Background

Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.

Results

To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90 K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.

Conclusions

Through evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.

中文翻译：

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苗期水稻生根能力的全基因组关联研究。

背景

水稻生根能力是一个复杂的农艺性状，表现出杂种优势，在水稻生长和生产中起着重要作用。双亲群体仅鉴定了几个数量性状基因座（QTL）。剖析水稻生根能力的遗传结构需要更多的基因或QTL。

结果

为了表征水稻生根能力的遗传基础，我们使用了以90 K单核苷酸多态性（SNP）阵列进行基因分型的天然水稻种群，以通过全基因组关联研究（GWAS）鉴定与生根相关性状相关的基因座。 。种群结构分析将自然种群分为两个亚组：in稻和粳稻。我们测量了四个用于评估水稻生根能力的特征，即根系生长能力（RGA），最大根长（MRL），根长（RL）和根数（RN）。使用在三个小组组成一个完整的人口，一个协会研究籼稻，以及一个用于粳稻鉴定出24个与生根能力相关性状相关的SNP。通过比较具有极端表型的种质之间的相对表达水平和DNA序列，结果表明LOC_Os05g11810在编码区具有非同义变异，这可能导致根数差异，并且LOC_Os04g09900和LOC_Os04g10060的表达水平密切相关。根长变化。

结论

通过对水稻生根能力的相关性状的评价和关联图谱的研究，为了解水稻生根能力的遗传基础提供了有用的信息，并为水稻根系育种确定了一些候选基因和分子标记。