Plant Genomics

Teacher

Dr Rukmini Mishra

Category

Core Courses

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Course Name:Plant Genomics

Code(Credit) : CUTM1441(3-1-0)

Course Objectives

•Deciphering the genetic makeup and protein population in an organism are among the elementary approaches in biological sciences.
•To provide an understanding in genomics and proteomics and, the different approaches and techniques employed in these fundamental fields of study.

Learning Outcomes

•Identifying various omics approaches and their role in understanding plant function.
•Design and develop experiments to understand and manipulate plant function.
•Analyse information from plant genomic research and recognise its potential applications in crop improvement.

Course Syllabus

Module I: Basics of Genomics

Introduction to genomics, Brief overview of prokaryotic and eukaryotic genome organization, Extra-chromosomal DNA: bacterial plasmids, Extra-chromosomal DNA: mitochondria and chloroplast

Practice: Demonstration of Polymerase chain reaction (PCR)

Module II: Genome mapping
Genetic and physical mapping, Markers for genetic mapping, FISH technique in gene mapping, comparative gene mapping

Practice: Demonstration of gene mapping

Module III: Genome sequencing projects

Human Genome Project, Genome sequencing projects for microbes, Genome sequencing projects for plants and animals, Accessing and retrieving genome project information from the web

Practice: Demonstration of web tools for genome analysis

Module IV: Comparative genomics

Identification and classification of organisms using 16S rRNA typing/sequencing, Identification and classification of organisms using SNPs, Use of genomes to understand evolution of eukaryotes, track emerging diseases and design new drugs, Determining gene location in genome sequence.

Practice: Phylogenetic analysis using genomic tools

Module V: Proteomics

Introduction to proteomics, Proteomics technologies- 2D-PAGE, isoelectric focusing, Mass spectrometry, MALDI-TOF, Yeast 2-hybrid system, Proteome databases.

Practice: Demonstration of 2D-PAGE gel

Module VI: Functional genomics and proteomics

Transcriptome analysis for identification and functional annotation of gene, Gene function- forward and reverse genetics, Protein chips and functional proteomics, Clinical and biomedical applications of proteomics; Introduction to metabolomics, lipidomics, metagenomics and systems biology.

Module VII: Emerging Technologies

Introduction to gene editing, ZFNs & TALENs, CRISPR/Cas System, Case studies of gene editing for crop improvement

Practice: Demonstration of gene cloning

Session Plan

Session 1

Session 2

Brief overview of prokaryotic and eukaryotic genome organization
https://www.youtube.com/watch?v=IQR7Fk5b8z8
https://www.youtube.com/watch?v=MsQHwXfYkAs

Session 4

Practice
Demonstration of PCR

https://www.youtube.com/watch?v=o_0dFor_syw

Session 5

Extra-chromosomal DNA: bacterial plasmids, Mitochondia and Chloroplast
https://www.youtube.com/watch?v=SdqJFA6mOkI

Session 6

Genetic and physical mapping
https://www.youtube.com/watch?v=ZeATszO-6e0

Session 7

Practice
Demonstration of Gene mapping

https://www.youtube.com/watch?v=ZeATszO-6e0&t=33s

Session 8

Markers for genetic mapping
https://www.youtube.com/watch?v=-H0ss1kDf_I

Session 9

FISH technique in gene mapping, Comparitive gene mapping
https://www.youtube.com/watch?v=LiRJoTi44TA

https://www.youtube.com/watch?v=qmefXRNFsq8

Session 13

Genome sequencing projects for microbes
https://www.youtube.com/watch?v=pNY7znelCN0

Session 14

Genome sequencing projects for plants and animals
https://www.youtube.com/watch?v=2JUu1WqidC4&t=1s

Session 15

Accessing and retrieving genome project information from the web
https://www.youtube.com/watch?v=5teoROLvijg

Session 16

Session 17

Identification and classification of organisms using SNPs
https://www.youtube.com/watch?v=DE9b1dxy_pE

Session 18

Practice
Phylogenetic analysis using genomic tools

https://www.youtube.com/watch?v=hlgB3aRyE_8

Session 19

Use of genomes to understand evolution of eukaryotes, track emerging diseases and design new drugs
https://www.youtube.com/watch?v=bDsfd6V-U1c

Session 20

Introduction to transcriptomics, DNA Microaaray, RNA Sequencing

https://www.youtube.com/watch?v=mYWVi7B-13c
https://www.youtube.com/watch?v=U1uQ_wBcO4U

Session 21

Introduction to proteomics
https://www.youtube.com/watch?v=5paHhTq87Ak

Session 22

Proteomics technologies- 2D-PAGE, isoelectric focusing
https://www.youtube.com/watch?v=KD1pXgWLKdU

Session 23

Practice
Demonstration of 2D-Page gel

https://www.youtube.com/watch?v=FHvblg338Gg

Session 25

Session 26

Session 27

Transcriptome analysis for identification and functional annotation of gene
https://www.youtube.com/watch?v=g0mmAgETTM8

Session 28

Gene function- forward and reverse genetics
https://www.youtube.com/watch?v=Paf5WRMizzQ

Session 29

Functional proteomics, Clinical and biomedical applications of Proteomes
https://www.youtube.com/watch?v=eHjPp1iSoGs

https://www.youtube.com/watch?v=E5PMZ52B_PY

Session 30

Introduction to metabolomics and Phenomics
https://www.youtube.com/watch?v=0mqz94bRma8

Session 31

Metagenomics and systems biology
https://www.youtube.com/watch?v=oLu6UdazPxM

Session 33

Practice
Demonstration of Gene cloning

https://www.youtube.com/watch?v=sjwNtQYLKeU

Session 36

Case Studies

Case Studies

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    Dr Rukmini Mishra

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    Dr Rukmini Mishra is presently working as an Assistant Professor (Botany), School of Applied Science, Centurion University of Technology and Management. She has a PhD in Agricultural Biotechnology from ICAR-National Rice Research Institute, India. After PhD, she received the prestigious Young Scientist Award from the Dept. of Science & Technology, SERB, Govt. of India to […]