Genome wide association study identifies candidate genes related to fatty acid components in upland cotton (Gossypium hirsutum L.)

As an important source of edible vegetable oil, cottonseed oil and its fatty acid composition that determines its nutritional value have attracted growing attention in recent years. For the identification of the quantitative trait loci (QTLs) underpinning cottonseed oil content and fatty acid components, 83 representative upland cotton accessions grown in multiple environments were used in a genome-wide association study (GWAS) base on a CottonSNP63K array. Two, 8, 35, 26, 1, 3, 7 and 50 QTLs were identified for myristicoleic acid, palmitic acid, palmitoleic acid, oleic acid, linoleic acid, linolenic acid, total fatty acids and oil content, respectively. Four stable QTLs related to oleic acid accumulation, including qOA-D11-1, qOA-A05-2, qOA-D01-1, and qOA-D07-4, were identified. The candidate genes for these QTLs were further suggested as Gh_D11G0990, Gh_A05G2242, Gh_D01G2016 and Gh_D07G1914, respectively, based on haplotype block analysis and strong and direct linkage disequilibrium between significant SNPs and the genes. The ectopic expression of Gh_D01G2016 in yeast resulted in reductions in oil content and oleic acid content by 18.1% and 9.91%, respectively. The identification of Gh_D01G2016 as a candidate gene in regulating oil synthesis not only facilitates the understanding of the intricate mechanism underpinning the cottonseed oil biosynthesis, but also provide a potentially useful tool for molecular breeding and genetic modification of cottonseed oil.