Integrative GWAS and transcriptomic analyses identify candidate genes associated with oil content and fatty acid composition in safflower

BACKGROUND: This study investigates the genetic basis of oil content, fatty acid (FA) composition, and seed yield in safflower (Carthamus tinctorius L.) to support breeding efforts aimed at improving oil quality and yield. A genome-wide association study (GWAS) was conducted on 262 safflower accessions using 4,545 SNP markers to identify genetic loci associated with oil-related traits. Additionally, RNA-seq was performed to analyze gene expression differences between high- and low-oleic safflower varieties. RESULTS: GWAS identified 64 significant genetic loci, with chromosome 10 showing a high concentration of markers linked to key oil traits, including oleic acid, linoleic acid, vaccenic acid, oil content, and oil yield. Transcriptome analysis revealed 206 genes involved in lipid metabolism, including those related to FA synthesis and oil accumulation. Several transcription factors were also identified as putative regulators of these processes. Real-time quantitative reverse transcription PCR (qRT-PCR) confirmed the expression levels of five selected differentially expressed genes, chosen based on statistical significance and functional relevance to lipid metabolism. CONCLUSIONS: The integration of GWAS and transcriptome analyses provided valuable insights into the genetic and molecular mechanisms underlying oil production in safflower. These findings can be applied to develop safflower varieties with enhanced oil content and quality, benefiting both agricultural and industrial applications.