title: Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm.
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.
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Xuehui
authors.initials: X
authors.lastname: Huang
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
authors.forename: Canyang
authors.initials: C
authors.lastname: Li
authors.forename: Ahong
authors.initials: A
authors.lastname: Wang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Wenjun
authors.initials: W
authors.lastname: Li
authors.forename: Yunli
authors.initials: Y
authors.lastname: Guo
authors.forename: Liuwei
authors.initials: L
authors.lastname: Deng
authors.forename: Chuanrang
authors.initials: C
authors.lastname: Zhu
authors.forename: Danlin
authors.initials: D
authors.lastname: Fan
authors.forename: Yiqi
authors.initials: Y
authors.lastname: Lu
authors.forename: Qijun
authors.initials: Q
authors.lastname: Weng
authors.forename: Kunyan
authors.initials: K
authors.lastname: Liu
authors.forename: Taoying
authors.initials: T
authors.lastname: Zhou
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Jing
authors.forename: Lizhen
authors.initials: L
authors.lastname: Si
authors.forename: Guojun
authors.initials: G
authors.lastname: Dong
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.forename: Tingting
authors.initials: T
authors.lastname: Lu
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.forename: Jiayang
authors.initials: J
authors.lastname: Li
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D002523:Edible Grain / Q000235:genetics; D035264:Flowers / Q000235:genetics; D020869:Gene Expression Profiling; D017343:Genes, Plant; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D006239:Haplotypes; D012275:Oryza / Q000235:genetics*; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA