Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome-wide association study (GWAS) using a combined population panel of indica and japonica rice varieties, and identified a total of 746 single nucleotide polymorphisms (SNPs) that were strongly associated with the chalk phenotype, covered 78 Quantitative Trait Loci (QTL) regions. Among them, 21 were high-value QTLs, as they explained at least 10 % of the phenotypic variance for PGC. A combined epistasis and GWAS was applied to dissect the genetics of the complex chalkiness trait, and its regulatory cascades were validated using gene regulatory networks. Promising novel epistatic interactions were found between the loci of chromosomes 6 (PGC6.1) and 7 (PGC7.8) that contributed to lower PGC. Based on haplotype mining only a few modern rice varieties confounded with a lower chalkiness, and they possess several PGC QTLs. The importance of PGC6.1 was validated through multi-parent advanced generation intercrosses and several low-chalk lines possessing superior haplotypes were identified. The results of this investigation have deciphered the underlying genetic networks that can reduce PGC to 2%, and will thus support future breeding programs to improve the grain quality of elite genetic material with high-yielding potentials.

中文翻译：

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全基因组关联耦合基因与基因相互作用研究揭示了影响稻谷垩白的主要效应位点中的新上位靶点

质量被评为优秀的稻米品种具有较低的谷物白垩度（PGC）百分比（PGC），低于2％，碾磨后的全谷物产量较高，从而为农民带来更高的经济回报。我们使用籼稻和粳稻的组合种群面板进行了全基因组关联研究 (GWAS)水稻品种，共鉴定了 746 个与粉笔表型密切相关的单核苷酸多态性 (SNP)，覆盖 78 个数量性状基因座 (QTL) 区域。其中，21 个是高价值 QTL，因为它们解释了 PGC 至少 10% 的表型变异。应用组合上位性和 GWAS 来剖析复杂白垩性状的遗传学，并使用基因调控网络验证其调控级联。在染色体 6 ( PGC6.1 ) 和 7 ( PGC7.8 )的基因座之间发现了有希望的新型上位相互作用，这有助于降低 PGC。基于单倍型挖掘，只有少数现代水稻品种混杂了较低的垩白性，并且它们具有多个PGC QTL。PGC6.1的重要性通过多亲先进代杂交进行了验证，并鉴定了几个具有优良单倍型的低粉笔系。这项调查的结果已经破译了可以将 PGC 降低到 2% 的潜在遗传网络，因此将支持未来的育种计划，以提高具有高产潜力的优良遗传材料的谷物质量。