Plant Genome. 2019 Mar;12(1). doi: 10.3835/plantgenome2017.09.0085.
Rice ( 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-), 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.
大米（L.）的终用途烹饪品质对全球的生产者和数十亿消费者来说至关重要。谷物品质是一个复杂的性状，受到遗传和环境因素的相互作用。解析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，对三个水稻多样性面板进行了全基因组关联（GWA）分析，即美国农业部水稻核心子集（1364 个品系）、微核心（MC）（去除非 MC 后 173 个品系）和高密度水稻微核心阵列（HDMC）（383 个品系），使用简单序列重复、单核苷酸多态性标记或两者兼用，揭示了与已知基因和以前未表征的基因组区域相关的大效应和小效应位点。GWA 结果中显著区域的聚类表明，多个谷物品质性状是一起遗传的。11 个新的候选基因位点和 7 个候选谷白垩质基因位点都参与了淀粉生物合成途径。这项研究强调了复杂基因型-表型关联中存在的错综复杂的多效关系，并深入了解了谷物品质改良的有效育种策略。
