbreeding: Definitions. Inbreeding depression –effect of inbreeding – degree of inbreeding depression –homozygous and heterozygous balance. Heterosis and luxuriance –manifestation of heterosis. Genetic basis – dominance hypothesisoverdominance hypothesis – similarities and differences. Physiological basis of heterosis- mitochondrial complementation –fixation of heterosis. Recurrent selection- types- simple- recurrent selection for general combining ability – for specific combining ability – reciprocal recurrent selection.
• Hybrids and synthetic varieties: Prcocedure – development of inbreds – evaluation of inbreds – phenotypic and top cross test, single cross evaluation, production of hybrid seeds- double cross and polycross hybrids. Role of cytoplasmic genetic male sterility and self incompatibility in hybrid seed production. Improvement of inbred lines- pedigree selection- backcross method – convergent improvement – gametic selection – merits and demerits – achievements

Unit II. Mutation Breeding and Ployploidy Breeding:

• Mutation Breeding: Introduction – spontaneous and induced mutation- mutation effects- molecular basis- base substitutionaddition and deletion. Mutagens- physical – chemical and radiation dose effects of non ionizing radiation on biological targets. Factors affecting radiation effects- biological,  environmental – water content, temperature, chemical factors, mechanism of action of radiations, mechanism of action of chemical mutagens, procedure of mutation breeding, recurrent irradiation, gamma garden, directed mutagenesis, application of mutation breeding, limitations and achievements.
• Polyploidy breeding: Definitions, types of changes in chromosome number – euploids and aneuploids – auto and allopolyploids. Aneuploids- nullisomics, monosomics, double monosomics and trisomics. Autopolyploids, autotriploids, autotetraploids, autohexaploids and autooctoploids. Allopolyploids, allotetraploids, allohexaploids, allooctoploids, morphological and cytological features. Production of autopolyploids: materials and agents usedmethod of treatment-merits and demerits-achievements

Unit III. Distant hybridization, quality breeding, Ideotype breeding,

Resistance Breeding, Breeding for stress resistance:

• Distant hybridization: History, barriers in production of distant hybrids-failure of zygote formation-failure of zygote developmentlethal genes-phenotypic disharmony between two parental genomes- chromosome elimination- incompatible cytoplasmendosperm abortion-failure of hybrid seedling development. Techniques of production of distant hybrids- sterility in distant hybrids- cytogenetic basis- genetic basis and cytoplasmic basisapplication of distant hybridization in crop improvement- alien chromosome addition and substitution lines–transfer of small chromosome segment–achievements and limitations
• Quality breeding: Introduction. Quality traits – morphologicalnutritional – geological –hulling and milling recovery- cooking quality- nutritional quality of rice, wheat, fiber colour, length and strength in cotton, elimination of toxic substances-lathyrismprotein and mineral content and quality. Laboratory evaluation for protein quality and quantity, problems and prospects of quality breeding.
• Ideotype breeding: Ideotype concepts, types, development of ideotypes, steps in development. Characters of a crop ideotype, selected crops’ ideotype; Barley, Rice, Cotton, Brassica – ideotype breeding- limitations
• Resistance breeding: Historical account, loss due to disease, variability in pathogen. Physiological races and pathotypes. Genetics of pathogenicity- disease development-disease escapedisease resistance, susceptible reaction- immune reaction, resistance-tolerance. Vertical and Horizontal  resistance- Mechanism of disease resistance–mechanical, hypersensitivity and nutritional. Genetics of disease resistance – oligogenic inheritance, gene for gene relationship–molecular basis for gene for gene relationship – polygenic inheritance.
• Methods of breeding for disease resistance: Testing for disease resistance – Disease epidemics, Insect resistance, mechanism of resistance, breeding methods, screening techniques, problems in insect , resistance breeding.
• Breeding for stress resistance:
  • Drought resistance; introduction – types of abiotic stresses – minimizing drought resistance – breeding methods – Genetics of drought resistance –Problems.
  • Mineral stresses: Salt affected soil- alkali soil, breeding for salinity resistance – effect of salinity stress, water stress, salt toxicity – salinity resistance, sources of salinity resistance breeding approach- Problems

Unit IV. Breeding of Crop plants:

Origin, taxonomy, cytogenetics and evolution of the following crops

• Cereals -Rice, Wheat, Maize
• Tuber Crops -Tapioca, Potato
• Fibre yielding -Cotton, Jute
• Plantation Crops -Rubber
• Sugar yielding -Sugar cane
• Narcotics -Nicotiana
• Vegetables -Allium, Tomato
• Oil yielding -Brassica, Arachis
• Pulses -Vigna
• Beverages -Coffee, Tea

Practicals

1. Heterosis Breeding

• Pepper Uthirankotta X Cheriakaniakkaden Panniyur
• Maize cob
• Sorghum

2. Mutation breeding

• Capsicum seed treated with chemicals. Drawings of control & treated seedlings showing morphological variations
• Figures of mutants – sunflower, tapioca

3. Polyploidy breeding

• Autopolyploids- colchicines treatment –i.Capsicum seed and seedling
• Polyploids – Evolutionary chart of the following;
  • Wheat – Triticum aestivum and Triticale
  • Cotton, Nicotiana, Brassica

4. Ideotype: - Super rice 2000

5. Resistance Breeding

6. Crops: Description on taxonomy, cytogenetics & evolution of all the  above mentioned crops.

 

BOT- 542. Developmental Genetics

Unit I. Cell differentiation and growth

• Cell Differentiation and Development: General characteristics of cell differentiation, effects of mutations in developmental processes, antennapaedia complex, the bithorax complex, segmental genes, Gap genes and pair rule genes in Drosophila, Effects of nuclear and cytoplasmic factors in development, environmental effects, maternal effects, nuclear cytoplasmic interactions with particular reference to Acetabularia
• Genes in development: Gene expression and regulation, chromatin and DNA methylation, signal transduction in development, the cell division cycle, cytoskeleton, cell adhesion and the extra-cellular matrix.
• Molecular mechanism of cell differentiation: Control at the level of transcription, translational control, amplification, gene  rearrangements.
• Growth and Development in Plants: Patterns of growth and differentiation; Gene expression and mutations regulating meristem function, embryogenesis, seedling, root, leaf and flower development. Homeotic genes, ABCD model in Arabidopsis flower, hormonal control of plant tissue development, effect of auxins on root and root formation, gibberellin promoted growth of plants, ethylene and triple response mutants, brassinosteroids and photomorphogenesis.

Unit II Developmental mechanisms

• Special cases of differentiation: Sex as a developmental phenotype,  factors influencing sex differentiations - environmental effects, hormonal effects, effects of ploidy, sex determination – monoecious and dioecious plants
• Biological Rhythms: Circadian rhythms, rhythm responses to  environment, clock mechanism.
• Photoperiodism : General principles , florigen concept.
• Photomorphogenesis: Phytochrome genes and their expression, control of photo-morphogenic responses. Dose-response relations in photo-morphogenesis, light induced chloroplast differentiation, effect of photoreceptors.
• Ageing : Cellular and molecular changes in ageing, mechanism of senescence, extra cellular ageing. Theories of ageing -theories involving induced damage, genetically programmed ageing and cell death, evidence from tissue culture. Difference between necrosis and apoptosis. Processes, pathways and proteins involved in apoptosis regulation. Factors and signals inducing cell death. Cell-types affected.

Unit III. Regulation of Cancer

• Tumourigenesis in plants: Characteristics of CGT cells, crown gall and plant transformation, Interaction between wound cell and bacteria, plasmids as tumour inducing principle.
• Carcinogenesis: Characteristics of cancer cells, cytological changes, Theories of carcinogenesis - Chromosomal somatic mutation, environmental carcinogenesis.
• Viruses that cause cell transformation: DNA tumour virus - papova virus, adenoviruses, RNA tumour virus, oncogenic retrovirus
• Oncogenes and cancer: Molecular basis, cell division signals and oncogenes, activation carcinogens - Chemical carcinogens, radiation as carcinogens tumour suppressor genes, teratomas, teratocarcinomas, teratogenesis.

Practicals

• Study of various developmental stages and polytene chromosomes of Drosophila
• Preparation of sex chromatin from cheek cells
• Angiosperm embryo development using bean seeds
• Early plant development – Pollen tube formation
• Study of plant tumours – galls, club root of cabbage
• Study of human cancers (blood cancer, breast cancer, uterine cervix cancer etc.) using permanent slides
• Problems

 

BOT- 541. Population Genetics

Unit I. Genetic Composition and Mendelian Population

• History: Gene frequencies and Genotype frequencies, Gene pool.
• Systems of Mating:
  • Random mating and Hardy-Weinberg Principle, Application of  Hardy-Weinberg principles-Test for Random mating, Test for sex-linked trait, Test for carrier gene frequency, Test for mode of inheritance, Test for multiple gene.
  • Non – random mating-Positive non-random mating-Negative non random mating.

Unit II. Factors affecting gene frequencies in natural populations

• Factors affecting random mating-Migration-Mutation and Selection, Mutation and Selection- balance, Selection against dominant genotype, Selection against recessive genotype, Selection for heterozygote .
• Random drift, Genetic Load, Founder effect.

Unit III Consanguinity in natural populations

• Inbreeding/Consangunity: Definition-Inbreeding co-efficient, degrees of inbreeding, Types of inbreeding, Harmful effects of inbreeding, Genetic effects of Inbreeding.

Practicals 25 problems pertaining to the above chapters.

 

BOT. 543 Biosystematics

Unit I. Historical background, Herbarium Taxonomic relations:

• Historical background: Rise of experimentally based taxonomy, Review of biosystematics, The challenge of new approaches to systematic.
• Herbarium: History and development of a herbarium, Functions of herbarium, different kinds of herbarium, important herbarium of the world. Method for preparing a herbarium.
• Morphology in relation to taxonomy.
  • External morphology: Vegetative features, reproductive features
  • Micrscopic morphology (epidermal characters) or ultrastructural systematics: Trichomes, epidermal cells, seed surface pattern, pollen wall  ornamentation, stomata, types of stomata
• Anatomy in relation to taxonomy: Taxonomic applications of anatomical features. Vegetative and floral anatomy, Floral anatomy in relation to taxonomy and phylogeny Eg, Apocyanaceae, Caesalpiniaceae , Papilonaceae, Saxifragaceae, Ranunculaceae, Leaf anatomy in relation to taxonomy Eg. Myrtales
• Embryology in relation to taxonomy: Basic embryological characters of taxonomic significance. Embryological characters, Taxonomic applications of embryological features. Eg. Scytopetalaceae, Loranthaceae. Cyperaceae. Trapa. Paeonia.
• Cytology in relation to taxonomy: Chromosome techniques, Chromosome banding as a tool in taxonomy, Chromosome number and size, Chromosome morphology- Chromosome morphology and relative size, Heterochromatin. Chromosome behaviour at meiosis. The genome, Natural karyotype. Genomic characters and classification. The importance of genomic characters for biosystematics. The taxonomic value of cytological data: General, Family level and above Generic level, Specific level and below in angiosperm families - Zingiberales, Liliaceae, Malvaceae. Cucurbitaceae, Araceae, Rubiaceae, Araliaceae Polyploidy and taxonomy ; Frequency of polyploidy, Types of polyploidy, Auto and allopolyploidy, Cryptic structural polyploidy, Segmental allopolyploidy and other situations.

Unit II Phytochemistry, plant reproductive strategies:

• Phytochemistry in relation to taxonomy: Chemotaxonomy- Origin and nature of chemotaxonomy. Compounds useful in plant taxonomy. Value of chemotaxonomy . Secondary metabolites, Distribution and description of directly visible chemical substances, chemical test characters, Plant products, Alkaloids. Flavonoid profiles as biosystematical aids. Chemical identification of plant cultivars. Chemistry of plant hybrids. Chemistry in taxonomic revisions. Eg. Brassica Leguminosae, Papaveraceae, Fumariaceae, Centrospermae.
• Numerical taxonomy: Principles and status of numerical taxonomy, Historical account of the  development of numerical taxonomy, Aims and objectives and nomenclature. Merits and demerits of numerical taxonomy. Applications of numerical taxonomy . Eg. Polemonium pulcherrimum and Chenopodiaceae.
• Plant reproductive strategies: Apomixis and biosystematics , Modes of  asexual reproduction, origin and fixation of apomixis. The evolutionary prospects of apomixis Eg. Potentilla tabernaemontana and Curculinoideae. Breeding systems and pollination mechanisms in plants and their use in biosystematics .
• Palynology in relation to taxonomy: Pollen morphological characters, Pollen morphoforms, Exine sculpturing, Pollen size and shape, Evolution of pollen morphological characters, Role of palynology in rrlation to taxonomy. Eg. Acanthaceae, Rubiaceae, Scrophulariaceae, Rutaceae , Malvaceae.

Unit III. Molecular systematics, serology, cytogeography in relation to taxonomy:

• Molecular systematics : Molecules and genomes in plant systematics- Techniques used in molecular taxonomy, Chloroplast DNA and the study of plant phylogeny,- present status and future prospects, Use of chloroplast DNA rearrangements in reconstructing plant phylogeny, Mitochondrial  DNA in plant systematics, Applications and limitations, Ribosomal RNA as a phylogenetic tool in plant systematics. Eg. Saxifragaceae, Asteraceae, Onagraceae, Brassica, Nymphales. Molecular approaches to plant evolution, Intraspecific cp DNA variation in systematic and phylogenetic implications. Molecular evidence and plant introgression, molecular data and polyploid evolution in plants. Molecular systematics and crop evolution.
• Serology in relation to taxonomy: Brief history of sero-taxonomy. Methods used in sero-taxonomy. Role of serology in taxonomy.
• Cytogeography and biosystematics: Cytogeography and structure of a group of related taxa Eg. Ranunculus plantagieus, Polycarpon polycarpoides, Erysimum grandiflorum. Cytogeography and historical botanical geography, The occurrence of other biosystematic methods on cytogeography.

 

Elective Courses

501 – Biophysics

Unit I. Bioenergetics, Tools and Technique in Biology:

• Bioenergetics: Concepts of Entropy, free energy, enthalpy, redox potential. Tools and Technique in Biology:
  • Microscopy: Principles and applications of light, phase contrast fluorescence, Polarizing, Scanning and transmission electron microscopy: cytophotometry and flow cytometry, video-micrometry, camera lucida and photomicrography.
• Centrifuges: Basic principles of sedimentation – Types of centrifuges and their uses – Preparative and Analytical centrifuge – Sedimentation equilibrium method, Sedimentation velocity meth od – Density Gradient Centrifugation – Isokinetic and isopycinic centrifugation – Differential centrifugation.
• Chromatography: General principles – Adsorption and Partition Chromatography – Thin layer chromatography, paper chromatography, Gasliquid chromatography (GLC), High performance liquid chromatography (HPLC), Ion-Exchange Chromatography and Affinity Chromatography.
• Electrophoresis: General principles – apparatus, methods and applications – Moving boundary, electrophoresis and zone electrophoresis – Paper electrophoresis thin layer column chromatography – starch gel, agarose gel and polyacrylamide gel electrophoresis – SDS, Non-SDS, DIS electrophoresis Isoelectric focusing, Istotachophoresis and immuno electrophoresis. Separation of nucleic southern blotting – DNA sequencer, DNA synthesizer.

Unit II. Spectroscopic techniques, X-ray diffraction Autoradiography:

• Spectroscopic techniques: General principles, Types of spectra and their biochemical usefulness, visible and UV spectrophotometry, Infra-red (IR) Circular Dichroism (CD), NMR, ESR and mass spectroscopy, Spectrofluorimetry, Luminometry, Atomic/Flame spectrophotometry, Atomic absorption and plasma emission spectroscopy.
• X-ray diffraction – Principles and Application: Radiation Biophysics: Types of radiation, interaction between radiation and matter – dosimetry,- radiation detectors.
• Autoradiography – Light microscope auto radiography – fibre auto radiography, High resolution auto radiography.

Practicals

• Different parts of microscope.
• Separation of compounds using Paper and Thin layer Chromatography
• Electrophoresis: Separation of protein using PAGE, immuno electrophoresis.
• Centrifuge: Separation of compound/materials using desktop and High speed centrifuge
• Spectrophotometry: Quantification of biological compounds using spectrophotometric method.
• Micrometry: Determination of pollen diameter, stomatal length and breadth using micrometry.
• Working of equipments like pH meter PCR machine etc.

 

BOT 505. Applied Palynology

Unit I. Area of study, Applied Palynology

• Area of study : Based on pollen or spore morphology, Basic Palynology (pollen, spore morphology, pollen ecology) and Applied palynology
• Applied Palynology: Melittopalynology, aeropalynology, palaeopalynology, iatropalynology, pharmacopalynology, copropalynology and forensic palynology.

Unit II. Basic palynology, palynological features

• Pollen –Spore morphology (Basic palynology):
  • Origin of exine, pollen wall structure and development, prime exine, sporopollenin (nature and composition), role of tapetum in pollen wall formation.
  • Pollen units: Monad, dyad, tetrad, polyad, pollinia, massula.
  • Polarity: Apolar, isopolar, hetropolar.
  • Shape: Pollen shape (tertiary): Radio symmetrical, bilateral, shape index in radio symmetrical grains (P/E X100). Shape types- oblate, suboblate, oblate-spheriod, spherical, prolatespheriodal, subprolate, prolate, perprolate.
  • Symmetry: Symmetric, Asymmetric.
  • Size: Based on Walker and Doyle (1975).
• Palynological features:
  • Aperture (primary): NPC System.
  • Exine surface ornamentation (secondary): projection typesspinate, spinulate, verrucate, gemmate, bacculate, tuberculate. Depression types- reticulate, lophate, fossulate, scrobiculate, punctate, pilate, psilate.
  • Exine strata: intine, exine with endo exine (base layer), mid exine (columella layer) and extoexine (the tectum, tegillum and supra tegillum).

 

BOT. 51A. Plant Tissue Culture

Unit I. Introduction

• History of plant tissue culture and cell culture

Unit II. Basic techniques& principles

• General laboratory facilities and requirements
• Media composition and preparation, sterilization techniques.
• Different types of media (MS, B5, White, SH, WPM, VW, Wimber etc)

Unit III. Growth and differentiation

• Callus culture- characteristic features, cytodifferentiation,  significance
• Suspension culture-different types, growth patterns, significance
• Organogenesis, chemical and physical factors, pathway of development
• Embryogenesis. Chemical and physical factors, pathway of development, Artificial seeds

Unit IV. Application of culture technologies to plant improvement

• Micropropagation protocol and application
• Anther culture protocol and application
• Protoplast culture and somatic hybridization protocols and application
• Cryopreservation –procedure and applications.
• Somoclonal variation-causes, merits and demerits.

 

BOT. 507 Transgenic Plants

Unit I. Basic concept of genetic engineering

• Genetic transformation of plants, Transgenic techniques, Steps for developing new crop verities

Unit II. Gene transfer methods

• Bacteri ne transfer in plants, Vector mediated gene transfer Creating recombinant DNA.

Unit III. Agrobacterium mediated gene transfer

• Tumor i nciple and the Ti plasmid, Agrobacterium mediated virus infection- agro infection.

Unit IV. Vectorless or direct DNA transfer

• Physical gene transfer methods, ElectroporationParticle bombardment/ microprojectile/ biolistic, Macroinjection, Microinjection

Unit V. Chemical gene transfer methods

Unit VI. Transgenic in crop improvement

• Resistance to biotic stresses, Insect resistance, Virus resistance, Disease resistance, Resistance to abiotic stresses, Transgenic for quality

UnitVII. Ethics of transgenic plants

 

BOT. 508 Biotechnology

Unit I. Somatic embryogenesis

• Ontogeny and development of somatic embryos. Factors affecting embryo formation application.

Unit II. Artificial- synthetic seeds

• Protocol and its significance.

Unit III. In vitro production of haploids

• In vitro production of haploids and uses of haploids, Androgenic methods, anther culture, microspore (pollen) culture, factors governing the success of androgenesis, uses of haploids in plant breeding, Gynogenic haploids, factors affecting gynogenesis.  Embryo rescue techniques, ovary, ovule, endosperm and embryo culture In vitro pollination and test tube fertilization, methodology, factors affecting seed set application. Green pod culture of orchids. Application.

Unit IV. Protoplast culture

• Protoplast isolation, different methods, production of protoplasts, protoplast culture, regeneration of plants, protoplast fusion, somatic hybridization, different types, fusion methods, identification and selection of hybrid cells. Cybrids, achievements and limitations. Significance of protoplast culture and somatic hybridization. Somatic hybridization for crop improvement.

Unit V. Secondary metabolites

• Secondary products found in plants, method of production – factors affecting yield. Bioreactors. Secondary metabolites detected in plant tissue culture. Root and hairy root culture. Methods of enhancement of secondary metabolite production in culture. Problem associated with secondary metabolite production .

Unit VI. Germplasm storage and cryopreservation

• Conservation of germplasm in vitro strategiesShort, medium and long term (cryopreservation) preservation application.

Unit VII. Transgenic plants

• Transgenic plants for crop improvement, Procedure and protocols of producing transgenic plants, Transgenic plants for molecular farming

Practical

• Preparation of culture media (MS)
• Stock solution preparation
• Sterilization of culture media
• Techniques of isolation, surface sterilization and inoculation of different explants.
• Direct and indirect organogesis (Medicinal plant)
• Preparation of artificial seeds
• Green pod(embryo culture) of orchid (Spathoglotis plicata).
• Protoplast isolation by enzymatic method
• Submit a record on the above work done.

 

BOT- 53A Phytochemicals

Unit I. Introduction:

• Major classes of plant chemicals-terpenoids, alkaloids and other nitrogen containing metabolites, phenolic compounds.

Unit II. Phytochemical databases:

• DR. Duke’s Phytochemical and ethnobotanical databases, NAPRALERT, MEDFLOR, USDA Phytochemical and ethnobotanical databases.

Unit III. Phytochemicals as nutraceuticals:

• With secial reference to vegetables and fruits from lant families such as Lilieaceae, CRUCIFERAE, solanaceae, Umbelliferae, Compositae and Rutaceae.

Unit IV. Phytochemicals in cosmetics:

• Brief description of properties and constituents of plants and plant arts used as Cosmetics and in Aromatherapy.

Unit V. Phytochemicals in disease prevention:

• Utility in treatment of cancer, diabetes, cardiovascular diseases. Mode of action-antioxidants, hormonal action, stimulation of enzymes, interference with DNA replication, antibacterial and antifungal effects, blocking and suppressing agents, phytoestrogens, isoflavanoids and lignans. Toxins such as glycoalkaloids, fucocoumarins, miscellaneous toxicants. Drug discovery and development.

Unit VI. Methods of isolation and analysis:

• Extraction techniques. Separation and Purification techniques-chromatography TLC, HPLC and GC. Detection techniques-UV-Vis spectroscopy, Infrared spectroscopy (IR) and Mass spectroscopy (MS), NMR spectroscopy.

Unit VII. Biotechnology and Phytochemical production:

• Engineering the plant metabolism. Methods of expression of foreign proteins in plants, production of pharmaceuticals and industrial enzymes, expression of whole proteins and pharmaceutically active peptides. Isolation and purification from plants.

 

BOT. 52A. Plant Cell Culture Technology

Unit I. Introduction: Plant metabolites and their importance

• Cell culture techniques: suspension culture- bioreactors, cell line selection, in vitro mutagensis, protoplast hybridization: consequences and applications.

Unit II. Secondary metabolite classes & groups

• Alkaloids- morphines, codeine, quinine, nicotine, cocaine, hyoscyamine,
• lysergic acid, taxol
• Terpenoids: Menthol, camphor, caroteniod, pigments
• Polyterpenes: rubber
• Phenyl propanoids: Anthocyanin, coumarins, favanoids, isoflavniods,
• stilbenes, tannins
• Quinones: Anthraquinones, benzoquinones, naphthoquinones
• Steroids: Diosegnin, sterols, ferruginol
• Exploitation of secondary metabolites in culture. Role of cell line selection, in vitro mutagenesis for exploitation. Biochemicals from cultured plant cells, productivity enhancement- optimization of medium and culture conditions, development of high yielding cell lines, elicitors, use of organ culture and two-phase system.

Unit III. Large scale exploitation of secondary metabolites

• Hairy root culture- advantages, commercial production of shikokonin, berberine, diosegnin, taxol, vincristine, vinblastine, scopolamine, ajmaline Biotransformation, Metabolic engineering - advantages and limitations.