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.

Course Outcomes

COs Course outcomes Mapping COs with POs (High-3, Medium-2, Low-1)
CO1 Understand various omics approaches and their role in understanding plant function PO1-3, PO2-3, PO3-3, PO4-2, PO5-2
CO2 Experiments to understand plant function PO1-3, PO2-3, PO4-2, PO5-2
CO3 Analyze the information from plant genomic research and recognize its potential applications in crop improvement PO1-3, PO2-3, PO3-3, PO4-2, PO5-3
CO4 Design and develop experiments to understand and manipulate plant function PO1-3, PO2-3, PO3-3, PO4-2, PO5-2

Course Syllabus

Module I  

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

Module II

Genome mapping: Molecular Mapping of Genome: Genetic mapping-linkage analysis, Choice of mapping populations, markers for genetic mapping; Physical mapping-tools for physical mapping of genes, cytogenetic maps.

Practice 1: Demonstration of gene mapping

Module III 

Genome sequencing: Chemical (Maxim and Gilbert's degradation method) methods of DNA sequencing; Genome sequencing strategies-Whole genome, clone-by-clone and hybrid approaches. Next generation sequencing technologies-454, Illumina, ABI SOliD, single molecule and nanopore sequencing. Human Genome Sequencing Project, Genome sequencing projects for  plants (Rice, Arabidopsis)

Practice 2: Demonstration of web tools for genome analysis

Module IV: 

Comparative genomics: Whole genome comparison; Tandem and segmental duplication; DNA based phylogenetic trees; Identification and classification of organisms using 16S rRNA typing/sequencing.

Practice 3: Phylogenetic analysis using genomic tools

Module V 

Transcriptomics: Global gene expression strategies-Northern blotting, Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS), Microarray-construction of microarrays-genomic arrays, cDNA arrays and oligo arrays, Transcriptome profiling.

Practice 4: RNA Isolation

Module VI

Proteomics: Protein interactions; DNA – protein Interactions, yeast two-hybrid systems; affinity tagging, pathway building. 2D-PAGE, isoelectric focusing, mass spectrometry, MALDI-TOF, LC-MS; Proteome databases; Protein sequencing: N-terminal sequencing- Ninhydrin test, Sanger’s method, Edman degradation; C-terminal sequencing-types of reducing agents; functional protein microarrays.

Practice 5: Protein separation using SDS-PAGE (Demonstration through virtual labs)

Module VII

Metabolomics: Introduction to metabolomics: Metabolome, Metabolite profiling, Metabolome fingerprinting, Role of Biomarker in metabolomics, Techniques for metabolome analysis.

Practice 6: Isolation of secondary metabolites using Soxellate apparatus

Text books

  1. Twyman, R.M. Principles of Proteomics. BIOS Scientific Publisher, New York. 2004.
  2. Singer M and Berg P Genes and Genomes: A Changing Perspective; University ScienceBooks, CA, USA, 1991.

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 3

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

Session 4

Molecular Mapping of Genome: Genetic mapping

https://www.youtube.com/watch?v=iXQrInXK5rs

Session 5

Linkage analysis, Choice of mapping populations, markers for genetic mapping

https://www.youtube.com/watch?v=9VKxTKsRWSI

Session 6

Methods and techniques used for genetic mapping; Physical mapping- tools for physical mapping of genes, cytogenetic maps.

https://www.youtube.com/watch?v=ZeATszO-6e0

https://www.youtube.com/watch?v=rK0GMdxKrjY

Session 7

Practice
Demonstration of genetic mapping

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

Session 8

Chemical (Maxim and Gilbert’s degradation method) and enzymatic (Sanger’s dideoxy synthetic method) methods of DNA sequencing

https://www.youtube.com/watch?v=PMO350j7sLU

https://www.youtube.com/watch?v=1ZEpNmjLjiU

Session 9

Session 10

Next generation sequencing technologies- 454, Illumina, ABI SOliD, single molecule and nanopore sequencing

https://www.youtube.com/watch?v=jFCD8Q6qSTM

https://www.youtube.com/watch?v=ToKUGz_YhC4

Session 12

Genome sequencing projects for plants (Rice, Arabidopsis)

https://www.youtube.com/watch?v=MQMBVupN03I

https://www.youtube.com/watch?v=zaMtf1pLzmU

Session 13

Practice 

Demonstration of web tools for genome analysis

https://www.youtube.com/watch?v=C2g37X_uMok
https://www.youtube.com/watch?v=42qZyXSH0Cc

Session 14

Whole genome comparison, Tandem and segmental duplication

https://www.youtube.com/watch?v=n9EQfS0xGLc

Session 15

DNA based phylogenetic trees

https://www.youtube.com/watch?v=JRh0BbsYJmQ

Session 16

Identification and classification of organisms using 16S rRNA typing/sequencing

https://www.youtube.com/watch?v=SM3YtWVneO8

Session 17

Practice
Phylogenetic analysis using genomic tools

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

Session 18

Global gene expression strategies- Northern blotting, Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS)

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

https://www.youtube.com/watch?v=9hVTPJ6ajYo

https://www.youtube.com/watch?v=G2Z1wuEOZUU

Session 19

Microarray- construction of microarrays – genomic arrays, cDNA arrays and oligo arrays

https://www.youtube.com/watch?v=k_1YSdmBmo0

Session 20

Session 21

Session 22

Session 23

Yeast two-hybrid systems, affinity tagging, pathway building, 2D-PAGE, isoelectric focusing

https://www.youtube.com/watch?v=w5Pvri4-cUA

https://www.youtube.com/watch?v=6fMW0hLqTi8

https://www.youtube.com/watch?v=MXNwBqK5AzA

Session 25

Session 26

Protein sequencing: N-terminal sequencing- Ninhydrin test, Sanger’s method

https://www.youtube.com/watch?v=p1qcA9ZoYDQ

https://www.youtube.com/watch?v=IiCmCB6pNhw

Session 27

Edman degradation; C-terminal sequencing-types of reducing agents; functional protein microarrays

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

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

https://www.youtube.com/watch?v=9TYgNWyENRE

 

Session 28

Practice 

Protein separation using SDS-PAGE (Demonstration through virtual labs)

https://www.youtube.com/watch?v=S7NIkBy38To

Session 29

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

Session 30

Metabolome, Metabolite profiling, Metabolome fingerprinting

https://www.youtube.com/watch?v=0cuTCimrSoM

https://www.youtube.com/watch?v=Dclwob9am90

Session 31

Role of Biomarker in metabolomics, Techniques for metabolome analysis

https://www.youtube.com/watch?v=0cuTCimrSoM

https://www.youtube.com/watch?v=L1svFdst5D8

Session 32

Practice 

Isolation of secondary metabolites using Soxellate apparatus

https://www.youtube.com/watch?v=SEicK9UT7pY

Case Studies

Case Studies

Our Main Teachers

Dr Rukmini Mishra

Assistant Professor
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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 […]