Rice grain oil is a valuable nutrient source. However, the genetic basis of oil biosynthesis in rice grains remains unclear. In this study, we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions. High variation for 11 oil-related traits was observed, and the oil composition of rice grains showed differentiation among the subpopulations. We identified 46 loci that are significantly associated with grain oil concentration or composition, 16 of which were detected in three recombinant inbred line populations. Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci, four of which (PAL6, LIN6, MYR2, and ARA6) were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations. Interestingly, population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice. Based on these results, we propose a possible oil biosynthetic pathway in rice grains. Collectively, our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.

米粒油是一种宝贵的营养来源。然而，水稻籽粒油脂生物合成的遗传基础仍不清楚。在这项研究中，我们对 533 个栽培水稻品种的不同面板中的油组成和油浓度进行了全基因组关联研究。观察到 11 个油相关性状的高变异，并且稻米的油组成在亚群之间显示出分化。我们确定了 46 个与谷物油浓度或组成显着相关的基因座，其中 16 个在三个重组自交系群体中检测到。从这 46 个基因座中鉴定出 26 个编码石油代谢相关酶的候选基因，其中 4 个（PAL6、LIN6、MYR2和ARA6) 被发现有助于石油成分的自然变化，并显示出亚群之间的差异。有趣的是，群体遗传分析显示在粳稻中选择了PAL6和LIN6 的特定单倍型。基于这些结果，我们提出了一种可能的水稻籽粒油生物合成途径。总的来说，我们的研究结果为水稻籽粒油生物合成的遗传基础提供了新的见解，并可以促进基于标记的水稻品种的育种，以提高油和籽粒质量。