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

Course Co-ordinator: Dr. Niranjan Chakraborty

Course Material Credits
Molecular Cell Biology and Genetics 3
Genomics 3
Plant Biology 3
Emerging Trends in Plant Sciences 2
Research Methodology 2
Term Paper- A review in an emerging area of research 1
Seminar 1

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 Molecular Cell 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)
  • Constituents of Plant Cells: Extracellular matrix, Cytoskeleton, and Organelles.
  • Cell Cycle Regulation: Phases of cell cycle, Restriction and check point, Cell division and cell growth, Cell cycle progression.
  • Enzyme Function.
  • Protein Turnover: Biosynthesis and degradation.
2. Molecular Biology (12 lectures)
  • Genetic Material: Genome organization, DNA  replication and recombination, Source of genetic variation (natural and  induced).
  • Gene Expression: Transcription, Cis-acting  elements and transcription factors, RNA editing and processing.
  • 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)
  • Law of Inheritance:  Mendelian principles, Concept of dominance,  Segregation and independent assortment, Codominance, Incomplete dominance, Gene  interactions, Pleiotropy, Linkage and crossing over.
  • Allelic and Non-allelic Interaction: Concept of  allele, Lethal alleles, Multiple alleles, Test of allelism, Complementation and  epistatsis.
  • Mutation: Types of  mutation, Repair mechanism, Role in genetic analysis and  evolution.
  • Cytoplasmic Inheritance: Basis and mechanism,  Role of organellar genes.
  • Recombination: Homologous and non-homologous recombination including transposition.
  • Structural and  Numerical Alterations of Chromosomes: Polyploidy, Aneuploidy, Chromosomal  rearrangements – deletion, duplication, inversion and translocation.
Suggested Reading
  • Nelson DL and Cox MM (2008) Lehninger “Principles of Biochemistry”. Fifth Edition, Freeman & Co Ltd., NY,  USA.
  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K  and Walter P (2008) Molecular Biology of the Cell. Fifth Edition, Garland  Science, NY, USA.
  • Voet D and Voet JG (2011)  Biochemistry. Fourth Edition, John Wiley & Sons, NY,  USA.
  • Lodish H, Berk A,  Zipursky SL, Matsudaira P, Baltimore D and Darnell J (2012) Molecular Cell  Biology. Seventh Edition, Taylor & Francis Publishers, NY,  USA.
  • Krebs JE, Goldstein ES  and Kilpatrick ST (2011) Lewin’s Genes X. Tenth Edition, Jones &  Bartlett Publishers, MA,  USA.
  • Latchman DS (2007)  Gene Regulation. Fifth Edition, Taylor & Francis Publishers, NY,  USA.
  • Brown TA (2007) Genomes.  Third Edition, Garland Science, NY, USA.
  • Snustad DP and Simmons MJ (2012) Principles of  Genetics. Sixth Edition, John Wiley  & Sons, NY, USA.



Total Credit : 3
Total Number of Lectures : 48
Course In-charge: Dr. Praveen Verma and Dr. Mukesh Jain
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 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 in-silico genomics and proteomics tools and methodologies. On the whole, the course will enhance overall comprehension of the subject, improve computational skills and eventually assist in proper planning, execution and analysis of research work.
1. Genome Analysis (5 lectures)
  • Basic concepts of genes, genome and genomics.
  • Cloning systems used in genomics (Cosmids, P1 bacteriophage, BAC and PAC cloning vectors).
  • Physical mapping of the genome.
2. Sequencing, Analyzing Genomes and Transcriptomes (15  lectures)
  • Sequencing strategies for the systematic  sequencing of complex genomes.
  • Analysis of sequenced model plant genomes (Arabidopsis and rice).
  • Next generation sequencing methods and their  assembly and annotation.
  • Principles of genome annotation and gene  prediction: tools and resources.
  • Introduction to various  sequence formats and different methods of database searches.
  • Connecting sequence to  function and plant genome databases.
3. Functional Genomics (6 lectures)
  • Strategies to find gene function at genome-wide  level: Gene tagging, Tilling and gene targeting.
  • Differential gene expression profiling:  Methodology and analysis.
4. Molecular Markers and Their Applications in Molecular Breeding  (12 lectures)
  • Overview, development and application of  molecular markers.
  • Methods of assessing genetic diversity and  germplasm characterization, DNA fingerprinting and its application.
  • Concept of linkage mapping: Principles, mapping  populations, recombination fractions, LOD score and establishment of linkage  groups, gene mapping tools and resources.
  • QTL analysis and concept of marker-assisted  selection in plant breeding.
  • Map-based gene isolation.
  • Allele mining, association mapping and their  applications in crop improvement.
  • Statistical approaches to biological systems.
5. Evolutionary and Comparative Genomics (4 lectures)
  • Introduction to genome evolution: Molecular  phylogenetics and applications.
  • Multiple sequence  alignments and phylogenetic analysis.
  • Evolution of exon and introns, Gene duplication,  Acquisition of new genes in non-coding regions, Multigene families: neo-,  pseudo-, and sub-functionalization.
  • Transposable elements and their role in genome  evolution.
  • Intergenome comparison for synteny analysis.
6. Protein Structure Analysis (6 lectures)
  • The peptide bond and structural  basis of protein function
  • From sequence to structure  and from structure to function
Suggested Reading
  • Brown, T.A. (2010) Gene cloning and DNA analysis: an introduction. West Sussex: Wiley-Blackwell, NJ, USA.
  • Xu Y (2010) Molecular Plant Breeding. CABI International, Wallingford, Oxfordshire, UK.
  • Caetano-Anolles G (2010) Evolutionary Genomics and Systems Biology. Wiley-Blackwell, Hoboken, NJ, USA.
  • Somers DJ, Langridge P, Gustafson JP (2011) Plant Genomics: Methods and Protocols, Methods in Molecular Biology. Humana Press Inc., NY, USA.
  • Pevsner J (2009) Bioinformatics and Functional Genomics. Wiley-Blackwell, Hoboken, NJ, USA.
  • Brown TA (2007) Genomes. Third Edition, Garland Science, NY, USA.
  • Galperin MY and Koonin EV (2003) Frontiers in Computational Genomics. Caister Academic Press, Norfolk, UK.
  • Primrose SB and Twyman R (2006) Principles of Gene Manipulation and Genomics. Seventh Edition, Wiley-Blackwell, NJ, USA.
  • Xu Y (2010) Molecular Plant Breeding. CABI International, Oxfordshire, UK.
  • Somers DJ, Langridge P and Gustafson JP (2011) Plant Genomics: Methods and Protocols, First Edition, Humana Press Inc., NY, USA.
In addition, recent literature will be suggested by the faculty during the course of teaching.



Plant Biology

Total Credit : 3
Total Number of Lectures : 48
Course In-charge:Dr. Subhra Chakraborty and Dr. Senthil Kumar Muthappa
The course will focus on major biochemical processes and regulatory  control that operate in plant development. With an increasing  awareness of environmental problems, the course will include various aspects of  stress biology, especially the biotic and abiotic stresses which illustrate mechanism/s  of stress tolerance in plants. Understanding the biology of plants, different  aspects of signal  transduction, and the impact of genetic engineering for crop improvement are many of prime  issues of this course that will continue to fuel the expansion of plant biology  research.
1. Biochemical Processes (10 lectures)
  • Photosynthesis:  Light harvesting complexes,Mechanism of electron transport, Chlorophyll  fluorescence,Photoprotective mechanism, CO2 fixation- C3, C4 and CAM pathways.
  • Respiration  and Photorespiration: Citric acid cycle,Plant mitochondrial electron transport  and ATP synthesis,Alternative oxidase, Photo respiratory pathway.

  • 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.
  • Plant Nutrients: Essential nutrients (macro-nutrient & micro-nutrient) and their deficiency disorders.
  • Nitrogen metabolism: Nitrogen fixation,Ammonia uptake and transport,Nitrate uptake and reduction.
  • Secondary Metabolism: Biosynthesis and uses of alkaloids, glycosides, terpenes and phenolics.
2. Development (8 lectures)
  • Molecular  basis of stem, leafand root development.
  • Molecular  basis of reproduction: Male and female gametophyte, Male sterility,  Fertilization, Seed, Apomixis.

3. Signal Transduction (10lectures)
  • Overview of cell signalling.
  • Membrane receptors and receptor proteins.
  • Secondary messengers: Ca2+/CaM, NO etc.
  • Kinase signalling and reversible phosphorylation.
  • Plant Hormones: Biosynthesis, perception, signaling and role in plant growth and development.
  • Light Signaling: Perception, signaling and role in plant growth and development.
  • Sugar Signaling: Perception, signaling and role in plant growth and development.
4. Plant Response to Environment (12 lectures)
  • 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.
  • Plant  Immunity:Genetics of immune response,Signal perception,Host-pathogen  interaction (bacteria, fungus, and virus).
  • Symbiosis:  Mycorrhizal and rhizobial interaction.
5. Genetic engineering & crop improvement (8  lectures)
  • Recombinant  DNA technology, cloning of genes and regulatory elements.
  • Gene  manipulation (over-expression and RNA interference).
  • Agronomic,  industrial and quality traits.
  • Bioethics,  Biosafety, Intellectual property rights and implications in plant research.
Suggested Reading
  • Buchanan B Gruissem W and Jones R (2000)Biochemistry & Molecular Biology of Plants. American Society of Plant Physiologists Press,  Rockville, MD, USA.

  • Nelson DL and Cox MM (2008) Lehninger “Principles of Biochemistry”. Fifth Edition,Freeman&  Co Ltd., NY,  USA.
  • Alberts  B Johnson A Lewis J Raff M Roberts K and Walter P (2008) Molecular Biology of  the Cell. Fifth Edition, Garland Science, NY, USA.
  • Lea  P and Leegood RC (1999) Plant Biochemistry & Molecular Biology.John Wiley & Sons, NY, USA.
  • Tropp  BE(2008) Molecular Biology: Genes to Proteins. Third edition,Jones & Bartlett Publishers, MA, USA.
Other updated literature will be suggested by  the concerned faculties during the course of teaching.


Emerging Trends in Plant Sciences


Total Credit : 2
Total Number of Lectures : 32
Course In-charge: Dr. Gitanjali Yadav and Dr. Jitendra K. Thakur
In the past decade,  our understanding about plant biology has immensely increased largely because  of the availability of enriched genomic information and emerging techniques in  plant biology. The course will broaden our understanding about the emerging  concepts of plant gene regulation at in-depth level involving micro-RNA  regulation and epigenetics. Various ‘Omic’-based studies, which broadened our  knowledge about various plant processes and plant functioning as a whole, will  be discussed. A brief account of emerging application of nanotechnology in  plant sciences are also included.
1. Regulation Biology (12 lectures)
  • RNA interference, RNA editing, Plant Mediator  Complex- discovery, phylogeny, structure and diverse roles.
  • Post-transcriptional and post-translational  regulation.

  • Chromatin remodeling, DNA methylation, Histone  modifications.
  • Epigenetic regulation in plants, Epigenomics and  its scopes, Paramutation, Genomic imprinting, RNA-mediated epigenetic phenomenon.
2. Stem Cells (8 lectures)
  • Stem cell concept, plant and animal stem cell  niches including totipotency.
  • Molecular regulation of shoot stem cell niche  and its importance.
  • Molecular regulation of root stem cell niche and  its importance. Comparison between stem cell niches of different organs.
  • Cambium stem cells and their role in vascular  development.
3. Nanotechnology in Plant Science (4 lectures)
  • Introduction to nanotechnology.
  • Application and limitation of novel  nanotechnology strategies in plant biotransformation.
4. Systems Biology (8 lectures)
  • Introduction to systems biology.
  • Tools of systems biology.
  • Modeling the biological pathway.
  • Gene regulatory / co-expression network analysis.
  • Primary / secondary metabolite networks of  plants: a case study.
Suggested Reading
  • Hartl DL and Jones EW (2005) Genetics: Analysis of  Genes and Genomes. Sixth  Edition, Sudbury, MA, USA.

  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K  and Walter P (2008) Molecular Biology of the Cell. Fifth Edition, Garland  Science, NY, USA.
  • Nelson DL and Cox MM (2008) Lehninger “Principles of Biochemistry”. Fifth Edition Freeman, NY, USA.
  • Taiz L and Zeiger E  (2010) Plant Physiology, Fifth Edition. Sinauer Associates, Sunderland, MA, USA.
  • Howell SH (1998) Molecular Genetics of Plant  Development. Cambridge  University Press, NY, USA.
  • Srivastava LM (2002) Plant Growth and  Development: Hormone and Environment. Academic Press, Amsterdam, The  Netherlands.
  • Overview and Implications of Nanotechnology (2008).
  • Nanotechnology in Agriculture and Food (2006).  European Nanotechnology Gateway.
In addition, recent literature will be suggested  by the concerned faculties during the course work.



Research Methodology

Total Credit : 2
Total Number of Lectures : 24
Course In-charge: Dr. Ashverya Laxmi and Dr. Swarup K. Parida
Our understanding  about the plant biology has increased largely because of the availability of  latest techniques and instruments. The ‘Research Methodology’ course will  broaden the understanding of students about general instrumentation and its  requirement in various day-to-day lab activities. Various techniques involved  in gene expression analysis such as Real-Time PCR and Microarray will be  introduced. A brief account of proteomics studies will also be given. An  elaborate account of various microscopic, sequencing and mapping techniques  will be given. Further, a detailed account of radioisotope and imaging tools  will be discussed with special emphasis to various aspects of radiation safety.  The functioning of various other instruments such as photometry,  chromatography, pulse-field gel electrophoresis will also be discussed.  Finally, the functioning and uses of computational network and computational  facility will also be introduced. The introduction and visualization of these  techniques/instrumentations will help students to know about their  usage/applications and help in designing experiments for their research work  accordingly.
  • General instrumentation.
  • Computer networks and computational facility.
  • Basic bioinformatic tools.
  • Radioisotope and imaging.
  • Photometry.
  • Chromatography.
  • Proteomics.
  • Sequencing, Real-Time PCR and pulse-field gel  electrophoresis.
  • Advanced microscopy.
  • Microarray.
Suggested Reading

  • Bisen PS and Sharma A (2012) Introduction to Instrumentation in Life Sciences. Taylor & Francis, California, USA.
  • Cazes J (2009) Encyclopedia of Chromatography. Taylor & Francis, Florida, USA.
  • Wilson K and Walker J (2000) Principles and Techniques of Practical Biochemistry.Fifth edition, Cambridge University Press, UK.
  • Tuimala J and Laine MM (2005) DNA Microarray Data Analysis. Second Edition, CSC Scientific Computing Ltd., Helsinki.
  • Berrar DP, Dubitzky W and Granzow M (2003) A Practical Approach to Microarray Data Analysis. Kluwer Academic Publishers, NY, USA.
  • Reinders J and Scickmann A (2009) Proteomics- Methods and Protocols. Humana Press, NY, USA.
  • Spector DL and Goldman RD (2006) Basic Methods in Microscopy. Protocols and Concepts from Cells: A Laboratory Manual. Cold Spring Harbor University Press, NY, USA.
  • Confocal Microscopy: Methods and Protocols (1999) In: Methods in Molecular Biology, Vol 122, Ed., Stephen W. Paddock, Humana Press Inc., Totoya, NJ.
  • Manual: Training course on safety aspect in the research applications of ionizing radiations (2005): Radiological Physics and Advisory Divisions, Atomic       Energy Regulatory Board, BARC.
  • Oliphant A, Barker DL, Stuelpnagel JR and Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping.       Biotechniques, 32, S56.
  • Fan JB, Chee MS and Gunderson KL (2006) Highly parallel genomic assays. Nat. Rev. Genet., 7, 632–44.