Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

• DOI: 10.1038/ng.1018
• Publication Date: 2011-12-04T18:36:47Z
• Authors: Xuehui Huang; Yan Zhao; Xinghua Wei; Canyang Li; Ahong Wang; Qiang Zhao; Wenjun Li; Yunli Guo; Liuwei Deng; Chuanrang Zhu; Danlin Fan; Yiqi Lu; Qijun Weng; Kunyan Liu; Taoying Zhou; Yufeng Jing; Lizhen Si; Guojun Dong; Tao Huang; Tingting Lu; Qi Feng; Qian Qian; Jiayang Li; Bin Han
• Keywords: Germ plasm; Genome-wide Association Study; Genetic Association; Association mapping; Subspecies; Oryza; Candidate gene; Imputation (statistics)

A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.