Course Name:Plant Genomics
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•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.
|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|
Genome organization: Introduction to genomics, Brief overview of prokaryotic and eukaryotic genome organization, Extra-chromosomal DNA: bacterial plasmids, Mitochondrial and chloroplast genomes
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
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
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
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
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)
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
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 […]