Genome-Wide Association Study of Abiotic Stress Resistance in Sunflower

Sustaining agricultural production under adverse environmental conditions, such as nutrient stress or high salinity, is a one of the major challenges. Genetic association studies (GWAS) have rapidly evolved into a powerful tool for investigating complex traits, including abiotic stress responses such as drought, salt, or low nutrients. Here, we report workflow steps in genome-scan study in sunflower (Helianthus annus L.) to identify quantitative traits from field screens of diverse genotypes and map specific naturally occurring stress tolerance loci. A set of 283 inbred lines capturing a large proportion of allelic and substantial phenotypic diversity served as germplasm diversity pool in this study. To test for associations, a total 477,211 SNPs generated from the whole-genome shotgun resequencing data were used in data analysis. We detail the data quality assessment and critical steps that provided the best quality data used for association mapping, analyze patterns of linkage disequilibrium and use the resulting dataset in a preliminary search for the genomic footprints of abiotic stress resistance.