Molecular Breeding Data Analytics
Hands-on course covering Molecular Markers, QTL Mapping, Marker-Assisted Selection, SNP/HapMap data, Population Structure (STRUCTURE), GWAS with TASSEL & GAPIT (R), Haplotype Analysis, and KASP Assay design for crop improvement and trait mapping.
Course Overview
Molecular Breeding Data Analytics is a hands-on, application-driven course that equips plant breeders, geneticists, and agri-research students with end-to-end skills for marker-assisted selection, QTL mapping, GWAS, and KASP-based genotyping. The curriculum spans wet-lab data preparation, software-based analysis, statistical interpretation, and reproducible R-based pipelines.
Module I — Molecular Breeding Data Handling and Analysis
Basics of Molecular Markers, QTL Mapping & Marker-Assisted Selection (MAS)
- Overview of molecular markers — SSR, SNP, AFLP, and others
- Principles and workflow of marker-assisted selection in crop improvement
- Applications of molecular markers in trait mapping and breeding programs
- QTL Mapping — Linkage Mapping, Association Mapping, and Linkage Disequilibrium
Genotyping of SSR Markers, Scoring & Data Generation
- Experimental design and protocol overview for SSR genotyping
- Allele scoring from gel or capillary electrophoresis
- Preparing data matrices for downstream analysis
Genetic Diversity Studies
- Estimating allelic diversity, heterozygosity, and PIC (Polymorphism Information Content)
- Construction and interpretation of dendrograms
Population Structure Analysis using STRUCTURE
- Bayesian clustering for genetic structure determination
- Preparing input files, parameter setting, and output interpretation
- Visualisation of population clusters and admixture
SNP Data Analysis — HapMap, Imputation, Filtering
- SNP data formats — HapMap and VCF
- Quality control — MAF, missing data, heterozygosity filters
- Imputation of missing genotypes — preparing data for GWAS
Module II — GWAS, Haplotypes & KASP Assay
GWAS using TASSEL Software
- GWAS principles — population structure correction, kinship matrix
- Step-by-step execution of GWAS in TASSEL with example datasets
- Interpreting Manhattan plots, Q-Q plots, and significant marker-trait associations
GWAS using GAPIT in R Studio
- Installing and working with the GAPIT R package
- Data formatting; model selection — GLM, MLM, FarmCPU
- Reproducible and automated GWAS pipelines in R
Candidate Gene-Based Association Studies
- Targeted association studies using known trait-related genes
- Strategies to pinpoint candidate genes near associated markers
- Genome browsers, gene annotations, and functional databases
- Prioritising candidate genes for validation and functional studies
Haplotype Analysis
- Definition and significance of haplotypes in genetic analysis
- Identifying haplotypes within LD regions
- Associating haplotypes with phenotypic traits
KASP Assay for SNP Marker Genotyping
- Overview of Kompetitive Allele-Specific PCR (KASP) technology
- Designing KASP assays for SNP markers and trait-linked alleles
- KASP data analysis and interpretation
Who Should Enrol
Plant breeders, agri-genomics researchers, MSc/PhD students in plant biotechnology, and crop scientists planning marker-assisted breeding programs or GWAS-driven trait discovery.
Next Batch Begins Soon — Admissions Open.