Course Name:Plant Genomics
Plant Genomics
Teacher
Dr Rukmini Mishra
Category
Core Courses
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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
- Twyman, R.M. Principles of Proteomics. BIOS Scientific Publisher, New York. 2004.
- Singer M and Berg P Genes and Genomes: A Changing Perspective; University ScienceBooks, CA, USA, 1991.
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 5
Linkage analysis, Choice of mapping populations, markers for genetic mapping
Session 6
Methods and techniques used for genetic mapping; Physical mapping- tools for physical mapping of genes, cytogenetic maps.
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
Session 9
Genome sequencing strategies- Whole genome, clone-by-clone and hybrid approaches
https://www.youtube.com/watch?v=NfLoJrssdYQ
Session 10
Next generation sequencing technologies- 454, Illumina, ABI SOliD, single molecule and nanopore sequencing
Session 12
Genome sequencing projects for plants (Rice, Arabidopsis)
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
Session 16
Identification and classification of organisms using 16S rRNA typing/sequencing
Session 17
Practice
Phylogenetic analysis using genomic tools
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
Session 19
Microarray- construction of microarrays – genomic arrays, cDNA arrays and oligo arrays
Session 22
Protein interactions; DNA – protein Interactions
Session 23
Yeast two-hybrid systems, affinity tagging, pathway building, 2D-PAGE, isoelectric focusing
https://www.youtube.com/watch?v=w5Pvri4-cUA
Session 24
Mass spectrometry, MALDI-TOF, LC-MS
https://www.youtube.com/watch?v=RuwbeA22rew
https://www.youtube.com/watch?v=0jeFpXHZ8W0
Session 26
Protein sequencing: N-terminal sequencing- Ninhydrin test, Sanger’s method
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)
Session 30
Metabolome, Metabolite profiling, Metabolome fingerprinting
Session 31
Role of Biomarker in metabolomics, Techniques for metabolome analysis
Session 32
Practice
Isolation of secondary metabolites using Soxellate apparatus
Case Studies
Case Studies
Our Main Teachers
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 […]