QTL mapping of major fatty acids and identification of candidate genes in cottonseed in an introgression line population from Gossypium hirsutum × Gossypium barbadense

Cottonseed as a by-product of cotton production is an important source of oil and proteins. In this study, the genetic basis of cottonseed fatty acid composition traits was studied through quantitative trait locus (QTL) mapping in an interspecific backcross inbred line (BIL) population of 250 lines grown. Based on 7709 single nucleotide polymorphic (SNP) markers, 117 QTLs were identified for the contents of all major fatty acids. Nine stable QTLs were detected in at least three environments, within which six genes were identified as candidate genes. Introduction of Gh_D06G0548, Gh_D06G0571, and Gh_D06G0763 into transformed yeasts led to significant increases in fatty acid contents, especially palmitoleic acid. These findings not only shed more light on the molecular regulations of fatty acid biosynthesis and oil accumulation in cottonseed, but also provide a list of candidate genes for enhancing cottonseed oil content and improving fatty acid composition and its nutritional value. •117 QTLs were identified for the contents of all major fatty acids in cottonseeds.•Nine major QTLs and eight QTL clusters were found to regulate fatty acid content.•Six candidate genes related to cottonseed fatty acids were identified.•Three genes were found to participate in the dynamic accumulation of fatty acids.•Introduction of three genes into yeasts led to increases in fatty acid contents.