National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
Nat Genet. 2011 Dec 4;44(1):32-9. doi: 10.1038/ng.1018.
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.
最近，高密度单倍型图谱使对中国水稻地方品种籼亚种的全基因组关联研究（GWAS）成为可能。在这里，我们将这种方法扩展到包括 Oryza sativa indica 和 Oryza sativa japonica 亚种在内的 950 个全球水稻品种的更大、更多样化的样本中，以进行额外的 GWAS。我们总共鉴定出 32 个与开花时间和 10 个与谷物相关的性状相关的新位点，表明更大的样本增加了使用 GWAS 检测与性状相关变体的能力。为了描述各种等位基因和复杂的遗传变异，我们开发了一个基于单倍型的从头组装水稻低覆盖率测序数据的分析框架。我们通过详细注释鉴定了 18 个相关位点的候选基因。这项研究表明，基于序列的 GWAS 和功能基因组注释的综合方法有可能将复杂性状与其在水稻中的因果多态性联系起来。
