Fluorogenic ribonuclease protection (FRIP) analysis of single nucleotide polymorphisms (SNPs) in Japanese rice (Oryza sativa L.) DNA for cultivar discrimination

Momoko Kitaoka, Takuya Wada, Takeshi Nishio, Masahiro Goto

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

A rapid and easy method to discriminate plant cultivars is indispensable to confirm food labeling. We established a fluorogenic ribonuclease protection (FRIP) assay to discriminate Japanese rice (Oryza sativa L.) cultivars based on single nucleotide polymorphisms (SNPs). The FRIP assay uses a hybridization technique between fluorescent probes and the target sequence prepared by run-off transcription, but the requirement of two PCR thermocycles is the problem when preparing template DNA for run-off transcription from rice genomic DNA. In this study, we designed new PCR primers with asymmetric melting temperatures. These primers amplified the target SNP marker containing a T7 RNA polymerase promoter sequence upstream of the target sequence in a single PCR. Moreover, 100 cultivars were discriminated with the patterns of 15 SNPs. The assay can be used as a rapid method of analysis to discriminate Japanese rice cultivars.

Original languageEnglish
Pages (from-to)2189-2193
Number of pages5
JournalBioscience, Biotechnology and Biochemistry
Volume74
Issue number11
DOIs
Publication statusPublished - Dec 10 2010

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Analytical Chemistry
  • Biochemistry
  • Applied Microbiology and Biotechnology
  • Molecular Biology
  • Organic Chemistry

Fingerprint Dive into the research topics of 'Fluorogenic ribonuclease protection (FRIP) analysis of single nucleotide polymorphisms (SNPs) in Japanese rice (Oryza sativa L.) DNA for cultivar discrimination'. Together they form a unique fingerprint.

  • Cite this