Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
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DOI：
10.1038/ng.1018
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发表时间：
2012-01-01
期刊：
影响因子：
30.8
通讯作者：
Han, Bin
中科院分区：
文献类型：
--
作者：
Huang, Xuehui;Zhao, Yan;Han, Bin
最近，一张高密度单倍型图谱在中国水稻地方品种的一个亚种群体中进行了全基因组关联研究。在这里，我们将这一方法扩展到全球950个水稻品种的更大和更多样化的样本，包括水稻亚种，包括水稻和水稻亚种，以执行额外的全球水稻气候分析。我们共发现了32个与开花时间相关的新基因座和10个与籽粒相关的性状，这表明更大的样本增加了利用GWAs检测性状相关变异的能力。为了表征不同的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水稻低覆盖率测序数据从头组装的分析框架。通过详细的注释，我们确定了18个相关基因座的候选基因。这项研究表明，基于序列的GWAS和功能基因组注释的集成方法有可能将复杂的性状与它们的因果多态相匹配。
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.