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PMID: 22158310 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.

Nature biotechnology ·Vol. 30 ·No. 1 ·2011-12-11 ·Pages 105-11

Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W

Abstract

Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.

MeSH Terms
Breeding Chromosome Mapping Evolution, Molecular Genetic Markers/genetics Genetic Variation Genome, Plant/genetics Linkage Disequilibrium Oryza/genetics Phylogeny Polymorphism, Single Nucleotide/genetics Population Selection, Genetic Sequence Analysis, DNA/methods
Chemicals
Genetic Markers
Authors & Affiliations
25 authors, click to expand affiliations / ORCID
Xu Xun
CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China.
Liu Xin
Ge Song
Jensen Jeffrey D
Hu Fengyi
Li Xin
Dong Yang
Gutenkunst Ryan N
Fang Lin
Huang Lei
Li Jingxiang
He Weiming
Zhang Guojie
Zheng Xiaoming
Zhang Fumin
Li Yingrui
Yu Chang
Kristiansen Karsten
Zhang Xiuqing
Wang Jian
Wright Mark
McCouch Susan
Nielsen Rasmus
Wang Jun
Wang Wen
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Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.2050
Published
2011-12-11
Epub
2011-00-11
Pages
105-11
Language
English
Region
United States
NLM ID
9604648
Subset
IM
External Links
PubMed source DOI: 10.1038/nbt.2050 View journal details
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