Identification of SNPs in closely related Temperate Japonica rice cultivars using restriction enzyme-phased sequencing

PLoS One. 2013;8(3):e60176. doi: 10.1371/journal.pone.0060176. Epub 2013 Mar 26.


Very low polymorphism in the germplasm typically used by breeding programs poses a significant bottleneck with regards to molecular breeding and the exploitation of breeding materials for quantitative trait analyses. California rice cultivars, derived from a very small base of temperate japonica germplasm and having a relatively brief breeding history, are a good example. In this study, we employed a reduced representation sequencing approach called Restriction Enzyme Site Comparative Analysis (RESCAN) to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in forty-five rice cultivars representing the majority of the 100 year-old breeding history in California. Over 20,000 putative SNPs were detected relative to the Nipponbare reference genome which enabled the identification and analysis of inheritance of pedigree haplotypes. Haplotype blocks distinguishing modern California cultivars from each other and from the ancestral short grain temperate japonica cultivars were easily identified. Reduced representation sequencing methods such as RESCAN are a valuable alternative to SNP chip genotyping and low coverage whole genome sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Restriction Enzymes / metabolism*
  • Genome, Plant / genetics
  • Genotype
  • Haplotypes / genetics
  • Oryza / genetics*
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA / methods*


  • DNA Restriction Enzymes

Grant support

This work was supported by USDA-ARS CRIS Project 5306-21000-017-00D ( and California Rice Research Board Project RB-3 ( The California Rice Research Board is a non-profit, California rice grower-funded body which awards grants primarily to public research institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.