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.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Huang X,Zhao Y,Wei X,Li C,Wang A,Zhao Q,Li W,Guo Y,Deng L,Zhu C,Fan D,Lu Y,Weng Q,Liu K,Zhou T,Jing Y,Si L,Dong G,Huang T,Lu T,Feng Q,Qian Q,Li J,Han B

doi

10.1038/ng.1018

subject

Has Abstract

pub_date

2011-12-04 00:00:00

pages

32-9

issue

1

eissn

1061-4036

issn

1546-1718

pii

ng.1018

journal_volume

44

pub_type

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