Methods in biotechnology

GENOMICS AND GENE DISCOVERY (5 CFU)Introduction to Genetics and Population Genetics (1 CFU)--> Basic Concepts in Formal Genetics: Introduction to foundational rules of genetic inheritance in plants.
--> Basics in Population Genetics: Understanding population structure, allelic frequencies, and evolutionary forces acting on plant genomes.
--> Mapping Traits: Principles of mapping monogenic and polygenic traits within plant populations. QTLs and Association Mapping in Breeding (1 CFU)--> Forward Genetics Pipelines: Proceeding from phenotype to genotype to detect major-effect loci.
--> Mapping Populations: Designing and utilizing Recombinant Inbred Lines (RILs), F2 populations, and multi-parental crosses.
--> From Cross-Based to Genome-Based Mapping: Transitioning from linkage mapping to high-resolution frameworks: Linkage Disequilibrium (LD), Genome-Wide Association Studies (GWAS), and controlling for population structure.
--> Practical Workshop: Hands-on applications of linkage disequilibrium and statistical approaches to map complex agronomic traits in plants. DNA Sequencing, Annotation and Comparative Genomics (1 CFU)--> DNA Sequencing Generations: Technical transition from 1st to 2nd Generation High-Depth Short-Read Sequencing (Illumina) and 3rd Generation Long-Read Sequencing (PacBio/Nanopore).
--> Overcoming Genome Complexity: Addressing large, highly repetitive plant genomes packed with transposable elements; selecting sequencing platforms to resolve Structural Variations (SVs).
--> Extracting Information: Reading, assembling, and performing in silico functional annotation using computational pipelines (e.g., BLAST, InterProScan) to filter protein domains, locate causal missense/nonsense mutations in exons, and evaluate cis-regulatory motifs in promoters.
--> Exploiting Information (Comparative Genomics): Utilizing synteny (conserved gene blocks across species) to map genomic architectures. Defining orthogroups (genes descending from a single ancestral sequence) to study gene family duplication, evolution, and function across divergent plant lineages.
--> Epigenomics and Pangenomics: Introduction to sequencing the epigenome and resequencing genomes to build a Pangenome, moving past single-reference genome limitations by defining the Core genome versus the Variable/Dispensable genome (presence-absence variations linked to environmental adaptation and stress tolerance). Molecular Plant Breeding and Gene Discovery (2 CFU)--> Molecular Markers at Work: Constructing complete haplotype blocks to track linked markers as inheritance units, significantly enhancing the accuracy of Marker-Assisted Selection (MAS).
--> Using Genomics for Gene Discovery: The formal workflow of positional cloning and fine mapping to narrow down initial chromosomal regions to specific physical spaces using finishing markers and crossover verification.
--> The Candidate Gene Approach: Selecting candidate genes based on sequence homology, predicted biological function, and dedicated crop expression databases (e.g., SoyBase, SolGenomics).
--> Practical Workshop: Active learning case studies on positional cloning, fine mapping, and candidate gene identification. FUNCTIONAL GENOMICS (4 CFU)Genes in Their Working Context (3.5 CFU)--> Techniques and Approaches in RNA Analysis: Simultaneous gene expression tracking and high-throughput transcriptomics; transitioning from individual gene analysis to whole-transcriptome tracking using microarray technologies and global RNA profiling.
--> Temporal and Spatial Assessment: Understanding how multiple gene networks and expression pathways react in tandem under varying environments, developmental stages, and stress conditions.
--> Reverse Genetics and Genome Modification Strategies: Proceeding from genotype to phenotype to establish gene function.
--> Random Chemical Mutagenesis: The mechanics of TILLING and EcoTILLING using mismatch-specific nucleases (CEL I) to flag point mutations without transgenesis.
--> Random Biological Mutagenesis: Managing T-DNA insertional mutagenesis libraries, analyzing segregation ratios (e.g., KanR phenotypic ratios), and tracking transposons.
--> Targeted Gene Manipulation and Silencing: Executing functional knockouts using CRISPR/Cas9 systems, or gene knockdowns via RNA interference (RNAi) and Virus-Induced Gene Silencing (VIGS).
--> The Gold Standard of Functional Validation: Utilizing genetic complementation in mutant backgrounds to definitively rescue phenotypes and prove gene-phenotype links.
--> Integration of Omics Platforms: Combining high-throughput content techniques (transcriptomics, proteomics, and phenomics) with advanced data analysis to predict cell modifications and model genotypic performance. Laboratory Activities (0.5 CFU)--> Practical Lab Sessions: Dedicated hands-on experimental activities focused on wet-lab RNA extraction, expression analysis protocols, and processing transcriptomic validation data.