BACKGROUND Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. RESULTS The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg- 1, ranging from 0.22 mg.mg-1 to 0.93 mg.mg- 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg- 1 (RM7309-135 bp on chromosome 9) to 0.45 mg.mg- 1 (RM297-180 bp on chromosome 2). RM297-180 bp showed the largest phenotypic effect value (0.44 mg.mg- 1 in 2016 and 0.45 mg.mg- 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297-175 bp (0.43 mg.mg- 1 in 2016 and 0.44 mg.mg- 1 in 2017). CONCLUSION Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.

中文翻译：

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利用关联图谱挖掘水稻中有效利用的有利等位基因。

背景技术湿式直接播种稻米可以替代传统的混泥土插秧稻米。前者用水量少，减少了劳动力需求。提高种子储备利用效率（SRUE）是促进该技术应用的关键因素。但是，控制此特征的QTL进行的研究很少。在这项研究中，进行了一个全基因组关联研究（GWAS），该研究使用了由542份水稻（Oryza sativa L.）材料组成的自然种群，并利用266个SSR标记对它们进行了基因分型。在研究人群中发现SRUE的大表型变异。结果两年（2016年和2017年）542份材料的平均SRUE为0.52 mg.mg-1，范围从0.22 mg.mg-1至0.93 mg.mg-1，变异系数为22.66％。总体，通过266对SSR标记在人群中检测到2879个标记等位基因，表明该人群中存在较大的遗传变异。使用普通线性模型方法，使用混合线性模型分析检测到了13个与SRUE相关的SSR标记基因座，并且还检测到13个基因座中的两个（RM7309和RM434），表型变异百分比（PVE）大于5％两年 除11号染色体外，13个关联基因座（P <0.01）位于所有染色体上，PVE介于5.05％（5号染色体上的RM5158）到12％（1号染色体上的RM297）。在这两个模型中都检测到了两个模型揭示的染色体6上的关联基因座RM7309和染色体9上的RM434。确定了23个有利的等位基因，其表型效应值（PEV）为0.10 mg。mg-1（染色体9上的RM7309-135 bp）至0.45 mg.mg-1（染色体2上的RM297-180 bp）。RM297-180 bp表现出最大的表型效应值（2016年为0.44 mg.mg-1,2017年为0.45 mg.mg-1），其中6.72％的成分携带该等位基因，典型的携带者是Manyedao，其次是RM297- 175 bp（2016年为0.43 mg.mg-1,2017年为0.44 mg.mg-1）。结论与先前的研究相比，确定了九个新的SRUE关联基因座。选择了最佳的亲本组合，以便对SRUE的更有利的等位基因进行金字塔化，并可以用于将来适合湿法直接播种的水稻材料的育种。携带该等位基因和典型携带者的72％的种质是Manyedao，其次是RM297-175 bp（2016年为0.43 mg.mg-1和2017年为0.44 mg.mg-1）。结论与先前的研究相比，确定了9个新的SRUE关联基因座。选择了最佳的亲本组合，以便对SRUE的更有利的等位基因进行金字塔化，并可以用于将来适合湿法直接播种的水稻材料的育种。携带该等位基因和典型携带者的72％的种质是Manyedao，其次是RM297-175 bp（2016年为0.43 mg.mg-1和2017年为0.44 mg.mg-1）。结论与先前的研究相比，确定了9个新的SRUE关联基因座。选择了最佳的亲本组合，以便对SRUE的更有利的等位基因进行金字塔化，并可以用于将来适合湿法直接播种的水稻材料的育种。