Soybean is a major oil crop in the world, and fatty acids are the predominant components for oil bio-synthesis and catabolism metabolisms and also are the most important energy resources for organisms. In view of this, two recombinant inbred line (RIL) populations (ZL-RIL and ZQ-RIL) and one natural population were evaluated for five individual seed fatty acid contents (palmitic acid, stearic acid, oleic acid, linoleic acid, and linolenic acid) under four different environments, simultaneously. In total, sixteen additive QTL clusters were identified in ZL-RIL population, and fifteen were stably expressed across multiple environments or had pleiotropic effects on various fatty acid contents. Furthermore, five and five of these 16 QTL clusters were verified in ZQ-RIL population and natural population, respectively. Among these consistent and stable QTL clusters, one QTL cluster controlling fatty acid on chromosome 5 with pleiotropic effect was identified under all of the environments in ZL-RIL and ZQ-RIL populations and also was validated in the natural population. Meanwhile, another stable QTL cluster was detected on chromosome 9 with pleiotropic effect under multiple environments in ZL-RIL population and was further verified by the natural population. More importantly, some causal genes, such as the genes on chromosome 9, involving in the fatty acid catabolism process were found in these stable QTL clusters, and some of them, such as Gm09G042000, Gm09G041500, and Gm09G047200 on chromosome 9, showed different expressions in ZL-RIL parents (Zheng92116 and Liaodou14) based on the transcriptome sequencing analysis at different seed developmental stages. Thus, the study results provided insights into the genetic basis and molecular markers for regulating seed fatty acid contents in soybean breeding program.

大豆是世界主要油料作物，脂肪酸是油脂生物合成和分解代谢的主要成分，也是生物体最重要的能源。鉴于此，对两个重组自交系（RIL）群体（ZL-RIL和ZQ-RIL）和一个自然群体的五种种子脂肪酸含量（棕榈酸、硬脂酸、油酸、亚油酸和亚麻酸）进行了评估。酸）同时在四种不同的环境下进行。ZL-RIL群体中总共鉴定出16个加性QTL簇，其中15个在多种环境中稳定表达或对各种脂肪酸含量具有多效性。此外，这16个QTL簇中的5个和5个分别在ZQ-RIL群体和自然群体中得到验证。在这些一致且稳定的QTL簇中，在ZL-RIL和ZQ-RIL群体的所有环境下都鉴定出了一个具有多效性的控制5号染色体上脂肪酸的QTL簇，并且也在自然群体中得到了验证。同时，在ZL-RIL群体中在9号染色体上检测到另一个在多种环境下具有多效性的稳定QTL簇，并得到自然群体的进一步验证。更重要的是，在这些稳定的QTL簇中发现了一些参与脂肪酸分解代谢过程的致病基因，如9号染色体上的基因，其中一些基因，如9号染色体上的Gm09G042000、Gm09G041500和Gm09G047200表现出不同的表达。基于不同种子发育阶段的转录组测序分析，发现ZL-RIL亲本（Zheng92116和Liaoodou14）。因此，该研究结果为大豆育种计划中调节种子脂肪酸含量的遗传基础和分子标记提供了见解。