Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus

Theor Appl Genet. 2004 May;108(7):1212-20. doi: 10.1007/s00122-003-1553-0. Epub 2004 Jan 23.


We assessed the utility of single-nucleotide polymorphisms (SNPs) and small insertion/deletion polymorphisms (InDels) as DNA markers in genetic analysis and breeding of rice. Toward this end, we surveyed SNPs and InDels in the chromosomal region containing the Piz and Piz-t rice blast resistance genes and developed PCR-based markers for typing the SNPs. Analysis of sequences from a blast-susceptible Japanese cultivar and two cultivars each containing one of these genes revealed that SNPs are abundant in the Piz and Piz-t regions (on average, one SNP every 248 bp), but the number of InDels was much lower. The dense distribution of SNPs facilitated the generation of SNP markers in the vicinity of the genes. For typing these SNPs, we used a modified allele-specific PCR method. Of the 49 candidate allele-specific markers, 33 unambiguously and reproducibly discriminated between the two alleles. We used the markers for mapping the Piz and Piz-t genes and evaluating the size of DNA segments introgressed from the Piz donor cultivar in Japanese near-isogenic lines containing Piz. Our findings suggest that, because of its ability to generate numerous markers within a target region and its simplicity in assaying genotypes, SNP genotyping with allele-specific PCR is a valuable tool for gene mapping, map-based cloning, and marker-assisted selection in crops, especially rice.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Blotting, Southern
  • Breeding / methods*
  • Chromosome Mapping
  • Crosses, Genetic
  • DNA Primers
  • Genetic Markers
  • Genotype
  • Immunity, Innate / genetics
  • Magnaporthe / immunology
  • Molecular Sequence Data
  • Mutation / genetics*
  • Oryza / genetics*
  • Phenotype*
  • Plant Diseases / microbiology
  • Polymerase Chain Reaction / methods
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA


  • DNA Primers
  • Genetic Markers