SSR- and SNP-related QTL underlying linolenic acid and other fatty acid contents in soybean seeds across multiple environments

Soybean fatty acids (FAs) are major sources of vegetable oil in the world. The FA composition of soybean is associated with the quality and nutritional value of its oil and food products. The polyunsaturated FAs, particularly linolenic acid (LN), are prone to oxidation by lipoxygenase isozymes and negatively affect the flavor and shelf-life of soybean products. The improvement of FA composition and the increase of oxidative stability has been a major goal of soybean breeding for decades. The objective of the present study was to identify quantitative trait loci (QTL) associated with the low LN and other FA contents in six environments. One hundred and twenty-five recombinant inbred lines (RILs) of F5:7, F5:8 and F5:9 generations derived by the single-seed-descent method from the cross of Hefeng 25 [LN 6.20%; linoleic acid (LI) 53.06%; oleic acid (OL) 19.75%; palmitic acid (PA) 12.16%; stearic acid (ST) 4.97%] and Dongnong L-5 (LN 2.53%; LI 59.30%; OL 24.24%; PA 10.0%; ST 3.99%) were used in this study. A total of 112 simple sequence repeat markers were used to construct a genetic linkage map. Six QTL associated with LN content, four QTL associated with LI content, four QTL associated with OL content, four QTL associated with PA content and one QTL associated with ST content were identified, and mapped onto different linkage groups (LGs). The QTL detected here explained 2.53–37.30% of phenotypic variation for individual FA in different environments or individual FA means. Of them, the beneficial alleles of QLNB2_1 (close to Satt726), QLNB2_2 (close to Fad3a-4) and QLND1b_1 (close to Satt701), which were associated with low LN content across various environments and LN means, were derived from Dongnong L-5. These three QTL might have great potential value in marker-assisted selection for low LN content in soybean seed.