Molecular Breeding and Bioinformatics

Course Name: Molecular Breeding and Bioinformatics

Course Code: MGPB 0506 (2-1-0)

Course Objective:  To impart knowledge and practical skills to use innovative approaches and Bioinformatics   in Plant Breeding.

CO-PO Mapping:

PSO-Program specific outcomes- M.Sc Ag

PSO1 : Impart knowledge and understanding of fundamental concepts and techniques of maintaining and enhancing soil fertility, crop production, crop management, crop improvement, biodiversity and sustainability of agriculture worldwide.

PSO2 : Develop the ability to know farming practices and their scope to improve in the rural areas and the environments.

PSO4 : Apply knowledge of Agri-business management and finance to develop profitable agricultural system.

Syllabus (Theory):

Unit I: Genotyping; Biochemical and Molecular markers; Morphological, biochemical and DNA-based markers (RFLP, RAPD, AFLP, SSR, SNPs, ESTs, etc.), Functional markers; Mapping populations (F₂s, back crosses, RILs, NILs and DH); Molecular mapping and tagging of agronomically important traits; Statistical tools in marker analysis.

Unit II: Allele mining; Marker-assisted selection for qualitative and quantitative traits; QTLs analysis in crop plants; Marker-assisted backcross breeding for rapid introgression; Genomics- assisted breeding; Generation of EDVs; Gene pyramiding.

Unit III: Introduction to Comparative Genomics; Large scale genome sequencing strategies; Human genome project; Arabidopsis genome project; Rice genome project; Comparative genomics tools; Introduction to proteomics; 2D gel electrophoresis; chromatography and sequencing by Edman degradation and mass spectrometry; Endopeptidases; Nanotechnology and its applications in crop improvement.

Unit IV; Recombinant DNA technology, transgenes, method of transformation, selectable markers and clean transformation techniques, vector-mediated gene transfer, physical methods of gene transfer; Production of transgenic plants in various field crops: cotton, wheat, maize, rice, soybean, oilseeds, sugarcane, etc. and commercial releases; Biotechnology applications in male sterility/ hybrid breeding, molecular farming; Application of Tissue culture in molecular breeding; MOs and related issues (risk and regulations); GMO; International regulations, biosafety issues of GMOs; Regulatory procedures in major countries including India, ethical, legal and social issues; Intellectual property rights; Introduction to bioinformatics: bioinformatics tools, biological data bases (primary and secondary), implications in crop improvement.

Syllabus (Practical):

Requirements for plant tissue culture laboratory; Techniques in plant tissue culture; Media components and media preparation; Aseptic manipulation of various explants, observations on the contaminants occurring in media, interpretations; Inoculation of explants, callus induction and plant regeneration; Standardizing the protocols for regeneration; Hardening of regenerated plants; Establishing a greenhouse and hardening procedures; Visit to commercial micro propagation unit; Transformation using Agrobacterium strains; GUS assay in transformed cells/ tissues; DNA isolation, DNA purity and quantification tests; Gel electrophoresis of proteins and isozymes, PCR-based DNA markers, gel scoring and data analysis for tagging and phylogenetic relationship; Construction of genetic linkage maps using computer software; NCBI Genomic Resources, GBFF, Swiss Prot, Blast n/ Blast p, Gene Prediction Tool, Expasy Resources, PUBMED and PMC, OMIM and OMIA, ORF finder; Comparative Genomic Resources: - Map Viewer (UCSC Browser and Ensembl); Primer designing- Primer 3/ Primer BLAST.

REFERENCES:

Azuaje F and Dopazo J. 2005. Data Analysis and Visualization in Genomics and Proteomics. John Wiley and Sons. Brown TA. 1991.

Essential Molecular Biology: a practical Approach. OXford university press, 2002, 2nd edition Chawala HS. 2000.

Introduction to Plant Biotechnology. OXford & IBH Publishing Co. Pvt. Ltd. Chopra VL and Nasim A. 1990.

Genetic Engineering and Biotechnology: Concepts, Methods and Applications. OXford & IBH. Gupta PK. 1997.

Elements of Biotechnology. Rastogi Publ. Hackett PB, Fuchs JA and Messing JW. 1988.

An Introduction to Recombinant DNA Technology Basic Experiments in Gene Manipulation. 2nd Ed. Benjamin Publ. Co. Jollès P and Jörnvall H. 2000.

Proteomics in Functional Genomics: Protein Structure Analysis. Birkhäuser.

Lewin B. 2017. Genes XII. Jones & Bartlett learning, 2017. Robert NT and Dennis JG. 2010.

Plant Tissue Culture, Development, and Biotechnology. CRC Press.

Sambrook J and Russel D. 2001.

Molecular Cloning - a Laboratory Manual. 3rd Ed. Cold SpringHarbor Lab. Press.

Singh BD. 2005. Biotechnology, Expanding Horizons. Kalyani Publishers, New Delhi.

Watson J. 2006. Recombinant DNA. Cold Spring harbor laboratory press.

Session Plan (Theory):

Session 1: Genotyping; Biochemical and Molecular markers

https://youtu.be/Quk-Dh65iHY

Session 2: Morphological, biochemical and DNA-based markers (RFLP, RAPD, AFLP, SSR, SNPs, ESTs, etc.)

https://youtu.be/swQ_pm4cR5o

Session 3: Functional markers; Mapping populations (F₂s, back crosses, RILs, NILs and DH)

https://youtu.be/VlQA3KEHGBE

Session 4: Molecular mapping and tagging of agronomically important traits

https://youtu.be/gGUxf-aL1DA

Session 5: Statistical tools in marker analysis

https://youtu.be/yoCF_zTKgdk

Session 6: Allele mining

https://youtu.be/0xkmgrlxK4c

Session 7: Marker-assisted selection for qualitative and quantitative traits

https://youtu.be/_OfDyT8E8dI

Session 8: QTLs analysis in crop plants

https://youtu.be/JN0B6AeAsZY

Session 9: Marker-assisted backcross breeding for rapid introgression

https://youtu.be/O0se5-VLAsk

Session 10: Genomics- assisted breeding

https://youtu.be/0RbZbWziQq8

Session 11: Generation of  EDVs

https://youtu.be/t0vp73-zC-c

Session 12: Gene pyramiding

https://youtu.be/irjOku53gmQ

Session 13: Introduction to Comparative Genomics

https://youtu.be/Irs65GAu1YM

Session 14: Large scale genome sequencing strategies

https://youtu.be/kvXgsYaVvQI

https://youtu.be/9czh_qUScVk

Session 15: Human genome project; Arabidopsis genome project

https://youtu.be/-hryHoTIHak

Session 16: Rice genome project

https://youtu.be/MQMBVupN03I

Session 17: Comparative genomics tools

https://youtu.be/kzrjcvIuqLk

Session 18: Introduction to proteomics; 2D gel electrophoresis; chromatography and sequencing by Edman degradation and mass spectrometry

https://youtu.be/vnW9kH0agcE

Session 19: Endopeptidases

https://youtu.be/fHMHMraljJM

Session 20: Nanotechnology and its applications in crop improvement.

https://youtu.be/TmCf3ey-MX8

Session 21: Recombinant DNA technology

https://youtu.be/K3BxuKGONCY

Session 22: Transgenes, method of transformation, selectable markers and clean transformation techniques

https://youtu.be/nD_8cXRiyYQ

Session 23: Vector-mediated gene transfer

https://youtu.be/D5aEKiez_nw

Session 24: Physical methods of  gene  transfer

https://youtu.be/43Zwdg56NIA

Session 25: Production of transgenic plants in various field crops: cotton, wheat, maize, rice

https://youtu.be/6GG634muj00

Session 26: Production of transgenic plants in various field crops: soybean, oilseeds, sugarcane, etc. and commercial releases

https://youtu.be/8rb_exM0kgY

Session 27: Biotechnology applications in male sterility/ hybrid breeding

https://youtu.be/yHfxoOUbVx0

Session 28: Molecular farming

https://youtu.be/1IF-Nv7dkI8

Session 29: Application of Tissue culture in molecular breeding

https://youtu.be/pt02DNHjQJI

Session 30: GMO; International regulations, biosafety issues of GMOs; Regulatory procedures in major countries including India, ethical, legal and social issues

https://youtu.be/E171qNrEesc

Session 31: Intellectual property rights

https://youtu.be/E171qNrEesc

Session 32: Introduction to bioinformatics: bioinformatics tools, biological data bases (primary and secondary), implications in crop improvement.

https://youtu.be/QvEEmR2nsD0

Session Plan (Practical):

Session 1: Requirements for plant tissue culture laboratory

https://youtu.be/H4QDv16u784

Session 2: Techniques in plant tissue culture

https://youtu.be/n9RGZ1jJt6s

Session 3: Media components and media preparation

https://youtu.be/cneascR3OEc

Session 4: Aseptic manipulation of various explants, observations on the contaminants occurring in media, interpretations

https://youtu.be/KHg_PyjQPwk

Session 5: Inoculation of explants, callus induction and plant regeneration

https://youtu.be/wYEyp8ir0Ko

Session 6: Standardizing the protocols for regeneration; Hardening of regenerated plants; establishing a greenhouse and hardening procedures

https://youtu.be/KyKBtqpoTuwhttps://youtu.be/9XbLoVW-j5U

Session 7: Transformation using Agrobacterium strains

https://youtu.be/riQz6U-YUm0

Session 8: Transformation using Agrobacterium strains; GUS assay in transformed cells/ tissues

https://youtu.be/wHWxqsfW8r4

Session 9: DNA isolation, DNA purity and quantification tests

https://youtu.be/tcPgdR9_t64

Session 10: Gel electrophoresis of proteins and isozymes, PCR-based DNA markers, gel scoring and data analysis for tagging

https://youtu.be/MhJT9yjnl88

Session 11: Phylogenetic relationship

https://youtu.be/JRh0BbsYJmQ

Session 12: Construction of genetic linkage maps using computer software; NCBI Genomic Resources, GBFF, Swiss Prot, Blast n/ Blast p

https://youtu.be/q4yHvpfsRpM

https://youtu.be/3nr_vAav5k0

https://youtu.be/iu2g6TYj7kk

Session 13: Gene Prediction Tool, Expasy Resources, PUBMED and PMC, OMIM and OMIA, ORF finder

https://youtu.be/iu2g6TYj7kk

https://youtu.be/Yt5njm-T_Bs

Session 14: Comparative Genomic Resources: - Map Viewer (UCSC Browser and Ensembl)

https://youtu.be/zxdgFet7wUA

Session 15: Primer designing- Primer 3/ Primer BLAST

https://youtu.be/BwPmVvvU5sk

Session 16: Visit to commercial micro propagation unit