Brassica Pathogen Genomics
GWAS and genomic mapping to identify Blackleg disease resistance in oilseed crops.
Project Overview
Investigated the genomic factors governing plant-pathogen interactions, specifically focusing on Blackleg (Leptosphaeria maculans) resistance in Brassica crops. This research was conducted during the Summer Down Under Research Internship (SDURI) program.
My Role
Genomics Intern. Responsible for genome-wide association study (GWAS) data analysis, gene annotation, and running bioinformatic pipelines.
Tools / Stack
Project Details
Implementation Roadmap
Development Process.
Obtain genotyping data for diverse lines of Brassica napus.
Run quality control and filtering steps on SNP arrays using PLINK.
Map resistance genes using genome-wide association study (GWAS) models in R.
Utilize the RGAugury pipeline to annotate resistance gene analogs (RGAs).
Pinpoint candidate loci overlapping with known defense pathways.
Case Study Analysis
Challenges & Outcomes.
Dealing with high levels of false positives in GWAS due to population structure in Brassica lines.
Implemented mixed linear models (MLM) incorporating kinship matrices and population structure covariates to control false positive rates.
Successfully annotated three novel resistance gene clusters that correlate with field-observed resistance against Blackleg disease.