High-resolution mapping of QTL for fatty acid composition in soybean using specific-locus amplified fragment sequencing

KEY MESSAGE: We constructed a high-density linkage map comprising 3541 markers developed by specific-locus amplified fragment sequencing, and identified 26 stable QTL including nine novel loci, for fatty acid composition in soybean. ABSTRACT: Soybean oil quality and stability are mainly determined by the fatty acid composition of the seed. In the present study, we constructed a high-density genetic linkage map using 200 recombinant inbred lines derived from a cross between cultivated soybean varieties Luheidou2 and Nanhuizao, and SNP markers developed by specific-locus amplified fragment sequencing (SLAF-seq). This map comprises 3541 markers on 20 linkage groups and spans a genetic distance of 2534.42 cM, with an average distance of 0.72 cM between adjacent markers. Inclusive composite interval mapping revealed 26 stable QTL for five fatty acids, explaining 0.4–37.0% of the phenotypic variance for individual fatty acids across environments. Of these QTL, nine are novel loci (qLA1, qLNA2_1, qPA4_1, qLA4_1, qPA6_1, qSA12_1, qPA16_1, qOA18_1, and qFA19_1). These stable QTL harbor three fatty acid biosynthesis genes (GmFabG, GmACP, and GmFAD8), and 66 genes encoding lipid-related transcription factors. These stable QTL and tightly linked SNP markers can be used for marker-assisted selection in soybean breeding programs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-017-2902-8) contains supplementary material, which is available to authorized users.