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

Xu, Xun, 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 and Wang, Wen (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology, 30 1: 105-111. doi:10.1038/nbt.2050


Author Xu, Xun
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
Title Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
Journal name Nature Biotechnology   Check publisher's open access policy
ISSN 1087-0156
1546-1696
Publication date 2012-01-01
Year available 2011
Sub-type Article (original research)
DOI 10.1038/nbt.2050
Open Access Status Not yet assessed
Volume 30
Issue 1
Start page 105
End page 111
Total pages 7
Place of publication New York, NY, United States
Publisher Nature Publishing Group
Language eng
Formatted 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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