Plant Genome. 2019 Mar;12(1). doi: 10.3835/plantgenome2018.04.0021.
The Rice Diversity Panel 1 (RDP1) was developed for genome-wide association (GWA) studies to explore five rice ( L.) subpopulations (, , , , and ). The RDP1 was evaluated for over 30 traits, including agronomic, panicle architecture, seed, and disease traits and genotyped with 700,000 single nucleotide polymorphisms (SNPs). Most rice grown in the southern United States is and thus the diversity in this subpopulation is interesting to U.S. breeders. Among the RDP1 accessions, 'Estrela' and 'NSFTV199' are both phenotypically and genotypically diverse, thus making them excellent parents for a biparental mapping population. The objectives were to (i) ascertain the GWA QTLs from the RDP1 GWA studies that overlapped with the QTLs uncovered in an Estrela × NSFTV199 recombinant inbred line (RIL) population evaluated for 15 yield traits, and (ii) identify known or novel genes potentially controlling specific yield component traits. The 256 RILs were genotyped with 132 simple sequence repeat markers and 70 QTLs were found. Perl scripts were developed for automatic identification of the underlying candidate genes in the GWA QTL regions. Approximately 100 GWA QTLs overlapped with 41 Estrela × NSFTV199 QTL (RIL QTL) regions and 47 known genes were identified. Two seed trait RIL QTLs with overlapping GWA QTLs were not associated with a known gene. Segregating SNPs in the overlapping GWA QTLs for RIL QTLs with high values will be evaluated as potential DNA markers useful to breeding programs for the associated yield trait.
水稻多样性面板 1（RDP1）是为全基因组关联（GWA）研究开发的，用于探索五个水稻（L.）亚群（、、、和）。RDP1 评估了 30 多个性状，包括农艺性状、穗结构、种子和疾病性状，并使用 70 万个单核苷酸多态性（SNP）进行了基因分型。美国南部种植的大多数水稻是，因此该亚群的多样性对美国种植者很感兴趣。在 RDP1 品种中，“Estrela”和“NSFTV199”在表型和基因型上都具有多样性，因此它们是构建双亲作图群体的优秀亲本。目标是（i）从 RDP1 的 GWA 研究中确定与在 Estrela×NSFTV199 重组自交系（RIL）群体中发现的 QTL 重叠的 GWA QTL，该群体评估了 15 个产量性状，（ii）鉴定可能控制特定产量组成性状的已知或新基因。用 132 个简单序列重复标记对 256 个 RIL 进行了基因分型，发现了 70 个 QTL。为自动识别 GWA QTL 区域中的潜在候选基因开发了 Perl 脚本。大约 100 个 GWA QTL 与 41 个 Estrela×NSFTV199 QTL（RIL QTL）区域重叠，鉴定出 47 个已知基因。两个与重叠 GWA QTL 相关的种子性状 RIL QTL 与已知基因无关。重叠 GWA QTL 中与高值 RIL QTL 相关的分离 SNP 将被评估为与相关产量性状的育种计划有用的潜在 DNA 标记。
