Genetic variation and association mapping for 12 agronomic traits in indica rice

Background: Increasing rice (Oryza sativa L.) yield is a crucial challenge for modern agriculture. The ideal plant architecture is considered to be critical to enhance rice yield. Elite plant morphological traits should include compact plant type, short stature, few unproductive tillers, thick and sturdy stems and erect leaves. To reveal the genetic variations of important morphological traits, 523 germplasm accessions were genotyped using the Illumina custom-designed array containing 5,291 single nucleotide polymorphisms (SNPs) and phenotyped in two independent environments. Genome-wide association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Results: In total, 126 and 172 significant loci were identified and these loci explained an average of 34.45 % and 39.09 % of the phenotypic variance in two environments, respectively, and 16 of 298 (~5.37 %) loci were detected across the two environments. For the 16 loci, 423 candidate gene...

背景：提升水稻（Oryza sativa L.）产量是现代农业面临的关键挑战。理想株型被认为是提高水稻产量的核心要素。优良植株形态性状应包含紧凑株型、矮秆、少量无效分蘖、粗壮茎秆以及直立叶片。为解析重要形态性状的遗传变异，本研究利用搭载5291个单核苷酸多态性（single nucleotide polymorphisms, SNPs）的定制化Illumina芯片，对523份种质资源材料进行基因型分型，并在两个独立环境中开展表型鉴定。本研究采用混合线性模型开展全基因组关联分析，以探究基因型与表型变异的关联。结果：在两个环境中分别鉴定到126个和172个显著关联位点，上述位点分别解释了两个环境下表型变异的平均34.45%与39.09%；在两个环境中均被检测到的位点共16个，占298个总位点的约5.37%。针对这16个位点，共筛选得到423个候选基因……