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

Xun Xu, Xin Liu, Song Ge, Jeffrey D. Jensen, Fengyi Hu, Xin Li, Yang Dong, Ryan N. Gutenkunst, Lin Fang, Lei Huang, Jingxiang Li, Weiming He, Guojie Zhang, Xiaoming Zheng, Fumin Zhang, Yingrui Li, Chang Yu, Karsten Kristiansen, Xiuqing Zhang, Jian WangMark Wright, Susan McCouch, Rasmus Nielsen, Jun Wang, Wen Wang

Research output: Contribution to journalArticlepeer-review

661 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)105-111
Number of pages7
JournalNature biotechnology
Issue number1
StatePublished - Jan 2012
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering


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