Genome-Wide Association Study Uncovers Candidate Genes Governing Oil Quality Traits in Sunflower (Helianthus annuus L.)

Sunflower is a globally important oilseed crop. Improving its fatty acid composition is crucial for enhancing oil quality and nutritional value. To dissect the genetic basis of quality traits, we performed genome resequencing on 203 sunflower inbred lines and conducted a genome-wide association study (GWAS) for five traits—oil content, stearic acid, palmitic acid, oleic acid, and linoleic acid—across three environments. We identified 103 significant single-nucleotide polymorphisms (SNPs) and 154 candidate genes. Notably, several associated loci were co-localized for multiple traits, suggesting pleiotropic effects or close genetic linkages. Integration with transcriptome data from developing seeds revealed that 66 candidate genes were expressed within 30 days after pollination, of which 12 showed significant differential expression between high- and low-oleic acid varieties. Functional characterization of a selected candidate, the ω-6 fatty acid desaturase gene (LOC110938218, designated HaDES8.11), demonstrated that the HaDES8.11-eGFP fusion protein localizes to the endoplasmic reticulum. Heterologous expression of HaDES8.11 in Arabidopsis thaliana significantly increased seed linoleic acid content while decreasing oleic acid content, confirming its role in fatty acid desaturation. Our study provides novel genetic insights and valuable candidate genes for the molecular breeding of sunflower with optimized oil quality.