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

Nature Genetics 44, 32–39 (2012) doi:10.1038/ng.1018

Abstract：

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.