Plant Biotechnology – Ph.D., Courses – Centre for Plant Molecular Biology and Biotechnology

Ph. D., (Ag.) Biotechnology (List of courses for Semester System, 2019)

S. No.	Course No.	Course Title	Credit hours
I. Major courses (15)
1.	MBB 601	Advances In Plant Molecular Biology	3+0
2.	MBB 602	Advances In Genetic Engineering	3+0
3.	MBB 603	Advances In Microbial Biotechnology	3+0
4.	MBB 604	Advances In Crop Biotechnology	2+0
5.	MBB 605	Advances in Genomics and Bioinformatics	3+0
6.	MBB 606	Commercial Plant Tissue Culture	1+0
Total Credits			15+0=15
II. Minor courses (8)
1.	GPB 604	Cellular and Chromosomal Manipulations in Crop Improvement	2+1
2.	PLP 605	Climate Change and Crop Growth	2+0
3.	PLP 611	Advances In Plant Responses To Abiotic Stresses	2+1
4.	PLP 603	Molecular Approaches for Improving physiological traits	2+0
5.	PAT 604	Molecular Basis Of Host-Pathogen Interaction	2+1
Total Credits			6+2=8
III. Supporting courses (5)
1.	GPB 601	Plant Genetic Resources And Their Utilization	2+0
2.	AGM 605	Microbial Gene Technology	2+1
4.	ENT 608	Advanced Host Plant Resistance	1+1
5.	MAT 604	Mathematical Modeling In Agricultural Sciences	1+1
Total Credits			4+1=5
IV. Doctoral Seminar-I			1+0
V. Doctoral Seminar-II			1+0
VI. Research			0+45
Total Credits			27+48=75

In addition, Compulsory Non-credit courses, as mentioned in the above M. Sc. (Agriculture) in Biotechnology program, have to undergo (if not undergone during MSc program).

Programme Outcomes (PO) of Ph. D., (Plant Biotechnology)

PO1	Knowledge: Applying the mechanisms and principles learnt to solve the problems in agriculture by using biotechnological techniques and tools.
PO2	Understanding the problems and finding out solutions: Identifying the research gaps in the agricultural field by practical exposure and working out the methodology for solving the problems through literature collection and experimentation.
PO3	Conducting research for solving the problems: After identifying a research problem, formulation of a research proposal by collecting literature and deriving the methodologies for implementing the research through several experiments, collection of data, analysis of data and finally interpreting the data for getting a solution to the research problem.
PO4	Gaining knowledge on modern tools and techniques: While solving new research issues methodologies will be optimized, new tools may be developed, undergoing the usage of sophisticated equipments and valuable softwares / tools to attain the solutions scientifically.
PO5	Work efficiency: Students’ working efficiency will be improved either individually or working under team environment. Understanding the value of time the productivity will be increased.
PO6	Professional Ethics: Apply ethical principles and commit to follow professional ethics and norms and guidelines in the practice of biotechnology responsibly.
PO7	Communication skills: Solutions found out for the research problems will be effectively communicated by way of writing research articles and presentations.
PO8	Biotechnology and society: Apply reasoning for the issues, informed by the contextual knowledge of the problems in hand and assess the risk associated with the societal, health, safety, legal and cultural issues of the problems and the consequent responsibilities relevant to the professional practice of the discipline.
PO9	Environment and sustainability: Understand the impact of the technological solutions developed through biotechnology in contexts of society and the environment, and demonstrate the knowledge need for sustainable development in judicious use of biotechnology tools and technique.
PO10	Life-long learning: Understanding the dynamism of biological sciences, technological changing needs are to be felt, positive attitude are to developed so as to prepare and engage in adapting to such changes through the process of life-long learning.

Ph. D., (Plant Biotechnology): Programme Specific Outcomes (PSO)

PSO1	Impart a high quality education in biotechnology among students to meet out future challenges in agriculture.
PSO2	Understand the nature and basic concepts of cell biology, Biochemistry, Molecular biology and bioinformatics.
PSO3	Analyze the complex problems of agriculture and address issues through use of modern tools and techniques in biotechnology.
PSO4	Perform experimental procedures as per established laboratory standards in the areas of Biochemistry, Molecular biology, Plant tissue culture, Genetic Engineering, Molecular Ecology, Molecular marker Technology and Bioinformatics.
PSO5	Understand the applications of biotechnology in all spheres of agriculture and develop crops with improved productivity thereby increasing farmers’ income, better human health and decreased environmental pollution.

Ph. D., (Ag.) Biotechnology

Major Courses

MBB 601 Advances in Plant Molecular Biology (3+0)

OBJECTIVE

To discuss the specialized topics and recent advances in the field of plant molecular biology

THEORY

Unit I : Forward and Reverse Genetics

Arabidopsis in molecular biology, Forward and Reverse Genetic Approaches, Transcriptional and post-transcriptional regulation of gene expression, isolation of promoters and other regulatory elements.

Unit II : Transcriptomics

RNA interference, Transcriptional gene silencing, Transcript and protein analysis, use of transcript profiling to study biological systems.

Unit III : Hormone regulated pathways

Hormone regulatory pathways: Ethylene, Cytokinin, Auxin and ABA, SA and JA; ABC Model of Floral Development, Molecular basis of self incompatibility. Signal transduction and receptors.

Unit IV : Abiotic stress

Molecular biology of abiotic stress responses: Cold, high temperature, submergence, dehydration, salinity and drought;

Unit V : Plant pathogen interactions

Molecular Biology of plant-pathogen interactions, molecular biology of Agrobacterium infection, Molecular biology of Rhizobium infection (molecular mechanisms in symbiosis), Programmed cell death in development and defense.

LECTURE SCHEDULE

1. Arabidopsis as a model plant in molecular biology

2. The genetic basis of a phenotype or trait

3. Expression of a phenotype by a particular gene

4. Reverse Genetic Approaches in functional genomics

5. Reverse Genetic Approaches in functional genomics (cont…)

6. Transcriptional and post-transcriptional regulation of gene expression

7. Transcriptional and post-transcriptional regulation of gene expression (cont…)

8. Promoters and their role in gene expression

9. Isolation of promoters and other regulatory elements

10. RNA interference – micro RNAs and small interfering RNAs

Mode of action in RNAi system

12. RNA dependent gene silencing

13. Transcriptional gene silencing

14. Post transcriptional gene silencing

15. RNA viruses in post transcriptional gene silencing

16. Suppression of gene silencing by plant viruses

17. Application of RNAi technology in plant biotechnology

18. Transcript analysis to study biological systems

19. Protein analysis to study biological systems

20. Regulation of cellular processes by different hormones

21. Role of hormones in flowering

22. Role of hormones in fruit ripening

23. Role of hormones in seed germination

24. Role of hormones in senescence

25. Mid semester exam

26. JA in signal transduction

27. ABC Model of Floral Development

28. Molecular basis of self incompatibility

29. Signal transduction – over view

30. Plasma membrane receptors

31. Protein kinases

32. G proteins in signal transduction

33. Principles of stress perception

34. Signal transduction pathway

35. Regulation of gene expression

36. Molecular biology of salinity stress tolerance in plants

37. Molecular biology of drought tolerance in plants

38. The heat shock response in higher plants

39. Molecular biology of low temperature response in plants

40. Molecular biology and genomics of flooding

41. Response and adaptation by plants to flooding stress

42. Molecular responses to dehydration in plants

43. Molecular mechanisms involved in Agrobacterium infection of plant cells

44. Molecular mechanisms involved in Agrobacterium infection of plant cells

45. (cotnd…)

46. Use of Agrobacterium as a biotechnological tool for genetic engineering

47. Molecular biology of Rhizobium infection

48. Nodulation genes

49. Nod factor signaling and infection in Rhizobium-legume symbiosis

50. Programmed cell death(PCD) or Apoptosis in plants

51. Occurrence and necessity of PCD for plant development

52. Occurrence and necessity of PCD for plant defense

SUGGESTED READINGS

1.	Buchanan B, Gruissen W & Jones R. 2015. Biochemistry and Molecular Biology of Plants. 2nd Ed, American Society of Plant Physiologists, USA.
2.	Krebs, JE, Goldstein ES &Kilpatrick ST 2017. Levin’s Genes XII. 12th Ed. Jones & Barlett Learning Publ.
3.	Malacinski GM & Freifelder D. 2008. Essentials of Molecular Biology. 4th Ed. Jones & Bartlett Publ.
4.	Nelson DL & Cox MM. 2017. Lehninger’s Principles of Biochemistry. 7th Ed. WHFreeman & Co.
5.	Watson JD, Bakee TA, Bell SP, Gann A, Levine M &Losick R. 2017. Molecular Biology of the Gene. 7th Ed. Pearson Education.

SUGGESTED WEBSITES

http://www.elsevier.com/wps/find/journaldescription.cws_home/journalof molecular biology

http://www.cellbio.com/elecpubs.html (molecular biology today – journal)

www.springer.com/life+sciences/plant+sciences/journal/11103(plant molecular biology)

http://www.ebooksx.com/Arabidopsis-Protocols-2nd-Edition-Methods-in-Molecular-Biology-_208282.html


MBB 602 Advances In Genetic Engineering		(3+0)
	OBJECTIVE
	To discuss specialized topics and advances in the field of genetic engineering and their application in crop improvement
	THEORY
	Unit I : Genetic Engineering Technologies

Overview of transgenic plants – current status of transgenic plants. Recent advances – cisgenesis and intragenesis, RNAi technology, targeted genome modification – CRISPR-Cas9 and advancements in CRISPR technology, gene drive. Regulated and tissue-specific expression of transgenes for crop improvement

Unit II : Engineering for stress resistance

Gene stacking; Pathway engineering; Marker-free transgenic development strategies. High through put phenotyping of transgenic plants. Case studies: Genetic engineering of herbicide resistance, Transgenic plants resistant to pests; Engineering for abiotic stress resistance

Unit III : Engineering for Quality traits and male sterility

Genetic Engineering food crops for quality – nutritional quality, starch composition, FA composition and shelf life. Genetic engineering for pollination control, Induction of male sterility in plants.

Unit IV : Production of recombinant proteins in plants

Molecular farming of plants for pharmaceutical applications advances in chloroplast transformation – production of therapeutic proteins in chloroplasts. Expression of recombinant proteins using viral vectors.

Unit V : Biosafety and Regulatory issues

Bio-safety studies – Environmental issues associated with transgenic crops; Food and feed safety issues; risk assessment – problem formulation; risk assessment for environment and food safety. Field studies with transgenic crops; National and international regulatory framework – Advances in biosafety regulation.

LECTURE SCHEDULE

	1.	An over-view of transformation methods
	2.	Advances in transformation methods
	3.	Current status of transgenic plant – global and national level
	4.	Benefits and impact of transgenic plants – global and national level
	5.	Cisgenesis and intragenesis
	6.	Cisgenesis vs transgenesis; examples
	7.	RNAi technology
	8.	Targeted genome modification – basics; ZFN and TALEN
	9.	CRISPR technology
	10.	Advances in CRISPR technology
	11.	Gene drive and its application in insect control
	12.	Marker-free transgenic plants
	13.	Regulated and tissue specific expression of target genes
	14.	Pathway engineering; case studies
	15.	High throughput genotyping of transgenic plants
16.		Genetic engineering for herbicide resistance; case studies
17.		Genetic engineering for insect resistance, Bt mediated insect resistance
18.		Improving Bt expression in plants; case studies
19.		Insect resistance genes of plant and other origin
20.		RNAi technology in insect control
21.		Genetic engineering for fungal disease resistance; case studies
22.		Genetic engineering for bacterial disease resistance; case studies
23.		Genetic engineering for viral disease resistance; case studies
24.		Application of RNAi and CRISPR technology for disease resistance – case studies
25.		Mid Semester Examination
26.		Engineering crops for abiotic stress resistance
27.		Abiotic resistance; case studies
28.		Genetic engineering for nutritional quality – protein, mineral
29.		Genetic engineering for nutritional quality – vitamins
30.		Genetic engineering for nutritional quality – fatty acid composition
31.		Genetic engineering for quality – starch composition, shelf life
32.		Genetic engineering for male sterility – strategies
33.		Genetic engineering for male sterility – Case study
34.		Molecular pharming in different systems
35.		Plant Molecular pharming for pharmaceutical proteins
36.		Production of antibodies; vaccines – case studies
37.		Advances in chloroplast transformation
38.		Production of therapeutic proteins in chloroplasts
39.		Transient expression of recombinant proteins using viral vectors
40.		First and second generation Viral vectors
41.		Transient expression – case studies
42.		Biosafety issues; Food safety concerns of transgenic plants
43.		Environmental issue associated with transgenic plants
44.		Principles of Risk assessment
45.		Problem formulation – basics
46.		Problem formulation – environmental risk assessment
47.		Problem formulation – risk assessment for food and feed safety
48.		Biosafety regulation at global level
49.		Biosafety regulations at national level; regulatory set up in India
50.		Conduct of confined field studies
51.		Advances in biosafety regulation; regulation of products derived from RNAi and CRISPR technologies

SUGGESTED READINGS

1.	Handbook of Plant Biotechnology, 2 volume set, Edited by Christou P and Klee H. Wiley publisher, 2004, 1488 pages.
2.	Molecular Farming- Plant made pharmaceuticals and technical proteins. Edited by Fischer R and Schillberg S, 2004, WILEY-VCH Verlag publisher
3.	Genetically Engineered Food: Methods and Detection, Edited by Heller KJ, Wiley-Blackwel, 2006, 287 pages
4.	Plant Biotechnology- The genetic manipulation of plants by Authors, Slater et al., 2008, Oxford University Press, 376 pages.
5.	Agrobacterium: From Biology to Biotechnology. Edited by Tzfira et al., Springer, 2008, 750 pages
6.	Recent Advances in Plant Biotechnology and Its Applications: Prof. Dr. Karl-Hermann Neumann Commemorative Volume. Edited by Ket N al., I. K. International Pvt Ltd, 2008, 694 pages.
7.	Genetically Modified and non-Genetically Modified Food Supply Chains: Co-Existence and Traceability. Edited by Bertheau Y., Wiley-Blackwell, 2012, 708 pages
8.	Plant Gene Containment, Edited by Oliver MJ and Li Y. Wiley-Blackwell, 2012, 224 pages.
9.	Improving Crop Productivity in Sustainable Agriculture. Edited by Tuteja et al , Wiley-Blackwel, 2013; 536 pages
10.	Plant Biotechnology – Experience and Future Prospects. Edited by Ricroch et al., Springer, 2014; 276 pages
11.	Genetic Modification and Food Quality: A Down to Earth Analysis, Blair, R and Regenstein JM., Wiley, 2015; 288 pages
12.	Plant Pathogen Resistance Biotechnology. Edited by Collinge DB, Wiley-Blackwel, 2016. 440 pages.
13.	Plant Biotechnology: Principles and Applications. Edited by Abdin MZ et al., Springer, 2017; 392 pages.
14.	Biotechnologies of Crop Improvement, Volume 2, Transgenic Approaches. Edited by Gosal SS and Wani SH, Springer International Publishing, 2018, 485 pages.

SUGGESTED WEBSITES

1.	http://cls.casa.colostate.edu/transgeniccrops/faqpopup.html
2.	http://www.isaaa.org/gmapprovaldatabase/

MBB 603 Advances in Microbial Biotechnology (3+0)

OBJECTIVE

The objectives of this course are to introduce the students to the field of microbiology with emphasis on biotechnological potential of microbes.

THEORY

Unit I : Microbial Diversity

Domain and Kingdom concepts in classification of microorganisms; Criteria for classification; Classification of Bacteria according to Bergey’s manual; use of DNA and RNA sequencing in classification; Molecular methods used in microbial classification; 16S rDNA sequencing and Ribosomal Database Project; Culture Collection and preservation.

Unit II : Microbial Growth Kinetics and physiology

Microbial growth – yield constants, continuous kinetics, methods of growth estimation; Nutrition; microbial metabolism; Fermentative metabolism- isolation, preservation and improvement of industrially important microorganisms.

Unit III : Bioprocessing

Fermentors – types-Batch, Fed batch and continuous fermentation-Immobilization of enzymes and cells; Fermentation medium; Scale-up principles; Down-stream processing, Product development regulation and safety.

Unit IV : Microbial Biotechnology Products – I

Recombinant and synthetic vaccines; Microbial insecticides; Microbial polysaccharides and polyesters; primary metabolites; secondary metabolites, microbial enzymes, Biotransformation.

Unit V : Microbial Biotechnology Products – II

Fuels and industrial chemicals; food and beverage fermentation; food additives and supplements; microbial biomass; biofuels; environmental biotechnology.

LECTURE SCHEDULE

Importance of the Identification and Classification of Microorganisms
Taxonomic Diversity of Bacteria
Characteristics of fungi and its classification
Classification of Bacteria according to Bergey’s manual
Molecular methods used in microbial classification
16S rDNA sequencing and Ribosomal Database Project
Convention of Biological Diversity, Microbial culture Preservation & Culture collection
Microbial Nutrition – Nutritional categories of microorganisms
Microbial growth kinetics – batch growth – continuous growth
Determination of growth of microbes – environmental influence on growth
Microbial metabolism
Microbial metabolism – regulating microbial metabolism
Fermentative metabolism
Isolation, screening of industrially important microorganisms
Strain improvement of industrially important microorganisms
Fermentation system – fermentor design and construction
Physical and chemical control in a fermentor
Fermentors/ bioreactors – types and classification
SSF – Factors that control SSF
Fermentation process development
Fermentation medium formulation
Principles and methods used for sterilization in fermentor
Scale up principles
Downstream processing – an overview
Large scale cell separation techniques
Mid Semester Examination
Cell disruption and Product recovery
Immobilization of cells and enzymes
Product development regulation and safety
Vaccines – recombinant and synthetic vaccines
Vaccines improvement – recent advances in vaccine development
Microbial Insecticide – Bt toxins
Microbial polysaccharides and its production
Microbial polyesters production
Microbial primary metabolites – Organic acid production
Microbial primary metabolites – Amino acid production
Microbial secondary metabolites – antibiotics
Commercial production of antibiotics
Physiology of antibiotic production
Commercial microbial enzymes production
Fuel and Industrial chemicals – overview
Biofuels – development and recent advances
Fermentation of diary products
Fermentation of traditional food products
Fermentation of dairy products
Microbial production of food additives and supplements
Microbial biomass production – SCP – different methods of SCP
Waste water and effluent treatment and composting
Biodegradation of xenobiotics
Genetic and metabolic aspects of biodegradation
Recent updates on trends, technologies and milestones in microbial biotechnology

SUGGESTED READINGS

Maloy SR, Cronan JE Jr., and Freifelder D, (2006), Microbial Genetics, Jones Bartlett

Publishers, Sudbury, Massachusetts.

Glazer, A.N and Nikaido, H. Eds. (2007). Microbial biotechnology: Fundamentals of

Applied Microbiology. Cambridge University Press.

Palanivelu P. (2016). Microbial Biotechnology and Biosafety Aspects – II Edition.

Twentyfirst Century Publications.

SUGGESTED WEBSITES

Microbial Biotechnology http://www.sfam.org.uk/en/journals/microbial-biotechnology.cfm
Microbial Biotechnology https://www.ncbi.nlm.nih.gov/pubmed/10631778

MBB 604 Advances in Crop Biotechnology (2+0)
OBJECTIVE
To discuss specialized topics on the application of genomics tools in specific crops.

THEORY
Unit I : Conventional and molecular techniques of crop improvement
Conventional and non-conventional techniques in crop improvement; Present status and recent developments on available genetic transformation and genomic tools for crop improvement. Diversity assessment, Germplasm characterization – diversity analysis; Molecular markers in Plant variety protection and hybrid purity testing.
Unit II : Methods of construction of genetic linkage maps
Mapping populations – F2s, RILs ,Backcross lines, NILs, NAM (Nested Association mapping), MAGIC (Multi-parent advanced generation inter-cross); Constructing molecular maps; integrating genetic, physical and molecular maps; GWAS (Genome Wide Association Studies); Navigating from genetic to physical map.
Unit III : Molecular mapping of complex traits and Marker Assisted Selection
Mapping simple and complex traits, QTL detection methods; Fine mapping ; Map based cloning/ positional cloning for gene discovery; Marker Assisted Selection (MAS); Gene/QTL introgression; MABB (Marker Assisted Back cross breeding) : Gene/QTL pyramiding strategies; Selected examples on marker assisted selection of qualitative and quantitative traits.
Unit IV : Genomic selection and High throughput genotyping platforms
Single Nucleotide Polymorphisms, Advances in SSR genotyping – Principle of Association mapping – GWAS ; DARTseq, SNP genotyping – Illumina’s Golden Gate Technology, Fluidigm; GBS (genotyping by sequencing),Nano pore sequencing-;Genomics Assisted Breeding ; Principles and methods of Genomic Selection.
Unit V : Application of Biotechnological tools in crop improvement
Discussion on application of molecular markers, genetic transformation and genomic tools for the genetic enhancement in some major field crops such as rice, wheat, maize, vigna, cotton, soybean, oilseeds, sugarcane etc., LECTURE
1.	Conventional versus non-conventional methods for crop improvement
2.	Recent developments on molecular markers for crop improvement
3.	Molecular markers for diversity assessment and hybrid purity testing
4.	Types of mapping populations – F2, RILs , NILS, Biparental mapping vs Multi-parent mapping, NAM (Nested Association mapping), MAIGIC
5.	Introduction to genome mapping- Construction of genetic linkage maps
6.	GWAS (Genome Wide Association Studies)
7.	Navigating from genetic to physical map
8.	Mapping simple and complex traits, QTL detection methods
9.	Map based cloning/ positional cloning for gene discovery
10.	Strategies in molecular breeding – Marker Assisted Selection (MAS); Genomics Assisted Breeding case studies
11.	Methods of Gene/QTL introgression
12.	MABB (Marker Assisted Back cross breeding) case studies
13.	Foreground and back ground selection for introgression of QTL
14.	Gene/QTL pyramiding strategies
15.	Crop databases and its application in mapping studies
16.	QTL mapping quantitative traits – days to flowering, plant height & grain yield
17.	Mid Semester Examination
18.	Meta analysis of QTLs
19.	QTL mapping quantitative traits – submergence, salinity, drought tolerance,
20.	QTL mapping for quantitative traits – nutritional traits, Nutrient use efficiency
21.	Association mapping strategy for complex traits improvement
22.	Synteny mapping in cereals
23.	Fine mapping traits with selected examples in cereal genomes
24.	Map-based positional cloning of agronomically important genes
25.	Marker assisted selection of qualitative traits
26.	Marker assisted selection of quantitative traits
27.	Genomic selection for crop improvement
28.	Application of biotechnological tools for genetic enhancement in rice
29.	Application of biotechnological tools for genetic enhancement in wheat
30.	Application of biotechnological tools for genetic enhancement in maize
31.	Application of biotechnological tools for genetic enhancement in cotton
32.	Application of biotechnological tools for genetic enhancement in Vigna & soybean
33.	Application of biotechnological tools for genetic enhancement in oilseeds
34.	Application of biotechnological tools for genetic enhancement in sugarcane

SUGGESTED READINGS

1.	D.J. Somers, (2009), Plant Genomics – Methods and Protocols, Humana Press, Business Media.
2.	C. Kole, A.G. Abott, (2008), Principles and Practices of Plant Genomics, Science Publishers.
3.	R.K. Varshney, R. Tuberosa, (2008). Genomics Assisted Crop Improvement, Springer.
4.	K. Meksem, G Kahl, (2005). The Handbook of Plant Genome Mapping: Genetic and Physical Mapping, Wiley-Blackwell.
5.	A.F. Griffiths et al, (2000). An Introduction to Genetic Analysis, WH Freeman & Co.
6.	Plant Molecular Breeding – http://base.dnsgb.com.ua/files/book/Agriculture/Plant Breeding/Plant-Molecular-Breeding.pdf
7.	Molecular Plant Breeding – http://download.bioon.com.cn/upload/201105/28152813_8350.pdf
8.	Molecular Markers and Marker-Assisted Breeding in Plants -http://cdn.intechopen.com/pdfs-wm/40178.pdf

MBB 605 Advances in Genomics and Bioinformatics	(3+0)
OBJECTIVE
To educate the students on the advances in genome analysis at various levels (DNA, mRNA and protein) and bioinformatics methods used in these analysis
THEORY
UNIT I: Genome analysis
Introduction to Genomics, Structural and Functional Genomics; Advances in Genome analysis – Advances in Genome mapping – QTL mapping, Association mapping, GWAS, MAGIC, Genomic Selection; DNA sequencing – Next generation sequencing methods, Advances in Whole genome sequencing; Genome sequencing projects and databases; Re-sequencing Projects – Rice 3K, Arabidopsis 1K and Human ENCODE etc., Phenomics, Speed Breeding
UNIT II: Transcriptomics
Regulation of gene expression; Functional genomics – Tools and Techniques; Transcriptomics – RTPCR, Northern, cDNA library, SSH Library, DD-RT-PCR, cDNA AFLP, SAGE, MPSS, Microarrays, RNA-Sequencing, small RNAs etc.,
Unit III: Proteomics, Metabolomics
Proteomics: Protein separation and 2D PAGE; mass spectrometry; LC-MS; Proteome databases; Protein microarrays; Structural Proteomics: Protein structure determination; Designing novel agrochemicals: Metabolomics; Phenomics
UNIT IV: Functional analysis of genes
Functional analysis of genes – Mutagenesis, Over-expression mutants, Knock out mutants; RNA-interference; Genome editing; Gene traps;; Yeast-two hybrid System; SNPs, TILLING, EcoTILLING; allele mining; Functional genomics projects in Rice, Arabidopsis; Applications of functional genomics in agriculture
UNIT V: Bioinformatics
Bioinformatics in genome sequence assembly and annotation; Gene prediction; Genomic databases – structure and data retrieval; Bioinformatics tools in microarrays, RNA-Seq and proteomics; Computational methods of miRNA prediction; In silico tools in protein structure prediction – Homology Modeling
THEORY SCHEDULE
1. Introduction to Genomics – Proteomics; Genomes
2. Organization in genome prokaryotes and eukaryotes
3. Physico-chemical properties of a genomes
4. Gene structure and Gene expression in prokaryotes and eukaryotes
5. Genetic exchange in prokaryotes and eukaryotes – principles
6. Introduction to genome maps – types – Genetic and physical maps
7. Introduction to molecular markers and its types
8. Genetic mapping – Linkage mapping
9. QTL mapping – principles & methods
10. Fine mapping of QTLs – Positional cloning
11. Association mapping – Principles, methods and applications
12. Marker Assisted Selection – Principles, methods and applications
13. Marker Assisted Back cross breeding – principles, methods and applications
14. Pyramiding multiple QTLs through marker assisted breeding
15. Advances in genotyping procedures – SSRs and SNPs
16. Marker Assisted Selection – Case studies – yield traits
17. Marker Assisted Selection – Case studies – abiotic stress tolerance
18. Marker Assisted Selection – Case studies – biotic stress tolerance
19. Advancements in MAS – NAM, MAGIC and Genomic Selection
20. Case studies in MAGIC and Genomic Selection
21. Introducing concepts of Phenomics and Speed breeding
22. Introduction to Physical mapping – types of physical maps
23. Methods of sequencing – Sanger method and Maxam & Gilbert method
24. Second and third generation sequencing methods
25. Metagenomics – 16s rRNA/shot gun
26. Genome sequencing strategies, tools and techniques
27. Genome sequencing assembly and annotation
28. Mid Semester Examination
29. Genome databases – humans, plants, microbes and animals
30. Genome databases – Re-sequencing of plant genomes (Rice, Arabidopsis)
31. Introduction to Functional genomics – Techniques in gene expression profiling
32. Transcriptomics – RT-PCR , Northern analysis
33. cDNA library screening – ESTs; DD-RT-PCR, cDNA AFLP – SAGE
34. Microarrays – Principle, methodology
35. Microarrays – data analysis and case studies
36. RNA sequencing – tools, techniques and data analysis
37. Case studies – Microarrays and RNA-Seq
38. Introduction to Proteomics – need for proteomics, Definition and types of proteomics; 2D PAGE
39. Mass spectrometry (LC-MS, Q-TOF, MALDI) and applications in proteomics
40. Applications of Proteomics in Agriculture, Designing novel agrochemicals
41. Metabolomics, Ionomics, Lipidomics, Glycomics, Phenomics
42. Assigning functions of a gene – Mutagenesis – Chemical, Physical and molecular mutagenesis
43. Over-Expression Mutants – Knock-out mutants; case studies
44. Genome editing – Principles and methods
45. Gene traps, Yeast two hybrid system etc.,
46. SNPs – Allele mining in crop improvement
47. Bioinformatics in miRNA prediction, validation and target prediction
48. Determination of Protein structure – computational tools
49. Bioinformatics in Modeling and Docking
50. Case studies in functional genomics
51. Case studies in Functional genomics
Suggested Readings
1. Stephen P. Hunt, Rick Livesey. 2009. Functional Genomics: A Practical Approach.
2. Christopher A. Cullis. 2005. Plant Genomics and Proteomics
3. Primrose. S. B. and Twyman. R. 2004. Principles of Genome Analysis and Genomics. Third edition University of York
4. Lesk A. M. 2014. Introduction to Bioinformatics. Oxford University Press, New York
5. Baxevanis AD and Ouellettee BFF. 2001. Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins. Wiley Interscience
6. Kessel A,2010. Introduction to Proteins: Structure, Function, and Motion, CRC Press
7. Weizhong Li and Adam Godzik. 2002. Discovering new genes with advanced homology detection. Trends in Biotechnology, 20:8, 315-316
8. Next-Generation DNA Sequencing Informatics, Second Edition by Stuart M. Brown. Cold Spring Harbor Laboratory Press (June 30, 2015) (Unit-1,2, and5)
Suggested websites
1. http://ocw.mit.edu/courses/
2. http://www.bx.psu.edu/old/courses/bx-fall10
3. http://www.ncbi.nlm.nih.gov/guide/training-tutorials/
4. http://www.ornl.gov/hgmis/medicine/pharma.html 161
5. http://www.bioinfo.rpi.edu/bystrc/courses/biol4540/biol4540.html
6. http://www.bioinfo.mbb.yale.edu/mbb452a/intro/
7. http://www.biology.ucsd.edu/others/dsmith/Bioinformatics.html
8. http://www.genome.org
9. www.tigr.org
10. http://www.ncbi.nlm.nih.gov/geo/
11. http://signal.salk.edu/cgi-bin/RiceGE
12. http://gene64.dna.affrc.go.jp/RPD

MBB 606 Commercial Plant Tissue Culture (1+0)
OBJECTIVE
To discuss the commercial applications of plant tissue culture in agriculture, horticulture, forestry medicine and industry.
THEORY Unit I : Techniques for Plant Mass Propagation through Tissue Culture
Commercial plant tissue culture lab organization. Micro propagation – plant multiplication, hardening – Low cost alternatives. Bio-reactors – Commercialized photoautotrophic micro propagation-automation technologies-Synthetic seed production.
Unit II : Commercial Scale Micropropagation
Commercial plant tissue culture and applications-case studies-banana, ornamentals, bamboo, sugarcane, plantation and tree crops, potato and medicinal plants.
Unit III : Quality Control and Guidelines for Certification & Accreditation of Labs
Quality control for plant tissue culture – Virus indexing and Genetic Fidelity testing. National certification system for TC plants-Guidelines and certification-TCCA, ATLs, TCPUs, TCPFs and RCs. Consortium of micro propagation research-commercial TC labs in India. Packing, transportation and quarantine for tissue cultured plants.
Unit IV : Plant cell cultures and applications
Cell suspension cultures, immobilization. Hairy root cultures – secondary metabolite production. Methods to enhance secondary metabolite production – precursor feeding, elicitation, immobilization, mutagenesis – Scale up through bioreactors. Production of useful compounds via biotransformation. Secondary metabolites of industrial and pharmaceutical importance – examples. Plant Stem Cell applications – cosmetic and therapeutic uses.
Unit V : Project preparation and recent developments
Project preparation for commercial plant tissue culture – management and marketing of TC plants. Recent patent applications in tissue culture – product and process patents. Visit to a commercial plant tissue culture laboratory.
LECTURE SCHEDULE
1.	Commercial plant tissue culture lab organization- Scope and Importance-overview
2.	Micro propagation – plant multiplication, hardening.
3.	Low cost alternatives in plant tissue culture.
4.	Commercialized photoautotrophic micro propagation-automation technologies-Synthetic seed production.
5.	Commercial plant tissue culture and applications-case studies-banana, ornamentals, bamboo
6.	Commercial plant tissue culture-sugarcane, plantation and tree crops, potato and medicinal plants.
7.	Quality control for plant tissue culture-Virus indexing and Genetic fidelity testing
8.	Mid Semester Examination
9.	National certification system for TC plants-Guidelines and certification-TCCA, ATLs, TCPUs, TCPFs and RCs.
10.	Consortium of micro propagation research-commercial TC labs in India.
11.	Packing, transportation and quarantine for tissue cultured plants.
12.	Establishment and maintenance of Cell suspension cultures. Hairy root cultures for secondary metabolite production.
13.	Bio-reactors – Design, types and considerations
14.	Methods to enhance secondary metabolite production – precursor feeding, elicitation, bio-transformation, immobilization, mutagenesis – Scale up through bioreactors.
15.	Secondary metabolites of industrial and pharmaceutical importance – examples. Plant Stem Cell applications – cosmetic and therapeutic uses.
16.	Project preparation for commercial plant tissue culture – management and marketing of TC plants.
17.	Recent patent applications in tissue culture – product and process patents. Visit to a commercial plant tissue culture laboratory.

SUGGESTED READINGS

1.	Bhojwani, S.S and Dantu, P. 2013. Plant Tissue Culture – An Introductory Text. Springer Publications
2.	Department of Biotechnology (2000) Plant tissue culture: from research to commercialization. A decade of support. Pub. DBT, Ministry of Science and Technology, Government of India
3.	Karl-Hermann Neumann, Ashwani Kumar and JafargholiImani. 2009. Plant Cell and Tissue Culture- A Tool in Biotechnology- Basics and Application. Springer-Verlag, Berlin Heidelberg
4.	Gamborg, O.L and G.C.Philips (eds.). 2013. Plant Cell, Tissue and Organ culture-Lab Manual. Springer Science & Business media.
5.	Razdan, M.K. 2003. Introduction to Plant Tissue Culture. (II Edn.). Science Publishers Inc, Enfield (NH) U.S.A.
6.	Roberta H. Smith, 2013. Plant tissue culture: Techniques and Experiments. Elsevier –Academic Press.
7.	Robert E. Bagwill. 2003. The legal aspects of plant tissue culture and patents . Patent and Trademark Office, U. S. Department of Commerce, Washington, D.C. 20231, U.S.A.
8.	George E.F., Hall, M.A. and De Klerk, G.J. 2008. Plant Propagation by Tissue Culture. Agritech. Publ. Herman, E.B. 2005-08. Media and Techniques for Growth, Regeneration and Storage. Agritech Publ.
9.	Teng, P.S. 2008. Bioscience Entrepreneurship in Asia. World Scientific.
10.	Trigiano, R.N and Gray D.J. 2011.Plant Tissue Culture Development and Biotechnology. CRC Press-Taylor and Francis group.pp.583

SUGGESTED WEBSITES

1.	DBT-NCSTCP guidelines: http://dbtncstcp.nic.in/
2.	Commercial Lab: https://www.saveer.com/planttissue.html
3.	NPTEL-Micropropagation: https://nptel.ac.in/courses/102103016/5
4.	PTC Lab-UAS-GKVK: http://planttissueculturelab.com/
5.	Cell Cultures: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915229/
6.	PTC Consumables Company: https://www.duchefa-biochemie.com/
7.	SPIC biotech: http://spic.in/spic-agro-biotech-centre-2/
8.	PTC lab supplies: https://phytotechlab.com/home

Minor courses

GPB 604 Cellular And Chromosomal Manipulations in Crop Improvement (2+1)

OBJECTIVE

This course focuses on the advanced techniques in analyzing chromosome structure and manipulations for genome analysis in crop species.

THEORY

Unit I:

Basics of cell – cell mechanisms – chemical foundations of cell – cell architecture – Prokaryote cells– Eukaryote cells – recent methods to study ultra structure of the cell – Membrane transport systems – cellular communications – evolution of cells and genetics of cell organelles – cell cycles and its control – role of CDK’s and cyclins – cell aging and cell death- Cytogenetic basis of differentiation in crop plants.

Unit II:

Totipotency – morphogenesis: in vivo and in vitro – different pathways of organogenesis and embryogenesis – applications of cellular manipulations – meristem culture – anther and pollen culture – ovule and ovary culture – embryo and endosperm culture – protoplast isolation, culture and fusion – in vitro mutant selection for biotic and abiotic stresses – In vitro germplasm conservation – somaclonal variation.

Unit III:

Organisation and structure of genome; genome size and variation – organelle genome and nuclear DNA organisation – variation in DNA content – AT/GC ratio – C value paradox – fine structure of gene : Introns and extrons – availability and advantages –

repetitive sequences.

Unit IV:

Karyotyping: importance and procedure – chromosome banding – distant hybridisation – barriers in interspecific and intergeneric hybridisation – role of wild species in crop improvement. Role of autopolyploidy and allopolyploidy in crop evolution and crop breeding.

Unit V:

Genome mapping – conventional and molecular based approaches – various types of markers – advantages and disadvantages – integration of classical linkage maps and molecular maps – linkage maps and comparative mapping – study of synteny in crops – physical mapping and techniques involved – transposon tagging – chromosome walking – centromere mapping – genome maps. MAS in introgression breeding and improvement of complex traits – plant gene transfer – Agrobacterium mediated gene transfer – recent approaches – genomics, proteomics, metabolomics and other related areas.

PRACTICALS

Chromosome banding – advanced techniques in chromosome study – fluorescent microscopy – media preparation – culture of different explants – meristem culture – anther culture – embryo culture – embryo rescue techniques – in vitro mutant selection – genomic DNA isolation – laboratory techniques involved in RFLP analysis – PCR based DNA analysis – techniques of plant gene transfer.

LECTURE SCHEDULE

Basics of cell and cell mechanisms. Chemical foundations of cell and cell architecture
Prokaryote cells vs Eukaryote cells: Recent methods to study ultra structure of the cell
Membrane transport systems; Cellular communications
Evolution of cells and genetics of cell organelles
Cell cycles and its control; Role of CDK’s and cyclins – cell aging and cell death
Cytogenetic basis of differentiation in crop plants
Totipotency of cells; Morphogenesis in vivo and in vitro
Different pathways of organogenesis and embryogenesis
Applications of cellular manipulations: Meristem culture in production of disease free

plants

Applications of cellular manipulations: Anther and pollen culture, ovule and ovary

culture

Applications of cellular manipulations: embryo and endosperm culture
Applications of cellular manipulations: protoplast isolation, culture and fusion
Applications of cellular manipulations: in vitro mutant selection for biotic stresses
Applications of cellular manipulations: in vitro mutant selection for abiotic stresses
Applications of cellular manipulations: In vitro germplasm conservation
Applications of cellular manipulations: somaclonal variation
Mid Semester Examination
Organisation and structure of genome: Genome size and variation
Organisation of organelle genome and nuclear DNA
Variation in DNA content – AT/GC ratio; C value paradox
Fine structure of gene; Introns and extrons; availability and advantages
Repetitive sequences and its role in crop evolution
Karyotyping – its importance and procedure; chromosome banding
Distant hybridisation; barriers in interspecific and intergeneric hybridisation; Role of wild species in crop improvement.
Role of autopolyploidy and allopolyploidy in crop evolution and crop breeding
Genome mapping – conventional approaches and molecular based genome mapping
Various types of molecular markers – advantages and disadvantages
Integration of classical linkage maps and molecular maps
Linkage maps and comparative mapping; study of synteny in crops
Physical mapping and techniques involved
Transposon tagging, chromosome walking and centromere mapping
Genome maps and MAS in introgression breeding and for improvement of complex traits
Plant gene transfer: Agrobacterium mediated gene transfer – recent approaches
Genomics, proteomics, metabolomics and other related areas.

PRACTICAL SCHEDULE

Chromosome banding
Fluorescent microscopy – its use in chromosome study and studying fertilization barriers
Media preparation and establishing culture
Cytological observation and chromosomal analysis in cultured cells
Methodologies for meristem culture
Pre-treatment for anther culture and methodologies in anther culture
Embryo culture and embryo rescue techniques
Protoplast isolation methods and fusion techniques
Steps involved in in vitro mutant selection
Steps in RFLP analysis – DNA extraction
Restriction enzyme digestion and Electrophoretic techniques
Southern hybridisation
Polymerase chain reaction techniques
RAPD and its application in mapping
Other PCR based markers and their application in mapping
Techniques of plant gene transfer
Final Practical Examination

SUGGESTED READINGS

Ammirato, P. V., Evans, D. A., Sharp, W. R. and Yamada, Y. (Eds.) 1984. Handbook of

Cell Culture. Vol. 3. Crop Species. Macmillan Publishing Co. New York. Collier

Macmillan Publishers. London. 620pp.

Bhojwani. S. S. ad Razdan, M. K. 1983. Plant Tissue Culture: Theory and Practice.

Elsevier, Amsterdam. 502pp.

Chaleff, R. S. 1981. Genetics of Higher Plants: Applications of Cell Culture. Cambridge

University Press, Cambridge. 184pp.

Clark, M. S and W. J. Wall. 1996. Chromosomes: The complex code. Chapman and Hall,

London. 345p

Evans, D. A., Sharp, W. R. and Ammirato, P. V. (Eds.) 1986. Handbook of Cell Culture.

Vol. 4. Techniques and Applications. Macmillan Publishing Co., New York Collier

Macmillan Publishers London. 697pp.

Foster, G. D and D. Twell. 1996. Plant gene isolation: Principles and practice. John

Wiley & Sons. Chichester. 426p.

Green, C. E. Somers, D. A., Hackett, W. P. and Beisboer, D. D. (Eds) 1987. Plant Tissue

and Cell Culture. Plant Biology. Vol. 3. Alan R. Liss Inc., New York. 509pp.

Gustfson, J. P (Ed.). 1984. Gene Manipulation in Crop Improvement. Plenum Press, New

York. 668p.

Paterson, A. H. (Ed). 1996. Genome Mapping in Plants. R. G. Landes Company, Austin.

330p.

Primrose, S. B. 1991. Molecular Biotechnology. Blackwell Scientific Publications,

London. 196p.

Schultz-Schaeffer, J. 1981. Cytogenetics: Plants, animals and human. Springer-Verlag,

Berlin.

Sybenga, 1985. Cytogenetics. Oxford University Press, London

PLP 605 Climate Change and Crop Growth (2+0)

OBJECTIVE

To impart knowledge about climate change and its implication on crop growth.

THEORY

Unit I : History of Climate Change and Water Cycle

History and evidences of climate change and its implications – International conventions and

initiatives on climate change – Effect of climate change on monsoons, hydrological cycle and water

availability – Impacts of climate change on Indian agriculture.

Unit II : GHG Emission and Ozone Hole

Natural and anthropogenic activities causing greenhouse gases (GHG) production – Influence of

agricultural practices on GHG production – Chemistry of temperature raise and ozone hole

formation by GHG – UV radiation effects on growth, physiological process and yield.

Unit III : Climate Change Drivers and Crop-Pest Interactions

Impact of climate change driver on phenology, distribution, and regeneration biology – Futureproof

crops for improving climate resilience – Projections of climate change effects on crop-weed,

crop-insect and crop-disease interaction.

Unit IV : Effect of Climate Change Drivers on Physiological Processes

Impact of elevated CO2, high temperature, drought, ozone, CH4, SO2, NO2 on phenology and yield

processes – Direct and indirect effects of climate change drivers on net carbon assimilation,

respiration, water relations and yield components – Interactive effect of elevated CO2 and

temperature on crop growth and productivity – Interactive effect of ozone, UV-B, SO2 on crop

growth and productivity.

Unit V : Crop Ecosystem Responses and Mitigation Strategies

Crop ecosystems responses to climate change – rice, wheat, maize, sorghum and millets,

legumes, cotton, sugarcane, mustard, vegetable, fruit and tuber crops – Approaches to improve

the crop adaptation to climate change by agronomic, plant breeding and biotechnological

methods – Carbon sequestration and carbon trading.

LECTURE SCHEDULE

History and evidences of climate change and its implications
International conventions and initiatives on climate change
Effect of climate change on monsoons and hydrological cycle
Effect of climate change on water availability
An overview of impacts of climate change on Indian agriculture
Natural and anthropogenic activities causing GHG production
Influence of agricultural practices on GHG production
Chemistry of global warming by GHG and ozone hole formation
Effect of UV radiation on growth, physiological process and yield
Impact of climate change driver on plant phenology, distribution, and regeneration

biology

Future-proof crops: challenges and strategies for climate resilience improvement
Impact of climate change drivers on crop-weed interaction

1067

Impact of climate change drivers on crop-insect interaction
Impact of climate change drivers on crop-disease interaction
An overview of effects of elevated ozone, CH4, SO2, NO2 on phenology and yield

processes

An overview of effects of elevated CO2, drought and high temperature on phenology,

and yield processes

Mid Semester Examination
Direct and indirect effects of climate change drivers on net carbon assimilation and

respiration

Direct and indirect effects of climate change on water relations and yield components
Interactive effect of elevated CO2 and temperature on crop growth and productivity
Interactive effect of ozone, UV-B, SO2 on crop growth and productivity
Crop ecosystems responses to climate change – rice
Crop ecosystems responses to climate change – wheat
Crop ecosystems responses to climate change – maize, sorghum and millets
Crop ecosystems responses to climate change – legumes and cotton
Crop ecosystems responses to climate change – sugarcane
Crop ecosystems responses to climate change – Mustard
Crop ecosystems responses to climate change – vegetables and tuber crops
Crop ecosystems responses to climate change – fruits crops
Agronomic approaches to improve the crop adaptation to climate change
Breeding approaches to improve the crop adaptation to climate change
Biotechnological approaches to improve the crop adaptation to climate change
Molecular mechanism of GHG effects on plants
Carbon sequestration and carbon trading

SUGGESTED READINGS

Reddy, K.R., and Hodges, H.F. 2000. Climate Change and Global Crop

Productivity. CABI.

Abrol, Y.P., and Gadgil, S. (Eds.). 1999. Rice in a Changing Climate.
Watson, R.T., Zinyowera, M.C., and Moss, R.H. 1998. The Regional Impacts of Climate

Change – an Assessment of Vulnerability. Cambridge University Press.

SUGGESTED WEBSITES

https://www.ipcc.ch/
https://www.globalchange.gov
https://www.nature.com/nclimate/

PLP 611 Advances In Plant Responses To Abiotic Stresses (2+1)

OBJECTIVE

To apprise the students regarding the physiological and molecular basis of abiotic stress responses in plants.

THEORY

Unit I : Water Stress

Abiotic stresses – Classification – impact on crop production – Water stress: Water deficit and

excess – Drought stress in plants – Development of water deficits – Physiological processes affected

by drought. Drought tolerance mechanisms – Physiological and morpho-anatomical traits for plant

adaptation to drought. Morpho-physiological responses to drought – Molecular responses of

plants to drought – Stress proteins – ABA mediated signaling and tolerance – antioxidant defenses

against drought stress. Approaches for the development of genotypes tolerant to drought.

Submergence stress / water logging – Plant responses to water logging – Anatomical, morphophysiological alterations – Physiological strategies, hormonal signaling and regulations and ROS metabolism for flooding tolerance. under water logging – Development of genotypes tolerant to

flooding – Molecular breeding.

Unit II : Salt Stress

Salt stress: Classification – Characteristics – Salinity stress: Salinity effects at cellular and whole

plant level. Physiological constraints imposed by salinity. Salinity tolerance – species variation –

Anatomical adaptation. Avoidance and tolerance mechanism of salt stress – SOS pathways and ion

homeostasis – Mechanisms of salt stress sensing and signaling – Key physiological mechanisms

conferring salinity tolerance in plants – Responses of plants under non-optimal soil pH- alkalinity,

sodicity. Molecular responses of plants to salinity – ABA mediated signaling and tolerance.

Approaches for the development of genotypes tolerant to salinity.

Unit III : High Temperature stress

Temperature stress – classification – High temperature/heat stress – Morpho-physiological and

biochemical changes in response to high temperature stress. High temperature stress tolerance

mechanisms – Heat-shock proteins (HSPs) – ROS Scavenging mechanisms. Molecular basis of

thermotolerance – APX, ChyB and CodA genes.

Unit IV : Low Temperature stress

Low temperature stress – chilling stress – Plant responses to chilling temperatures – phase

transition of membranes. Effects of chilling on biochemical and molecular processes – Signal

transduction pathways. Freezing stress – Physiological responses – phase transition – ice

nucleation and super cooling. Low temperature stress tolerance mechanisms – variation in fatty

acid composition – Cryoprotection – Role of ABA, LEA, DHN and antifreeze proteins on cold

tolerance. Molecular basis of freezing tolerance – CBF gene – cold response pathway – ICE1

pathway for cold regulation.

Unit V : Radiation stress

Radiation stress – Introduction – High light intensity –Responses of plants to high light – ROS

production – photo inhibition. Characters of heliophytes and sciophytes. Mechanism of high light

stress tolerance – Anatomical, physiological and molecular basis of adaptations to high light. Low

light intensity- Physiological responses of plant to low light – etiolation, plastid development and

adaptive mechanisms – gene expression. Crosstalk between plant hormones under abiotic

stresses. Heavy-metal stress in plants – Physiological responses and adaptations. Use of

exogenous protectants in mitigating abiotic stress effects in plants.

PRACTICALS

Stress imposition and quantification: Drought induction using different methods, Determination of

osmotic potential and osmotic adjustment – WUE – aerenchyma cells under flooding stress –

structural carbohydrates- Screening techniques for salt tolerance – Estimation of sodium

potassium ratios – antioxidant enzyme systems – lipid peroxidation – CSI and Sullivan’s heat

tolerance test/Membrane integrity – chlorophylls under high and low light conditions -Estimation

of GABA content – desaturase enzyme – Gene expression analysis in stress affected plants using

RT-PCR- Phenotyping approaches for water and salt stress – Bioinformatics platforms for sequence

and structure analysis of stress proteins.

LECTURE SCHEDULE

Abiotic stresses – Classification – impact on crop production – Water stress: Water

deficit and excess – Drought stress in plants – Development of water deficits –

Physiological processes affected by drought.

Drought tolerance mechanisms: Postponement, avoidance and tolerance –

Understanding the physiological and morpho-anatomical traits for plant adaptation to

drought – phenology, root system, anatomical modifications to reduce water loss.

Physiological responses of plants to drought – oxidative damage – ROS scavenging

system, Osmoprotectants – osmotic adjustment – chlorophyll fluorescence and

reflection indices,

Effective use of water/WUE – Carbon isotope discrimination, nutrient uptake and

assimilation.

Molecular responses of plants to drought – Stress proteins – ABA mediated signaling

and tolerance – antioxidant defenses against drought stress.

Approaches for the development of genotypes tolerant to drought – Molecular

breeding

Biotechnological approaches to improving drought tolerance- Identification of

candidate for water stress tolerance

Submergence stress / flooding / waterlogging – Plant responses to waterlogging –

morphological and anatomical alterations – Physiology and metabolism – Nutrient

uptake and transport.

Plant’s adaptation to waterlogging – Physiological strategies and hormonal signaling

and regulations for flooding tolerance – Phytohormone-mediated stomatal response,

escape and quiescence strategies in plants under flooding stress.

ROS metabolism under waterlogging – antioxidant defense – signal transduction

pathways that regulate hypoxia responses – Development of genotypes tolerant to

flooding – Molecular breeding.

Salt stress: Classification – Characteristics – Salinity stress: Salinity effects at cellular

and whole plant level.

Physiological constraints imposed by salinity – impact on plant growth, osmotic stress,

ionic imbalance, oxidative stress – metabolic disturbances – photosynthesis, Na+

toxicity, Cl- toxicity.

Salinity tolerance – species variation – genetic variability, salt glands and bladders,

changes in the root anatomy, control over leaf transpiration.

Avoidance and tolerance mechanism of salt stress – SOS pathways and ion homeostasis

– Mechanisms of salt stress sensing and signaling – Key physiological mechanisms

conferring salinity tolerance in plants- salt exclusion, extrusion and sequestration

mechanisms

Responses of plants under non-optimal soil pH- alkalinity, sodicity.
Molecular responses of plants to salinity – ABA mediated signaling and tolerance
Mid Semester Examination
Approaches for the development of genotypes tolerant to salinity – Molecular breeding
Biotechnological approaches to improving salinity tolerance- Identification of

candidate genes for salt stress tolerance.

Temperature stress – classification – High temperature/heat stress – Morphophysiological

and biochemical changes in response to high temperature – effect on

membrane property and photosynthesis

Response of plants to high temperature – photosynthetic machinery – pigments,

photosyntem I & II, electron transport chain, oxygen evolving complex, thylakoid

membranes – CO2 fixation, stomatal activity – production of reactive oxygen species.

High temperature stress tolerance mechanisms – membrane state, structure and

composition, role of osmolytes – Membrane stability – cytosol Ca signaling

High temperature tolerance mechanisms – Heat-shock proteins (HSPs), – ROS

Scavenging mechanisms – enzymatic and non enzymatic detoxification of ROS.

Molecular basis of thermo tolerance – APX, ChyB and CodA genes.

Low temperature stress – chilling stress – Plant responses to chilling temperatures –

stunted stature, chilling injuries – phase transition of membranes – altered

metabolisms.

Effects of chilling on biochemical and molecular processes – photosynthesis – lipids –

sugars – compatible solutes – ROS – stress-related proteins.

Signal transduction pathways in response to chilling – calcium, protein kinases/protein

phosphatases, lipid signaling, reactive oxygen species and nitric oxide.

Freezing stress – Physiological responses – phase transition – ice nucleation and super

cooling – Low temperature stress tolerance mechanisms – variation in fatty acid

composition – Cryoprotection – Role of ABA, LEA and DHN – antifreeze proteins on cold

tolerance.

Molecular basis of freezing tolerance – CBF gene – cold response pathway – ICE1

pathway for cold regulation.

Radiation stress – Introduction –High light intensity –Responses of plants to high light –

ROS production – photo inhibition – photo oxidation. Characters of heliophytes and

sciophytes.

Mechanism of high light stress tolerance – Anatomical, physiological and molecular

basis of adaptations to high light –

Low light intensity- Physiological responses of plant to low light – etiolation, plastid

development and adaptive mechanisms – gene expression – Phytochromes and

hormones.

Crosstalk between plant hormones under abiotic stresses.
Heavy-metal stress in plants – Physiological responses and adaptations.
Use of exogenous protectants in mitigating abiotic stress effects in plants

PRACTICAL SCHEDULE

Drought induction using different methods
Determination of osmotic potential and osmotic adjustment
Determination of water use efficiency at single leaf and whole plant level.
Study of aerenchyma cells under flooding stress
Estimation of structural carbohydrate contents under flooding stress
Screening techniques for salt tolerance – Hydroponics and pot culture experiments to

induce salt stress

Estimation of sodium potassium ratios in leaves and roots of plants under salt stress
Estimation of antioxidant enzyme systems under different stresses
Determination of lipid peroxidation by estimating MDA content
Assessment of high temperature tolerance – CSI and Sullivan’s heat tolerance

test/Membrane integrity

Observation and estimation of chlorophylls in leaves under high and low light

conditions.

Estimation of GABA content
Estimation of desaturase enzyme activity
Genomic/plasmid DNA/RNA isolation – Gene expression analysis in stress affected

plants using RT-PCR

Assessing plant stress indices using Chlorophyll fluorescence
Phenotyping approaches for water and salt stress
Final Practical Examination

SUGGESTED READINGS

Parvaiz Ahmad, M.M. Azooz, M.N.V. Prasad. 2013. Salt Stress in Plants- Signalling,

Omics and Adaptations. Springer Science+Business Media New York.

S. M. Zargar, M. Y. Zargar (eds.), 2018. Abiotic Stress-Mediated Sensing and Signaling

in Plants: An Omics Perspective, https://doi.org/10.1007/978-981-10-7479-0_1.

Springer Nature Singapore Pte Ltd.

J.M. Al-Khayri et al. (eds.), 2013. Advances in Plant Breeding Strategies: Agronomic,

Abiotic and Biotic Stress Traits, DOI 10.1007/978-3-319-22518-0_1. Springer

International Publishing Switzerland.

Sergey Shabala. 2017. Plant Stress Physiology, 2nd Edition. CAB International.UK
Ammar El-Akhdar, 2010. Advances in molecular breeding towards drought and salt

tolerant crops.

Madhava Rao KV, Raghavendra, AS and Janardhan Reddy K. 2006. Physiology and

Molecular Biology of Stress Tolerance in Plants.

SUGGESTED WEBSITES

Plantsress.com
www.plantphysiol.org

PLP 603 Molecular Approaches For Improving Physiological Traits (2+0)

OBJECTIVE

To impart knowledge to improve the physiological traits using molecular approaches; To understand the principles and methods of breeding and molecular genetics of crop improvement.

THEORY

Unit I : Physiological traits and phenotyping

Physiological traits – Major physiological process and metabolisms –Growth – Photosynthesis –

Water Use Efficiency – Nutrient Use Efficiency – Trait based breeding – Advantages -Phenotyping

of large germplasm -Concept of segregation, independent assortment and linkage.

Unit II : Development of Mapping populations

Concept of molecular markers – Types of marker systems – Development of mapping populations

– Advantages of association mapping – concept of linkage, LD decay and population structure –

Statistical analysis for phenotypic and molecular data. Assessment of genetic parameters –

Strategies for QTL introgression – Marker Assisted Selection (MAS). Map based cloning – novel

genes – Allele mining.

Unit III : Transgenic approaches

Introduction to GMOs – application in crop improvement – gene mining – sequence structure –

function analysis – bioinformatics tools, identification of candidate genes for various physiological

process associated with specific traits -potential benefits of transgenic crops.

Unit IV : Gene cloning and transformation

Cloning full-length candidate genes – stress inducible promoters – strategies – gene stackingtissue

specific expression –functional validation of genes -Transformation of crop plants-

Agrobacterium -particle gun – scorable and selectable markers.

Unit V : Evaluation of transgenics and Bio-safety regulations

Selection of transformants- molecular analysis – qRT-PCR – Southern – Northern analysis –

immunoassays -estimation of copy number – Evaluation of transgenics on the basis of gene

function. Generation of T1 populations – event characterization -Issues related to Bio-safety and

Registration of Transgenic Agricultural Organisms- methods to detect GMOs.

LECTURE SCHEDULE

Physiological traits with relevance to growth and development.
Physiological traits associated with photosynthetic parameters
Physiological traits associated with abiotic stress tolerance and nutrient acquisition.
Approaches for accurate phenotyping of large germplasm accessions and/or mapping populations.
The advantages of “Trait based” breeding approaches and its advantages.
Concept of segregation, independent assortment and linkage.
The concept of molecular markers, various types of Dominant and Co-dominant marker systems.
Relevance and development of mapping populations
Genetic analysis using marker systems.
Advantages of association mapping and the concept of linkage, LD decay and

population structure.

Statistical analysis to assess the variance in phenotypic traits and molecular data.
Assessment of genetic parameters such as heritability, genetic advance etc.
Strategies for QTL introgression and Marker Assisted Selection (MAS).
Map based cloning of novel genes and alleles.
Allele mining
Transgenic approach in improving physiological processes- Introduction to GMOs and

application in crop improvement

Mid Semester Examination
Gene mining, sequence structure & function analysis using bioinformatics tools.
Identification of candidate genes associated with photosynthetic efficiency
Identification of candidate genes associated with water use efficiency
Identification of candidate genes associated with nutrient acquisition.
Cloning full-length candidate genes.
Promoters : Types; Markers : Selectable and scorable markers.
Strategies to clone and characterize and make constructs for specific crops.
Gene stacking strategies and tissue specific expression and functional validation of

genes.

Transformation of crop plants –Vectors and direct Agrobacterium based transformation.
Transformation of crop plants – Particle gun transformation
Selection of transformants- molecular analysis on the basis of qRT – PCR, Southern,

Northern analysis and immunoassays.

Estimation of copy number.
Concept of desirable number of independent events.
Evaluation of transgenics on basis of empirical/physiological/biochemical process

under specific conditions on the basis of gene function.

Generation of T1 populations, event characterization and generation of molecular data

as per the regulatory requirements.

Issues related to Biosafety and Registration of Transgenic Agricultural Organisms.
Methods to detect GMOs from agricultural products.

SUGGESTED READINGS

Arbind,K. Choudhary et al., 2018. Integrated Physiological and Molecular approaches

to improvement of abiotic stress tolerance in pulse crops of semi-arid tropics. The crop

Journal, 6(2).

NishanthBhanu et al., 2016. Molecular mapping and breeding of Physiological traits.

Advances in Plant and Agriculture Research. 3(6).

Allele mining – an approach to discover allelic variation in crops. 2017. Editors.

Bhanu,Singh and Hemantharaj.

SUGGESTED WEBSITES

http://bioinformatics.psb.ugent.be/webtools/plantcare/html/
http://pgrc.ipk-gatersleben.de/cr-est/
http://www.ncbi.nlm.nih.gov

PAT 604 Molecular Basis of Host-Pathogen Interaction (2+1)

OBJECTIVE

To understand the concepts of molecular biology and biotechnology in relation to host-pathogen

interactions

THEORY

Unit I :

Molecular basis of host-pathogen interactions-pathogen virulence, aggressiveness, regulation of

infection processes-cAMP signaling and MAP kinase pathways-genetics of virulencepathogenicity

genes in plant pathogens, toxins-mode of action-role of toxins in disease development- cell wall -and cutin-degrading enzymes, hormones, extracellular polysaccharides variability in plant pathogens, mechanisms of variability, physiological races of pathogens

Unit II :

Host plant resistance-vertical and horizontal resistance, non-host resistance-recognition system,

elicitors-endogenous and exogenous elicitors, general and race-specific elicitors-receptor sites

for elicitor, chemical nature of elicitors-signal transduction- intracellular signal transduction second

messenger systems-calcium ion- protein kinases- phospholipases- proton pump- ATPases-G-proteins- H2O2- ethylene- systemic signal transduction- oligogalacuronides- salicylic acid-jasmonic acid- ethylene- abscissic acid-signal crosstalk, signal molecules, quorum sensing suppressors

Unit III :

Genetics of disease resistance- Gene-for-gene theory, avirulence (avr) genes, characteristics of

avr gene-coded proteins, hrp genes, protein-for-protein, Resistance (R) genes of plants, R -gene

expression and transcription profiling, mapping and cloning of resistance genes, structure and

classes of resistance genes, genomic organization of resistance genes

Unit IV :

Host defence mechanisms, morphological and anatomical resistance, phytoanticipins-phenolics,

glucosinolates, cyanogenic glucosides, saponins, steroid alkaloids, dienes, induced structural

and biochemical defences- cell wall modifications-papilla-callose deposition, HRGP

accumulation-lignification-suberization – phytoalexins, defence -related proteins, hypersensitive

reaction and its mechanisms, reactive oxygen species, systemic acquired resistance

Unit V :

Biotechnology and disease management-Different methods of Gene transfer-development of

disease resistance plants using genetic engineering approaches; fungal resistance-resistance

genes, antifungal protein genes-chitinase, glucanase, TLP, RIP, Thionins, lipid transfer proteins,

antimicrobial peptides, expression of phytoalexins, detoxification genes, peroxidase,

polygalacturonase-inhibiting protein, NPR1 protein; bacterial resistance-lytic peptides,

lysozymes, detoxification genens, cloned resistance genes, plant defense genes; Virus resistancepathogen-

derived resistance- coat protein, movement protein, replicase, satellite RNA, RNA

silencing, antibody-based resistance, cloned resistance genes, antiviral protein genes; biosafety

issues related to GM crops.

PRACTICALS

Isolation of elicitor from fungal mycelium, Purification of elicitor, Isolation and purification of toxin,

Estimation of total phenols, Assay of PAL and PO, Estimation of lignin content, Analysis of PR–

proteins by SDS-PAGE, Assay of β-1, 3 – glucanase activity, Assay of chitinase activity, Purification

of chitinase, Western blot analysis of defense-related proteins, Isolation of DNA and analysis,

Isolation of RNA and analysis, Extraction of plasmids, Bacterial transformation, Cloning and

characterization of defense related genes

LECTURE SCHEDULE

Molecular basis of host-pathogen interaction- pathogen virulence, aggressiveness
Regulation of infection processes – cAMP signaling and MAP kinase pathways
Pathogenicity genes in plant pathogens – toxins- toxins-mode of action-role of toxins in

disease development

Pathogenicity genes in plant pathogens-cell wall and cutin-degrading enzymes,

hormones

Extracellular polysaccharides
Variability in plant pathogens- mechanisms of variability and physiological races of

pathogens

Host plant resistance-vertical and horizontal resistance, non-host resistance
Elicitors-endogenous and exogenous elicitors, general and race-specific elicitors
Chemical nature of elicitors
Receptor sites for elicitors
Signal transduction- intracellular signal transduction- second messenger systemscalcium

ion- protein kinases- phospholipases- proton pump- ATPases- G-proteins-

H2O2- ethylene-

Systemic signal transduction- oligogalacuronides- salicylic acid- jasmonic acidethylene-

abscissic acid

Signal crosstalk and Quorum sensing
Suppressors
Genetics of disease resistance- Gene-for-gene theory
Avirulence (avr) genes, characteristics of avr gene-coded proteins, hrp genes,
Mid Semester Examination
Resistance (R) genes of plants, R-gene expression and transcription profiling
Mapping and cloning of resistance genes
Structure and classes of resistance genes, genomic organization of resistance genes
Host defence mechanisms- morphological and anatomical resistance- Phytoanticipinsphenolics,

glucosinolates, cyanogenic glucosides, saponins, steroid alkaloids, dienes,

Induced structural and biochemical defences- cell wall modifications-papilla-callose

deposition, HRGP accumulation-lignification-suberization

phytoalexins
Defense-related proteins
Hypersensitive reaction and its mechanisms
Reactive oxygen species
Systemic acquired resistance
Biotechnology and disease management-Different methods of Gene transfer
Transgenic plants with fungal resistance- cloned resistance genes, antifungal protein

genes-chitinase, glucanase, TLP, RIP, Thionins, lipid transfer proteins, antimicrobial

peptides,

Expression of phytoalexins, detoxification genes, peroxidise, polygalacturonaseinhibiting

protein, NPR1 protein

Bacterial resistance-lytic peptides, lysozymes, detoxification genens, cloned resistance

genes, plant defense genes

Virus resistance-pathogen-derived resistance- coat protein, movement protein,

replicase, satellite RNA, RNA silencing,

33 & 34 Antibody-based resistance, cloned resistance genes, antiviral protein genes and

Biosafety issues related to GM crops.

PRACTICAL SCHEDULE

Isolation of elicitor from fungal mycelium
Purification of elicitor
Isolation and purification of toxin
Estimation of total phenols
Assay of PAL and PO
Estimation of lignin content
Analysis of PR– proteins by SDS-PAGE
Assay of β-1, 3 – glucanase activity
Assay of chitinase activity
Purification of chitinase
Western blot analysis of defense-related proteins
Isolation of DNA and analysis
Isolation of RNA and analysis
Extraction of plasmids
Bacterial transformation
Cloning and characterization of defense related genes
Final Practical Examination

SUGGESTED READINGS

1.Datta, S.K. and Muthukrishnan, S. 1999. Pathogenesis- Related Proteins in Plants, CRC

Press, Florida, USA, p. 291

2.Goodman, R.N., Kiraly, Z. and Wood, K.R. 1986. The Biochemistry and physiology of

plant diseases. University of Missouri Press, Columbia, MO, USA pp. 433.

3.Gurr, S.J. Mc Pherson, M.J. and Bowles, D.J. 1992. Molecular Plant Pathology: A Practical

approach Vol. II. IRL Press, Oxford, England, p. 304.

4.Punja, Z.K. 2004. Fungal Disease Resistance in Plants – Biochemistry, Molecular Biology

and Genetic Engineering, Food Products Press (Haworth Press), New York, p. 266.

5.Punja, Z.K., De Boer, S.H., Sanfacon, H.2008. Biotechnology and Plant Disease

Management, CABI Publishing, P. 574.

6.Vidhyasekaran, P. 1988. Physiology of disease resistance in plants. Vol. I. CRC Press,

Florida, p. 149.

7.Vidhyasekaran, P. 1988. Physiology of disease resistance in plants. Vol. II. CRC Press,

Florida, p. 127.

8.Vidhyasekaran, P. 1997. Fungal pathogenesis in plants and crops: Molecular biology

and host defense mechanisms. Marcel Dekker, New York p. 553.

Chet I. 1993. Biotechnology in Plant Disease Control. Jhon Wiley & Sons, New York.
Mathew JD. 2003. Molecular Plant Pathology.Bios Scientific Publ.,UK.

11.Ronald PC. 2007. Plant-Pathogen Interactions: Methods in Molecular Biology.Humana

Press, New Jersey.

SUGGESTED WEBSITES

www.scirp.org/journal/PaperInformation.aspx?paperID=3471
www.cplbookshop.com/glossary/G392.html
www.ovid.com/…/product_CABI-Plant-Science-Book-Collection_13051
www.aensiweb.com/aejsa/2008/1-18.pdf
https://www.overdrive.com/mims-pathogenesis-of-infectious-disease
http://www.crcpress.com/product/isbn/9780849398674
www.apsnet.org/edcenter/advanced/topics/…/PHI-BiologicalControl.pdf
http://link.springer.com/chapter/10.1007/978-94-011-2656-4_7#page-1
http://www.cabdirect.org/abstracts/20113026296.html

III. Supporting Courses

GPB 601 Plant Genetic Resources and Their Utilization (2+0)

OBJECTIVE

To provide information about Plant Genetic Resources exploration, collection, evaluation,

documentation, maintenance and use of plant genetic resources for crop improvement.

THEORY

Unit I :

Historical perspectives and need for PGR conservation; Importance of plant genetic resources;

Taxonomical classification of cultivated plants; Gene pool: primary, secondary and tertiary;

Centres of origin and global pattern of diversity; Principles, strategies and practices of

exploration, collection, characterization, evaluation and cataloging of PGR; Plant quarantine and

phytosanitary certification; Germplasm introduction and exchange. Germplasm conservation- in

situ, ex situ, and on-farm; short, medium and long term conservation strategies for conservation

of orthodox seed and vegetatively propagated crops; Registration of plant genetic resources.

Principles of in vitro and cryopreservation.

Unit II :

PGR data base management; Multivariate and clustering analysis, descriptors; National and

international protocols for PGR management; PGR for food and agriculture (PGRFA); PGR access

and benefit sharing; Role of CGIAR system in the germplasm exchange.

Unit III :

Journey from wild to domestication; Genetic enhancement- need for genetic enhancement;

Genetic enhancement in pre Mendelian era and 21st century; Genetic enhancement and plant

breeding; Reasons for failure in genetic enhancement; Sources of genes/ traits- novel genes for

quality. Distant Hybridization: Inter-specific, inter-generic hybridization, scope and limitations,

techniques to overcome the limitations, Post-genomic tools for genetic enhancement of

germplasm.

Unit IV :

Utilization of genetic resources, concept of core and mini-core collections, genetic

enhancement/Prebreeding for crop improvement including hybrid development- Use of

Genomic tools in PGR management, Economic evaluation of biodiversity conservation and

biodiversity assessment.

Unit V :

Intellectual Property Rights (IPR) – issues and concerns – PGR – Plant Breeders’ rights – Farmers’

rights – PGR in strengthening Plant Breeding research system. Implications of World Trade

Organisations (WTO), General Agreement on Trade and Tariff (GATT), Trade Related Intellectual

Property Rights (TRIPs), Plant Variety Protection (PVP) and Convention on Biological Diversity

(CBD) on PGR.

LECTURE SCHEDULE

Historical perspectives and need for PGR conservation and importance of plant genetic

resources

Taxonomical classification of cultivated plants
Gene pool: primary, secondary and tertiary
Centres of origin and global pattern of crop diversity
Basic genetic resources and need for transgenes
Exploration, collection, characterization, evaluation and cataloging of PGR
Plant quarantine and phytosanitary certification
Germplasm introduction and exchange
In vitro conservation of PGR and status cryopreservation techniques
Germplasm conservation- in situ, ex situ, and on-farm strategies
Registration of plant genetic resources: Need and procedures
PGR data base management: Taxonomical Plant descriptors
National and international protocols for PGR management
PGR for food and agriculture: PGR access and benefit sharing
Role of CGIAR system in the germplasm conservation and exchange
Exploitation of landraces and wild relatives in genetic enhancement of crops
Mid Semester Examination
Impediments in using landraces and wild relatives in genetic enhancement
Need for novel genes for genetic enhancement of crop species: Pros and cons
Wide hybridization as a tool of genetic enhancement- Success stories in crops for

enhanced yield and quality

Plant genome projects and their implications on the exploitation PGR
PGR as a source for gene identification and transfer to cultivated crops
PGR and genomics in future crop improvement
Maintenance of core and mini-core collections of PGR
Economic evaluation of biodiversity conservation and biodiversity assessment
Who owns the plant genetic resources
Plant Breeders’ Rights, Farmers’ Rights in the context of using PGR
Legislations and Acts associated with PGR
Intellectual Property Rights (IPR) – issues and concerns associated with PGR use
Plant Breeders’ rights – Farmers’ rights and PGR
Use of Genomic tools in PGR management
Implications of World Trade Organizations (WTO), General Agreement on Trade and

Tariff (GATT) on PGR exchange

Convention on Biological Diversity and PGR
Indian Plant Variety Protection Bill and Biodiversity Bill- An analysis

SUGGESTED READINGS

Frankel OH & Bennett E. 1970. Genetic Resources in Plants – their Exploration and

Conservation. Blackwell.

Gautam PL, Dass BS, Srivastava U & Duhoon SS. 1998. Plant Germplasm Collecting:

Principles and Procedures. NBPGR, New Delhi.

Painting KA, Perry MC, Denning RA & Ayad WG. 1993. Guide Book for Genetic

Resources Documentation. IPGRI, Rome, Italy.

Paroda RS & Arora RK. 1991. Plant Genetic Resources, Conservation and Management.

Concepts and Approaches. IPGRI Regional office for South and South Asia, New Delhi.

Puzone L & Hazekamp TH. 1996. Characterization and Documentation of Genetic Resources Utilizing Multimedia Database. NBPGR, New Delhi.
Rana RS, Sapra RL, Agrawal RC & Gambhir R. 1991. Plant Genetic Resources, Documentation and Information Management. NBPGR, New Delhi.
Singh RJ & Jauhar PP. 2005. Genetic Resources, Chromosomal Engineering and Crop Improvement. Vol. I. Grain Legumes, Vol. II. Cereals. CRC Press, Taylor & Francis Group, USA.

AGM 605 Microbial Gene Technology (2+1)

OBJECTIVE

To make students familiarize with microbial genomes for use in recombinant DNA technology.

THEORY

Unit I : Introduction

Molecular concepts in microbial genetics – genetic elements – Molecular aspects of gene

expression – genotypic and phenotypic variation – regulation of gene expression – ‘Lac’ operon

and operon models.

Unit II : Molecular analysis-I

Development of microbial molecular biology – tools and techniques-extra chromosomal and

chromosomal DNAs – Analysis of DNA-Electrophoresis – DNA manipulative enzymes – Polymerase

Chain Reaction (PCR) – different versions of PCR- application of PCR methods

Unit III : Gene recombinant technology

Cloning vectors based on plasmids, phages, cosmids – construction of recombinant DNA

molecules-Introduction of recombinant DNA into bacterial cells- Transformation, transduction,

conjugation, electroporation.

Unit IV : Construction of DNA library

Construction of genomic library and cDNA library – Identification of correct clone through

primers, probes & antibodies – DNA sequencing – Methods in Genome sequencing – expression

of cloned genes in homologous & heterologous hosts – 16S rRNA, molecular markers, GFP, lacZ,

GUS.

Unit V : Molecular analysis-II

Application in microbial taxonomy and ecology – Expression in recipient cell – methods of scoring

markers – DNA hybridization, southern blotting, western – western blot techniques – screening

for DNA polymorphism – RAPD- VNTRs- SSRs- Gene tagging and techniques for DNA finger

printing.

PRACTICALS

Isolation of bacterial genomic DNA – Isolation of plasmid DNA from bacteria – Agarose gel

electrophoresis of DNA – Restriction digestion of DNA -Restriction mapping – Ligation of DNA

molecules – Microbial DNA amplification by PCR, random primers, specific primers –

Transformation of E.coli-screening of transformants – expression of cloned genes in E.coli plasmid

curing in beneficial microbes-bacterial conjugation- transposon mutagenesis- lysogenic

and lytic phage-phage DNA isolation.

LECTURE SCHEDULE

Microbial genetics – Genetic elements in microbes
Tools & techniques for molecular biology
Genetic and phenotypic variation
Molecular aspects of gene expression
lac operon and other operon models, fine structure
Types of plasmids and plasmid controlled characters
Conjugation and fertility factor in bacteria
Transposons mutagenesis
Bacterial transformation – theory and concept
Mapping of genes by transformation
Transduction – Generalized and specialized transduction
Mutation in microorganisms – spontaneous and induced
Mutagens – mechanism, mutation frequency & and reversion
Preparation of DNA from microbial cells
DNA manipulative enzymes
Plasmids as cloning vectors for E. coli
Mid Semester Examination
Bacteriophages as cloning vectors for E. coli
Cloning vectors for other microbes
Polymerase Chain Reaction
Construction of genomic library and cDNA Library
Direct and indirect selection of clones
DNA analysis for clone identification
Protein analysis for clone identification
Studies on the cloned genes
Genome structure and genome sequencing
DNA sequence analysis- Chemical and enzymatic methods
Methods of scoring markers.
DNA hybridization techniques – southern, northern and western blot.
Screening for polymorphism – RFLP, AFLP, UNTRS etc.,
Gene expression vectors
Production of recombinant proteins in E.coli
Production of recombinant proteins in eukaryotic cells
Problems with the production of recombinant proteins

PRACTICAL SCHEDULE

Isolation of bacterial genomic DNA
Isolation of plasmid DNA from E. coli
Agarose gel electrophoresis of DNA
Plasmid curing in bacteria
Conjugation in bacteria
Induction of mutation in microbes by Chemical agents
Induction of mutation in microbes by physical agents
Restriction digestion of plasmid and genomic DNA
Size determination of DNA molecules
Restriction mapping
Elution of DNA from Agarose gel
Ligation of DNA molecules
Preparation of E.coli competent cells
Transformation of E.coli -lacZ selection of recombinant E.coli
Expression of cloned gene in E. coli (SDS-PAGE of proteins)
Microbial DNA amplification by PCR
Final Practical Examination

SUGGESTED READINGS

Ausubel. F.M., R.Brent, R.E.Kingston, D.D.Moore, J.G.Seidman, J.A.Smith and K. Struhl.

1999.

Short Protocols in Molecular Biology. Fourth Edition. John Wiley & Sons, Inc. New York.
Brown. T.A. 2001. Gene Cloning and DNA Analysis: An Introduction. Fourth Edition.

Blackwell Science Inc., Oxford, UK.

Primrose. S., R. Twyman and B. Old. 2001. Principles of Gene Manipulation. Sixth
Sambrook, J., E.F. Fritsch and T. Maniatis. 2000. Molecular Cloning: A laboratory

Manuel. Hird Edition. Cold Spring Harbor Press, New York.

Streips, U.N. and R.E. Yasbin. 2006. Modern Microbial Genetics. Wiley – Liss. John

Wiley & sons, Inc. Publication, NY.

ENT 608 Advanced Host Plant Resistance (1+1)

OBJECTIVE

To familiarize the students with recent advances in resistance of plants to insects and acquaint with

the techniques for assessment and evaluation of resistance in crop plants.

THEORY

Unit I :

Importance of plant resistance, historical perspective, desirable morphological, anatomical and

biochemical adaptations of resistance; assembly of plant species – gene pool; insect sources –

behaviour in relation to host plant factors.

Unit II :

Physical and chemical environment conferring resistance in plants, role of trypsin inhibitors and

protease inhibitors in plant resistance; biochemistry of induced resistance – signal transduction

pathways, methyl jasmonate pathways, polyphenol oxidase pathways, salicylic acid pathways;

effects of induced resistance; exogenous application of elicitors.

Unit III :

Biotechnological approaches in host plant resistance- genetic manipulation of secondary plant

substances; incorporation of resistant gene in crop varieties; marker-aided selection in resistance

breeding.

Unit IV :

Estimation of plant resistance based on plant damage- screening and damage rating; evaluation

based on insect responses;

Unit V :

Techniques and determination of categories of plant resistance; breakdown of resistance in crop

varieties.

PRACTICALS

Understanding mechanisms of resistance for orientation, feeding, oviposition etc., allelochemical

bases of insect resistance; macroculturing of test insects like aphids, leaf/plant hoppers, mites and

stored grain pests; field screening- microplot techniques, infester row technique, spreader row

technique and plant nurseries; determination of antixenosis index, antibiosis index, tolerance

index, plant resistance index.

LECTURE SCHEDULE

Importance of plant resistance – Historical perspective.
Mechanisms of resistance – Desirable morphological adaptation of resistance.
Desirable anatomical and biochemical adaptations of resistance.
Assembly of plant species – gene pool – wild relatives of select crops.
Behaviour of insects in relation to the host plant factors.
Bio-physical and bio-chemical basis for resistance in plants.
Role of enzyme inhibitors – trypsin inhibitors and protease in plant resistance.
Mid Semester Examination
Biochemistry of induced resistance.
Synthesis of secondary metabolites in plants – signals transduction pathways – methyl

jasmonate pathways.

Poly phenol oxidase pathways salicylic acid pathways – effects of induced resistance –

exogenous applications of elicitors.

Biotechnological approaches in host plant resistance – genetic manipulations of

secondary plant substances.

Incorporation of resistance gene in crop varieties.
Marker – aided selection in resistance breeding.
Estimation of plant resistance based on plant damage – screening and damage rating;
Evaluation based on insect responses techniques and determination of categories of

plant resistance.

Break down of resistance in crop varieties

PRACTICAL SCHEDULE

Lab experiments to understand resistance of plant for orientation
Lab experiment to understand resistance of plants for feeding
Laboratory experiment to understand the resistance of the plants for oviposition.
Laboratory experiment to know the allelo chemical bases of insect’s resistance through

EAG.

Mass culturing of phytophagous insects – leaf and plant hoppers
Mass culturing of phytophagous insects – mites and stored grain pests
Field screening and estimation of plant resistance based on plant damage(rice, cotton)
Microplot techniques to estimate plant resistance based on plant damage (Rice)
Screening techniques in rice for resistance to lepidopterous pests
No choice and multiple choice tests for feeding and oviposition (Spodoptera litura,

white fly)

Seedling box screening and field screening with infester row
Screening plant nurseries – spreader row techniques
Determination of FPLI, anti xenosis index, antibiosis index and tolerance index – rice

BPH

Determination of FPLI, anti xenosis index, antibiosis index and tolerance index – rice

WBPH

Determination of FPLI, anti xenosis index, antibiosis index and tolerance index – rice

Visit to National/ International Institutes in India
Final Practical Examination

SUGGESTED READINGS

Panda N. 1979. Principles of Host Plant Resistance to Insects. Allenheld, Osum & Co., New

York.

Rosenthal GA & Janzen DH. (Eds.). 1979. Herbivores – their Interactions with Secondary

Plant Metabolites. Vol. I, II. Academic Press, New York.

Sadasivam S & Thayumanavan B. 2003. Molecular Host Plant Resistance to Pests. Marcel

Dekker, New York.

Smith CM, Khan ZR & Pathak MD. 1994. Techniques for Evaluating Insect Resistance in

Crop Plants. CRC Press, Boca Raton, Florida.

Chelliah, S. and S. Uthamasamy (Eds) 1995. Host Plant Resistance to Pests : Principles

and Practices, APC Publications Private Limited., New Delhi

Dhaliwal. G. S. and V. K. Dilwari (Eds) 1993. Advances in Host Plant Resistance to

Insects. Kalyani publishers, New Delhi 443p.

Panda. N. and G. S. Khush 1995. Host Plant Resistance to Insects CAB. International in

Association with International Rice Research Institute, Philippines, 426p

Painter, R. H 1951. Insects Resistance in Crop Plants Macmillan, New York, 520p

MAT 604 Mathematical Modeling In Agricultural Sciences (1+1)

OBJECTIVE

To Provide a good understanding of Mathematical modeling techniques and their various

applications in Agricultural research.

THEORY

Unit I : Matrices

Review of matrix Algebra – Matrix-Types – Algebra of matrices – inverse of a matrix by adjoint

method – Solving simultaneous equations using matrix inverse and Cramer’s rule-Leslie matrix –

simple applications in Population Dynamics.

Unit II : Calculus

Differentiation – definition – methods of differentiation – Partial differentiation –Increasing and

decreasing function-Maxima and minima of single and several variables without constraints.

Integration – methods of integration (method of substitution, method of partial fractions) and

Integration by parts (simple problems). Formation – First order: Variable separable – Homogenous – Linear Differential Equations – Second order differential equation with constant coefficient with RHS x n e and x  Growth rate – Relative growth rate – Application of calculating integration in area, volume and surface area – Estimating growth function from growth rate and relative growth rates.

Unit III : Mathematical models

Systems – Definitions – Components of a system – Modeling approach – Different kinds of

models – Mathematical model – their classification and properties – Simulation – Definition –

Examples.

Unit IV : Growth models and spacing models

Growth Models – uses in Agriculture – Linear – Stage wise – Exponential – Logistic – Richards –

Gempertz and Mitcherlich

Unit V : Response models

Yield response models in single and multiple inputs – Quadratic – Square root – Mitcherlich’s

response models – single input – Quadratic and square response models for several inputs –

Estimating physical and Economic optimum.

PRACTICALS

Problems in Algebra of matrices – inverse of a matrix by adjoint method – Solving simultaneous

equations using matrix inverse and Cramer’s rule. Leslie matrix – simple applications in

Population Dynamics. Problems in Differentiation- methods of differentiation- Partial

differentiation – increasing and decreasing function-Maxima and minima of single and several

variables without constraints. Problems in Integration method of substitution, method of partial

fractions and Integration by parts (simple problems). Problems in First order differential

equations – Variable separable – Homogenous – Linear Differential Equations – Second order

differential equation with constant coefficient with RHS x n e and x Problems in Growth rate –

Relative growth rate, Application of calculating integration in area, volume and surface area –

Estimating growth function from growth rate and relative growth rates. Problems in Mathematical

model – their classification and properties – Simulation – Examples – Growth Models – Linear –

Stage wise – Exponential – Logistic – Richards – Gempertz and Mitcherlich. Problems in Yield

response models in single and multiple inputs – Quadratic – Square root – Mitcherlich’s response

models – single input – Quadratic and square response models for several inputs – Estimating

physical and Economic optimum.

LECTURE SCHEDULE

Review of basic Algebra – Matrix-Types
Algebra of matrices – inverse of a matrix by adjoint method
Solving simultaneous equations using matrix inverse and Cramer’s rule
Leslie matrix – Simple applications in Population Dynamics.
Differentiation – definition – methods of differentiation.
Increasing and decreasing function-Maxima and minima of single variable
Maxima and minima of several variables without constraints.
Mid Semester Examination
Differential equations – Formation – First order – Variable separable and Homogenous

method.

Systems – Definitions – Components of a system – Modeling approach
Different kinds of models – Mathematical model – their classification and properties
Simulation – Definition – Examples.
Growth Models – uses in Agriculture – Linear – Stage wise – Exponential
Logistic – Richards – Gempertz and Mitcherlich
Yield response models in single and multiple inputs
Quadratic – Square root – Mitcherlich’s response models – single input
Quadratic and square response models for several inputs – Estimating physical and

Economic optimum.

PRACTICAL SCHEDULE

Problems in Algebra of matrices – inverse of a matrix by adjoint method
Solving simultaneous equations using matrix inverse and Cramer’s rule.
Problems in Leslie matrix – simple applications in Population Dynamics.
Problems in Differentiation- methods of differentiation
Problems in Partial differentiation – Increasing and decreasing function
Problems in – Maxima and minima of single and several variables without constraints.
Problems in Integration method of substitution, method of partial fractions
Problems in Integration by parts (simple problems)
Problems in First order differential equations – Variable separable – Homogenous –

Linear Differential Equations.

Solving Second order differential equation with constant coefficient with RHS

nx x e and 

Problems in Growth rate – Relative growth rate, Application of calculating integration in

area, volume and surface area – Estimating growth function from growth rate and relative

growth rates.

Problems in Mathematical model – their classification and properties
Problems in Simulation – Examples – Growth Models – Linear – Stage wise – Exponential

– Logistic – Richards – Gempertz and Mitcherlich.

Problems in Yield response models in single and multiple inputs
Problems in Quadratic – Square root – Mitcherlich’s response models – single input
Problems in – Quadratic and square response models for several inputs.
Final Practical Examination

SUGGESTED READINGS

Ranganathan C.R.(2006) “A First Course in Mathematical Models of population

Growth(with MATLAB Programs)”, Associated Publishing Company, New Delhi.

Batschelet Edward(2004) Introduction to Mathematics for Life sciences 5th edition,

Springer Verlog publishers.

Manickavasagam Pillai, T. K and Natarajan, T. 1989. Calculus, Viswanathan

Publications, Madras.

Mehta, B. C. and G. M. K. Madnani.(2005) Mathematics for Economists, Sultan Chand &

Sons, New Delhi.

SUGGESTED WEBSITES

www.sonoma.edu/users/w/wilsonst/Courses/Math_131/lp/default.html
http://en.wikipedia.org/wiki/Decision_analysis
http://en.wikipedia.org/wiki/Data_analysis