Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.

中文翻译：

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综合组学分析阐明了大豆种子重量和含油量的遗传基础

在过去的几十年里，传统育种对关键农艺性状的协同优化极大地提高了作物生产力。然而，产量和质量相关性状协调调控的遗传基础仍然知之甚少。在这里，我们使用 421 个大豆 (Glycine max) 种质，结合全基因组关联研究 (GWAS) 和全转录组关联研究 (TWAS)，剖析了种子重量和含油量的遗传结构。我们通过 GWAS 分别鉴定了 26 个和 33 个与种子重量和含油量显着相关的基因位点，并根据群体转录组检测了调节 3,347 个基因表达的 5,276 个表达数量性状位点 (eQTL)。有趣的是，由两个 eQTL 热点调控的基因模块 (IC79) 与种子重量和含油量均表现出显着相关性。TWAS 进一步对种子性状的 22 个候选因果基因进行了优先排序，其中包括编码钠泵蛋白的重量和种子油调节器 1 (GmRWOS1)。GmRWOS1 被证实可以通过基因敲除和过度表达来多效性调节种子重量和含油量。值得注意的是，GmRWOS1 的等位基因变异在大豆驯化过程中受到强烈选择。该研究揭示了大豆种子重量和含油量调控的遗传基础和网络，为通过分子育种提高大豆产量和品质提供了宝贵的资源。