Ph. D. Programme


Course Work for Ph.D. Students
National Institute of Plant Genome Research

Course Co-ordinator: Dr. Praveen Verma
Course Material Credits
Molecular Cell Biology and Genetics 3
Genomics 3
Plant Biology 3
Emerging Trends in Plant Sciences 1
Research Methodology 4
Seminar 1
Total 15
Molecular Cell Biology and Genetics
Total Credit : 3
Total Number of Lectures : 48
Course In-charge: Dr. Manoj Majee & Dr. Naveen Chandra Bisht
Fundamental knowledge of General Biology and Genetics is the basis of unraveling nature’s secret hidden in biological system. The students are expected to refresh their knowledge on cellular biology, molecular biology and genetics through this course. Emphasis will be given to explain the topics giving relevant examples that might help Ph.D. students in designing their experiments and interpretation of their observations.
1. Cellular Biology (16 lectures)
  1. Constituents of Plant Cells: Extracellular matrix, Cytoskeleton, and Organelles.
  2. Cell Cycle and Regulation: Phases of cell cycle, Restriction and check point, Cell division and cell growth, Cell cycle progression.
  3. Enzyme: Nomenclature, Classification, Kinetics, Mechanism and regulation.
  4. Protein Turnover: Biosynthesis and degradation of proteins.
2. Molecular Biology (12 lectures)
  1. Genetic Material: Genome organization, DNA replication and recombination, Source of genetic variation (natural and induced).
  2. Gene Expression: Transcription, Cis-acting elements and transcription factors, RNA editing and processing.
  3. Protein Targeting and Trafficking: Protein trafficking (classical and non-classical pathways), ER and Golgi dynamics, Protein sorting and trafficking, Dynamics of membrane-bound protein, Mechanism of protein secretion.
3. Genetics (20 Lectures)
  1. Law of Inheritance: Mendelian principles, Concept of dominance, Segregation and independent assortment, Co-dominance, Incomplete dominance, Gene interactions, Pleiotropy, Linkage and crossing over.
  2. Allelic and Non-allelic Interaction: Concept of allele, Lethal alleles, Multiple alleles, Test of allelism, Complementation and epistatsis.
  3. Mutation: Types of mutation, Repair mechanism, Role in genetic analysis and evolution.
  4. Cytoplasmic Inheritance: Basis and mechanism, Role of organellar genes.
  5. Recombination: Homologous and non-homologous recombination including transposition.
  6. Structural and Numerical Alterations of Chromosomes: Polyploidy, Aneuploidy, Chromosomal rearrangements - deletion, duplication, inversion and translocation.
Genomics
Total Credit : 3
Total Number of Lectures : 48
Course In-charge: Dr. Praveen Verma and Dr. Aashish Ranjan
The primary objective of this course is to familiarize students with fundamental concepts of plant structural, functional and comparative genomics and make them aware of novel genomics-assisted advanced technologies including various traditional as well as modern genetic and molecular breeding approaches having potential applications in crop improvement. This course further aims at helping students gain a deeper understanding of the latest novel in- silico genomics and proteomics tools and methodologies. On the whole, the course will enhance the students overall comprehension of the subject, improve their computational skills and eventually assist in proper planning, execution and analysis of their research work.
1. Genome Analysis (5 lectures)
  1. Basic concepts of genes, Genome and genomics.
  2. Cloning systems used in genomics (Cosmids, P1 bacteriophage, BAC and PAC cloning vectors).
  3. Physical mapping of the genome.
2. Sequencing, Analyzing Genomes and Transcriptomes (15 lectures)
  1. Sequencing strategies for the systematic sequencing of complex genomes.
  2. Analysis of sequenced model plant genomes (Arabidopsis and rice).
  3. Next generation sequencing methods and their assembly and annotation.
  4. Principles of genome annotation and gene prediction: tools and resources.
  5. Introduction to various sequence formats and different methods of database searches.
  6. Connecting sequence to function and plant genome databases.
3. Functional Genomics (6 lectures)
  1. Strategies to find gene function at genome-wide level: Gene tagging, Tillingand gene targeting.
  2. Differential gene expression profiling: Methodologyand analysis.
4. Molecular Markers and Their Applications in Molecular Breeding (12 lectures)
  1. Overview,development and application of molecular markers.
  2. Methods of assessing genetic diversity and germplasm characterization, DNA fingerprinting and its application.
  3. Concept of linkage mapping: principles, mapping populations, recombination fractions, LOD score and establishment of linkage groups, gene mapping tools and resources.
  4. QTL analysis and concept of marker-assisted selection in plant breeding.
  5. Map-based gene isolation.
  6. Allele mining, Association mapping and their applications in crop improvement.
  7. Statistical approaches to biological systems.
5. Evolutionary and Comparative Genomics (4 lectures)
  1. Introduction to genome evolution: Molecular phylogenetics and applications.
  2. Multiple sequence alignments and phylogenetic analysis.
  3. Evolution of exon and introns, Gene duplication, Acquisition of new genes in non-coding regions, and Multigene families: neo-, pseudo-, and sub-functionalization.
  4. Transposable elements and their role in genome evolution.
  5. Intergenome comparison for synteny analysis.
6. Protein Structure Analysis (6 lectures)
  1. The peptide bond and structural basis of protein function
  2. From sequence to structure and from structure to function
Plant Biology
Total Credit : 3
Total Number of Lectures : 48
Course In-charge:Dr. Senthil-Kumar Muthappa and Dr. Pinky Agarwal
1. Biochemical Processes (10 lectures)
  1. Photosynthesis: Light harvesting complexes, Mechanism of electron transport, Chlorophyll fluorescence, Photoprotective mechanism, CO2 fixation- C3, C4 and CAM pathways.
  2. Respiration and Photorespiration: Citric acid cycle, Plant mitochondrial electron transport and ATP synthesis, Alternative oxidase, Photo respiratory pathway.
  3. Water and Solute Transport and Photo-assimilates Translocation: Uptake, transport and translocation of water, ions, solutes and macromolecules from soil, through cells, across membranes, through xylem and phloem, Transpiration, Mechanism of loading and unloading of photo-assimilates.
  4. Plant Nutrients: Essential nutrients (macro-nutrient & micro-nutrient) and their deficiency disorders.
  5. Nitrogen metabolism: Nitrogen fixation, Ammonia uptake and transport, Nitrate uptake and reduction.
  6. Secondary Metabolism: Biosynthesis and uses of alkaloids, Glycosides, Terpenes and phenolics.
2. Development (8 lectures)
  1. Molecular basis of stem, leaf and root development.
  2. Molecular basis of reproduction: Male and female gametophyte, Male sterility, Fertilization, Seed, Apomixis.
3. Signal Transduction (10lectures)
  1. Overview of cell signalling.
  2. Membrane receptors and receptor proteins.
  3. Secondary messengers: Ca2+/CaM, NO etc.
  4. Kinase signalling and reversible phosphorylation.
  5. Plant Hormones: Biosynthesis, perception, signaling and role in plant growth and development.
  6. Light Signaling: Perception, signaling and role in plant growth and development.
  7. Sugar Signaling: Perception, signaling and role in plant growth and development.
4. Plant Response to Environment (12 lectures)
  1. Abiotic Stress: Drought, Salinity, Light, Temperature and heavy metals. Stress perception, Adverse effect of stresses on plant growth and development, Cellular, physiological and biochemical responses to stresses.
  2. Plant Immunity: Genetics of immune response, Signal perception, Host-pathogen interaction (bacteria, fungus, and virus).
  3. Symbiosis: Mycorrhizal and rhizobial interaction.
5. Genetic engineering & crop improvement (8 lectures)
  1. Recombinant DNA technology, cloning of genes and regulatory elements.
  2. Methods of gene manipulation (over-expression and RNA interference).
  3. Plant genetic transformation, cis-genics and transgenics.
  4. Agronomic, industrial and quality traits.
  5. Bioethics, Biosafety, Intellectual property rights and implications in plant research.
Emerging Trends in Plant Sciences
Total Credit : 1
Total Number of Lectures : 16
Course In-charge: Dr. Jitendra K. Thakur and Dr. Ananda K. Sarkar
1. Regulation Biology (8 lectures)
  1. RNA interference, RNA editing, Plant Mediator Complex- discovery, phylogeny, structure and diverse roles.
  2. Post-transcriptional and post-translational regulation.
  3. Chromatin remodeling, DNA methylation, histone modifications.
  4. Epigenetic regulation in plants, Epigenomics and its scopes, Paramutation, Genomic imprinting, RNA-mediated epigenetic phenomenon.
2. Stem Cells (4 lectures)
  1. Stem cell concept in plant, Comparison between animal and plant stem cell niches.
  2. Molecular regulation of shoot stem cell niche and its importance.
  3. Molecular regulation of root stem cell niche and its importance. Comparison between stem cell niches of different organs.
  4. Cambium stem cells and their role in vascular development.
4. Systems Biology (4 lectures)
  1. Introduction to systems biology.
  2. Tools of systems biology (different ‘omics’).
  3. Modeling the biological pathway.
  4. Gene regulatory / co-expression network analysis.
  5. A case study: Primary / secondary metabolite networks of plants.
Research Methodology
Total Credit : 4
Total Number of Lectures : 64
Course In-charge: Dr. Jitender Giri and Dr. Swarup K. Parida
  Topic Lectures
1. Computer networks and computational facility 2
2. Computational biology, R-program, NGS data analysis, whole genome assembly and annotation 7
3. Basic bioinformatic tools 3
4. General instrumentation 2
5. Radioisotope and imaging 2
6. Photometry 2
7. Chromatography & Metabolomics 4
8. Proteomics and Mass spectroscopy 4
9. Real-Time PCR 2
10. Intellectual property rights (IPR) 2
11. Advanced microscopy 3
12. Scientific Ethics 2
13. Biosafety 2
14. Genotyping tools 3
15. Biostatistics 6
16. X-ray crystallography and NMR 4
17. Plant Transformation 2
18. Research writing skills (term paper) 12