Rice SNP Markers


  • Parida et.al 2012 reported validation of 362 SNPs out of total 384 putative SNPs. Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Table.
  • Chen et.al 2011 identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing using 54,465 SNPs between the genomes of two indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, . From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Table1,Table2.
  • McNally et.al 2009 reported 160,000 non-redundant SNPs using resequencing of 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. These comprehensive SNP data can be obtained at oryzaSNP or at OryzaSNP Consortium.
  • Feltus et.al. 2005 aligned drafts of two rice subspecies, indica and japonica, and analyzed levels and patterns of genetic diversity. After filtering multiple copy and low quality sequence, 408,898 candidate DNA polymorphisms (SNPs/INDELs) were discerned between the two subspecies. Download.
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