AI in Plant Genomics: GWAS, Genomic Prediction & Climate-Resilient Crop Breeding

Aim

Workshop Objectives

Workshop Structure

Day 1: Plant GWAS, SNP Analysis & Trait-Associated Gene Discovery

Topics Covered

• Plant genomic datasets, SNP markers and quantitative trait analysis
• SNP quality control, filtering and population structure analysis
• Genome-wide association studies (GWAS) using GAPIT
• Manhattan plots, Q–Q plots and candidate genomic region identification
• Functional annotation of significant SNPs and candidate gene prioritization

Hands-On: Analyze a real wheat genomic dataset, perform SNP filtering and PCA, run GWAS, visualize genetic associations and identify candidate genomic regions.

Tools: R, GAPIT, tidyverse, RStudio

Day 2: AI-Based Genomic Prediction, Machine Learning & Genomic Selection

Topics Covered

• Genomic selection and genome-wide marker-based prediction
• Genomic BLUP (GBLUP) and ridge regression models
• Random Forest for genomic trait prediction
• Model validation, predictive accuracy and breeding value estimation
• Feature importance analysis and interpretation of genomic prediction models

Hands-On: Build genomic prediction models using SNP markers, compare GBLUP and Random Forest performance, evaluate predictive accuracy and rank candidate breeding lines.

Tools: R, rrBLUP, Python, Scikit-learn, Google Colab

Day 3: Genotype-by-Environment Modeling, Climate Adaptation & AI-Driven Crop Selection

Topics Covered

• Genotype-by-environment (G×E) interactions and crop adaptability
• Integration of genomic, phenotypic and environmental data
• Machine learning for multi-environment crop performance prediction
• Yield stability analysis and AI-assisted breeding line prioritization
• Multi-environment genomic selection and identification of climate-adaptive breeding candidates

Hands-On: Integrate genomic and environmental datasets, predict crop performance across environments, assess yield stability and prioritize promising breeding lines.

Tools: Python, Pandas, Scikit-learn, Matplotlib, Google Colab

Important Dates

Workshop Outcomes

Fee Structure