Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm |
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Authors: | Huang Xuehui Zhao Yan Wei Xinghua Li Canyang Wang Ahong Zhao Qiang Li Wenjun Guo Yunli Deng Liuwei Zhu Chuanrang Fan Danlin Lu Yiqi Weng Qijun Liu Kunyan Zhou Taoying Jing Yufeng Si Lizhen Dong Guojun Huang Tao Lu Tingting Feng Qi Qian Qian Li Jiayang Han Bin |
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Institution: | National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. |
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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. |
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