The most important objectives of soybean (Glycine max (L.) Merr.) breeding are to increase oil content and to improve oil quality. Although the biochemical processes of oil accumulation in oilseeds are very clear, knowledge of their underlying genetic mechanisms and regulation is limited. We performed RNA-Seq of soybean seeds from six accessions with high, medium and low seed oil contents. Through comparative genome analysis, promoter-enrichment study, and protein–protein interaction (PPI) analysis, 80 lipid-metabolism-related genes and 31 transcription factors were detected. The pathways of fatty acid elongation, desaturation and export from plastid (P = 2.53E-4), and triacylglycerol biosynthesis (P = 2.31E-8), were significantly over-represented in accessions with high total oil content. Further, in an integration analysis of RNA-Seq and a genome-wide association study (GWAS) database, 62 candidate genes were found to be associated with seed oil content, 73 with oleic acid content, and 83 with linolenic acid content. Of these, 60 genes were found to be involved mainly in metabolism of lipids (25), carbohydrates (24), and amino acids (11). Thirty are known oil-synthesis-related genes; LOX1, CYP93D1 and GPT2 for oil content, SAD and FAD2 for oleic acid, and FAD2, CYP89A6 and GPT2 for linolenic acid were detected twice. There were 22 genes found to be associated with at least two oil-related traits, and of 154 pairs of PPIs, two genes for each pair of 95 PPIs (62%) were found to be associated with various oil-related traits, indicating the genetic foundations of oil-related traits. Three transcription factor genes were found to be associated with oil-related traits: HRE2 (Glyma.10G016500), ERF12 (Glyma.13G236600) and WRKY6 (Glyma.15G110300). This study provides an efficient strategy for further discovery of mechanisms of oil composition and accumulation.

大豆育种（Glycine max（L.）Merr。）的最重要目标是增加油含量和改善油质。尽管油籽中油积累的生化过程非常清楚，但对其潜在的遗传机制和调控的了解仍然有限。我们从高，中，低种子油含量的六个种质中进行了大豆种子的RNA测序。通过比较基因组分析，启动子富集研究和蛋白质-蛋白质相互作用（PPI）分析，检测到80个与脂质代谢相关的基因和31个转录因子。质体的脂肪酸延伸，去饱和和输出途径（P = 2.53E-4）和三酰基甘油的生物合成（P= 2.31E-8），在总油含量高的种质中明显超标。此外，在RNA-Seq的整合分析和全基因组关联研究（GWAS）数据库中，发现62个候选基因与种子油含量，73个与油酸含量和83个与亚麻酸含量相关。其中，发现60个基因主要参与脂质（25），碳水化合物（24）和氨基酸（11）的代谢。已知有三十种与油合成有关的基因；LOX1，CYP93D1和GPT2用于含油量，SAD和FAD2用于油酸，FAD2，CYP89A6和GPT2对亚麻酸进行了两次检测。发现22个基因与至少两个与石油有关的性状相关，在154对PPI中，每对95个PPI的两个基因（62％）被发现与各种与石油有关的性状相关，表明石油相关性状的遗传基础。发现三个与油性相关的转录因子基因：HRE2（Glyma.10G016500），ERF12（Glyma.13G236600）和WRKY6（Glyma.15G110300）。该研究为进一步发现油的组成和聚集机理提供了有效的策略。