Genome-wide association study of rice grain width variation

文献类型： 外文期刊

第一作者： Zheng, Xiao-Ming

作者： Zheng, Xiao-Ming;Gong, Tingting;Qiao, Weihua;Wang, Junrui;Liu, Sha;Yang, Qingwen;Zheng, Xiao-Ming;Olsen, Kenneth M.;Gong, Tingting;Xue, Dayuan;Ou, Hong-Ling

作者机构：

关键词： grain size; genome-wide association study (GWAS); General Linear Model (GLM); Mixed Linear Model (MLM); Oryza sativa; rice

期刊名称：GENOME （ 影响因子：2.166； 五年影响因子：2.474 ）

ISSN： 0831-2796

年卷期： 2018 年 61 卷 4 期

页码：

收录情况： SCI

摘要： Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1.9 million genome-wide SNPs in a sample of 570 cultivated and wild rice accessions, we performed GWAS with two complementary models, GLM and MLM. The models yielded 10 and 33 significant associations, respectively, and jointly yielded seven candidate locus regions, two of which have been previously identified. Analyses of nucleotide diversity and haplotype distributions at these loci revealed signatures of selection and patterns consistent with adaptive introgression of grain width alleles across rice variety groups. The results provide a 50% increase in the total number of rice grain width loci mapped to date and support a polygenic model whereby grain width is shaped by gene-by-environment interactions. These loci can potentially serve as candidates for studies of adaptive seed size variation in wild grass species.

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