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 Genetjournal_title
Nature geneticsauthors
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 Bdoi
10.1038/ng.1018subject
Has Abstractpub_date
2011-12-04 00:00:00pages
32-9issue
1eissn
1061-4036issn
1546-1718pii
ng.1018journal_volume
44pub_type
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