PDF(Pubmed)
Abstract：
Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.
摘要：
直接播种的干水稻（dry-DSR）通常是深播种的，以避免灌溉的需要，因此，幼苗出苗是影响植物林分和产量的关键性状。为了培育耗水量少、气候适应性强的精英品种，了解在深播种的干DSR中产生的基因组区域和潜在基因将是非常有利的。用290万个单核苷酸多态性（SNP）评估了470个水稻种质（RDP1加上3KRGP的aus子集）的组合多样性面板，以鉴定与田间干DSR性状和受控环境性状的关联实验。使用全基因组关联研究(GWAS)分析，我们在1,2,4,5,6,7,9,10和11号染色体上发现了18个独特的QTL,解释了表型变异在2.6%到17.8%之间.三个QTL，即,qSOE-1.1，qEMERG-AUS-1.2和qEMERG-AUS-7.1与先前报道的中胚轴长度QTL位于同一位置。在确定的QTL中，一半与Aus的出现有关，六个是aus遗传组特有的。基于功能注释，我们确定了11个令人信服的候选基因，主要调节植物激素途径，如细胞分裂素，生长素,赤霉素,还有茉莉酸.先前的研究表明，这些植物激素在深播下的中胚轴长度中起关键作用。这项研究为aus和in作为理想的遗传资源的重要性提供了新的见解，以挖掘水稻深播耐受性的有利等位基因。本研究中鉴定的候选基因和标记标记的理想等位基因应直接有益于水稻育种计划。
