Genome-wide association studies of 14 agronomic traits in rice landraces.
Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.
National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
Xuehui
X
Huang
Xinghua
X
Wei
Tao
T
Sang
Qiang
Q
Zhao
Qi
Q
Feng
Yan
Y
Zhao
Canyang
C
Li
Chuanrang
C
Zhu
Tingting
T
Lu
Zhiwu
Z
Zhang
Meng
M
Li
Danlin
D
Fan
Yunli
Y
Guo
Ahong
A
Wang
Lu
L
Wang
Liuwei
L
Deng
Wenjun
W
Li
Yiqi
Y
Lu
Qijun
Q
Weng
Kunyan
K
Liu
Tao
T
Huang
Taoying
T
Zhou
Yufeng
Y
Jing
Wei
W
Li
Zhang
Z
Lin
Edward S
ES
Buckler
Qian
Q
Qian
Qi-Fa
QF
Zhang
Jiayang
J
Li
Bin
B
Han
D000383:Agriculture; D001483:Base Sequence; D002681:China; D032461:Chromosomes, Plant; D018556:Crops, Agricultural / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005843:Geography; D015810:Linkage Disequilibrium; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci