Rice (Oryza sativa L.) end‐use cooking quality is vital for producers and billions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality provides essential information for improved breeding strategies to enhance desirable traits that are stable across variable climatic and environmental conditions. In this study, genome‐wide association (GWA) analysis of three rice diversity panels, the USDA rice core subset (1364 accessions), the minicore (MC) (173 accessions after removing non‐sativa), and the high density rice array–MC (HDMC) (383 accessions), with simple sequence repeats, single nucleotide polymorphic markers, or both, revealed large‐ and small‐effect loci associated with known genes and previously uncharacterized genomic regions. Clustering of the significant regions in the GWA results suggests that multiple grain quality traits are inherited together. The 11 novel candidate loci for grain quality traits and the seven candidates for grain chalk identified are involved in the starch biosynthesis pathway. This study highlights the intricate pleiotropic relationships that exist in complex genotype–phenotypic associations and gives a greater insight into effective breeding strategies for grain quality improvement.

中文翻译：

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三种不同水稻种质资源对谷粒品质性状的调控

稻（稻L.）最终使用蒸煮品质是全球生产和十亿消费者的关键。谷物质量是具有相互影响的遗传和环境因素的复杂特征。解读与谷物品质相关的复杂遗传结构，为改进育种策略提供了重要信息，以增强在不同气候和环境条件下稳定的理想性状。在这项研究中，对三个水稻多样性小组的全基因组关联（GWA）分析，USDA水稻核心子集（1364个登录号），迷你核心（MC）（去除非苜蓿后的173个登录号）），以及具有简单序列重复和/或单核苷酸多态性标记的高密度水稻阵列MC（HDMC）（383份），揭示了与已知基因和以前未鉴定的基因组区域相关的大，小效应基因座。GWA结果中重要区域的聚类表明，多个谷物品质性状是一起遗传的。淀粉生物合成途径涉及11个新的谷物品质性状候选基因座和7个已鉴定的谷物白垩基因候选物。这项研究突出了复杂的基因型-表型关联中存在的复杂多效性关系，并为提高谷物质量的有效育种策略提供了更深入的了解。