Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice ac
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alysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions 1,2†
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Xiuxiu Li , Zhuo Chen , Guomin Zhang , Hongwei Lu , Peng Qin , Ming Qi , Ying Yu , 1 1 1 4 5,6 3 Bingke Jiao , Xianfeng Zhao , Qiang Gao , Hao Wang , Yunyu Wu , Juntao Ma , 3 3 3 1 1 7 Liyan Zhang , Yongli Wang , Lingwei Deng , Shanguo Yao , Zhukuang Cheng , Diqiu Yu , 1 1 1 5,6* 4* 1,2* LihuangZhu , Yongbiao Xue , Chengcai Chu , Aihong Li , Shigui Li & Chengzhi Liang 1
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese
Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; 3 Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; 4 Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 2
Chengdu 611130, China; Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225009, China; 6 Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China; 7 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China 5
Received January 15, 2020; accepted March 16, 2020; published online April 15, 2020
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. rice, Chinese cultivars, whole-genome resequencing, multi-environmental phenotyping, genome-wide association studies, favorable alleles Citation:
Li, X., Chen, Z., Zhang, G., Lu, H., Qin, P., Qi, M., Yu, Y., Jiao, B., Zhao, X., Gao, Q., et al. (2020). Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice acce
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