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

被引：756

作者：

Huang, Xuehui ^{[1
,2
]}

Zhao, Yan ^{[1
,2
]}

Wei, Xinghua ^{[3
]}

Li, Canyang ^{[1
]}

Wang, Ahong ^{[1
]}

Zhao, Qiang ^{[1
]}

Li, Wenjun ^{[1
]}

Guo, Yunli ^{[1
]}

Deng, Liuwei ^{[1
]}

Zhu, Chuanrang ^{[1
]}

Fan, Danlin ^{[1
]}

Lu, Yiqi ^{[1
]}

Weng, Qijun ^{[1
]}

Liu, Kunyan ^{[1
]}

Zhou, Taoying ^{[1
]}

Jing, Yufeng ^{[1
]}

Si, Lizhen ^{[1
]}

Dong, Guojun ^{[1
]}

Huang, Tao ^{[1
]}

Lu, Tingting ^{[1
]}

Feng, Qi ^{[1
]}

Qian, Qian ^{[3
]}

Li, Jiayang ^{[4
]}

Han, Bin ^{[1
,2
]}

机构：

[1] Chinese Acad Sci, Natl Ctr Gene Res, Natl Ctr Plant Gene Res Shanghai, Inst Plant Physiol & Ecol,Shanghai Inst Biol Sci, Shanghai, Peoples R China

[2] Chinese Acad Sci, Key Lab Genome Sci & Informat, Beijing Inst Genom, Beijing, Peoples R China

[3] Chinese Acad Agr Sci, China Natl Rice Res Inst, State Key Lab Rice Biol, Hangzhou, Peoples R China

[4] Chinese Acad Sci, Natl Ctr Plant Gene Res, Inst Genet & Dev Biol, Beijing, Peoples R China

来源：

NATURE GENETICS | 2012年 / 44卷 / 01期

基金：

中国国家自然科学基金;

关键词：

SPATIAL GENE-EXPRESSION; ARABIDOPSIS-THALIANA; NATURAL VARIATION; MAPPING POPULATION; OPEN SOFTWARE; MAJOR QTL; ENCODES; PROTEIN; LOCUS; DOMESTICATION;

D O I：

10.1038/ng.1018

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：32 / U53

页数：10

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