Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions

文献类型： 外文期刊

第一作者： Li, Xiuxiu

作者： Li, Xiuxiu;Chen, Zhuo;Lu, Hongwei;Qi, Ming;Yu, Ying;Jiao, Bingke;Zhao, Xianfeng;Gao, Qiang;Yao, Shanguo;Cheng, Zhukuang;Zhu, Lihuang;Xue, Yongbiao;Chu, Chengcai;Liang, Chengzhi;Li, Xiuxiu;Chen, Zhuo;Lu, Hongwei;Liang, Chengzhi;Zhang, Guomin;Ma, Juntao;Zhang, Liyan;Wang, Yongli;Deng, Lingwei;Qin, Peng;Wang, Hao;Li, Shigui;Wu, Yunyu;Li, Aihong;Wu, Yunyu;Li, Aihong;Yu, Diqiu

作者机构：

关键词： rice; Chinese cultivars; whole-genome resequencing; multi-environmental phenotyping; genome-wide association studies; favorable alleles

期刊名称：SCIENCE CHINA-LIFE SCIENCES （ 影响因子：6.038； 五年影响因子：4.754 ）

ISSN： 1674-7305

年卷期： 2020 年 63 卷 11 期

页码：

收录情况： SCI

摘要： Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies (GWAS). Several rice populations have been re-sequenced in the past decade; however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.

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