Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association.
Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association.
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DOI：
10.3390/plants12040927
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发表时间：
2023-02-17
期刊：
影响因子：
--
通讯作者：
Yu S
中科院分区：
文献类型：
--
作者：
Wang W;Qiu X;Wang Z;Xie T;Sun W;Xu J;Zhang F;Yu S
全麦大米被推荐用于天然健康饮食，因为与精米或白米相比，全麦大米具有高营养和健康益处。全谷物含有多种颜色（如棕色、红色和黑色）的果皮，与口味和商业品质相关。全谷物或糙米的颜色属性通常不理想，需要改进。为了破译全粒稻米颜色变异的遗传基础，我们对 682 个稻米品种的稻谷颜色三个参数（亮度、红色和黄色）进行了全基因组关联分析。确定了 26 个颜色参数基因座，这意味着谷物颜色受到多基因控制。其中，一些主效应位点与先前鉴定的基因如Rc和Rd共定位。为了消除 Rc 在影响谷物颜色的其他基因座上可能存在的掩码，我们在排除了色素（红米和黑米）的面板子集中进行了关联分析。检测到 18 个位点或 SNP 与亚群中的谷物颜色相关，其中许多以前从未报道过。使用近等基因系验证了 1 号和 9 号染色体上的两个显着峰值 SNP 区域。基于SNP区域内注释基因的差异表达分析和汇集的极端样本的代谢分析，我们发现至少三个注释基因作为参与与果皮颜色相关的黄酮类代谢途径的潜在候选基因。这些结果为了解稻米颜色的遗传基础提供了见解，并促进基因组育种，以改善全粒稻的外观和商业质量。
Whole grain rice is recommended in a natural healthy diet because of its high nutritional and healthful benefits compared to polished or white rice. The whole grain contains the pericarp with many assorted colors (such as brown, red, and black) associated with taste and commercial quality. The color attributes of whole grain or brown rice are usually undesirable and need to be improved. To decipher the genetic basis of color variation in the whole grain rice, we conducted a genome-wide association analysis of three parameters of grain colors (brightness, redness, and yellowness) in a panel of 682 rice accessions. Twenty-six loci were identified for the color parameters, implying that grain color is under polygenic control. Among them, some major-effect loci were co-localized with the previously identified genes such as Rc and Rd. To eliminate the possible mask of Rc on other loci influencing grain color, we performed the association analysis in a subset of the panel that excluded the pigmented (red and black) rice. Eighteen loci or SNPs were detected to be associated with grain color in the subpopulation, many of which were not reported before. Two significant peak SNP regions on chromosomes 1 and 9 were validated using near-isogenic lines. Based on differential expression analysis of annotated genes within the SNP regions and metabolic analysis of pooled extreme samples, we found at least three annotated genes as potential candidates involved in the flavonoid metabolic pathway related to pericarp color. These results provide insights into the genetic basis of rice grain color and facilitate genomic breeding to improve appearance and commercial quality of whole grain rice.
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