International Rice Research Institute (IRRI), Laguna 4031, Philippines.
University of the Southern Mindanao, Kabacan, Cotabato 9407, Philippines.
Genes (Basel). 2019 Jan 8;10(1):30. doi: 10.3390/genes10010030.
Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were and and and respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.
有色稻米富含营养，也是营养、谷物品质、抗病虫害等性状的有价值基因/数量性状位点（QTL）的良好来源，可用于水稻育种。利用高密度单核苷酸多态性（SNP）进行全基因组关联分析有助于精确检测 QTL 和基因。我们利用 22112 个 SNP 在 152 份有色稻品种中进行了全基因组关联分析，以定位营养、农艺和细菌性条斑病（BLB）抗性性状的 QTL。除花青素含量和 BLB 抗性外，大多数性状的表现均呈现出广泛的变化和正态分布。结构和主成分分析显示存在两个亚群。连锁不平衡（LD）分析显示，74.3%的标记对处于完全 LD 状态，平均 LD 距离为 1000 kb，有趣的是，36%的 LD 对小于 5 Kb，表明该群体中存在高重组。总共鉴定出 10 个性状的 57 个 QTL，这些 QTL 的表型方差解释（PVE）在 9%至 18%之间变化。有趣的是，30 个（53%）QTL 与已知或功能相关的基因共定位。一些与籽粒锌（Zn）和 BLB 抗性相关的重要候选基因分别是 、 、 、 。锌和花青素含量都很高的红米品种 Sayllebon 可能是培育营养丰富水稻的宝贵材料。总体而言，本研究中鉴定的 QTL 可用于 QTL 聚合以及基因组选择。一些新的 QTL 可以通过精细定位和功能表征进一步验证。结果表明，有色稻米是矿物质元素和抗氧化化合物的宝贵资源；它还可以为抗病性以及产量构成性状提供新的等位基因。因此，进一步探索和利用更多的有色稻品种用于育种具有很大的机会。
