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

Research output: Contribution to journalJournal articlepeer-review

  • 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
  • Xiuqing Zhang
  • Jian Wang
  • Mark Wright
  • Susan McCouch
  • Jun Wang
  • Wen Wang
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 x 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
JournalNature Biotechnology
Volume30
Issue number1
Pages (from-to)105-111
Number of pages7
ISSN1087-0156
DOIs
Publication statusPublished - 2012

ID: 40903649