The Rice Diversity Panel 1 (RDP1) was developed for genome‐wide association (GWA) studies to explore five rice (Oryza sativa L.) subpopulations (indica, aus, aromatic, temperate japonica, and tropical japonica). 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 tropical japonica and thus the diversity in this subpopulation is interesting to U.S. breeders. Among the RDP1 tropical japonica 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 tropical japonica 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 R² values will be evaluated as potential DNA markers useful to breeding programs for the associated yield trait.

中文翻译：

---

通过基因组-全关联图谱鉴定热带粳稻×热带粳稻双亲作图群体的产量构成特征。

水稻多样性研究小组1（RDP1）专为全基因组关联（GWA）研究而开发，旨在探索5个水稻（Oryza sativa L.）亚种群（in，澳大利亚，芳香族，温带粳稻和热带粳稻）。RDP1被评估超过30个性状，包括农艺，穗构型，种子和疾病性状，并具有700,000个单核苷酸多态性（SNP）的基因型。美国南部种植的大多数稻米是热带粳稻，因此，这一子种群的多样性对美国育种家来说很有趣。在RDP1热带粳稻中品名“ Estrela”和“ NSFTV199”在表型和基因型上都不同，因此使其成为双亲作图群体的优良亲本。目的是（i）从RDP1 GWA研究确定与在Estrela×NSFTV199热带粳稻中发现的QTL重叠的GWA QTL。重组近交系（RIL）群体评估了15个产量性状，并且（ii）识别可能控制特定产量成分性状的已知或新颖基因。用132个简单序列重复标记对256个RIL进行基因分型，发现70个QTL。开发Perl脚本以自动识别GWA QTL区域中的潜在候选基因。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。具有重叠的GWA QTL的两个种子性状RIL QTL与已知基因无关。对于具有高R ²值的RIL QTL，在重叠GWA QTL中分离SNP将被评估为潜在的DNA标记，可用于育种相关产量性状的程序。