Dot-blot-SNP analysis for practical plant breeding and cultivar identification in rice

K. Shirasawa, S. Shiokai, M. Yamaguchi, S. Kishitani, T. Nishio

Research output: Contribution to journalArticlepeer-review

42 Citations (Scopus)

Abstract

We report dot-blot hybridization with allele-specific oligonucleotides for single nucleotide polymorphisms (SNPs) analysis to be applicable for practical plant breeding and cultivar identification. Competitive hybridization of a digoxigenin-labeled oligonucleotide having the sequence of a mutant allele (or a wild-type allele) together with an unlabeled oligonucleotide having the sequence of a wild-type allele (or a mutant allele) was highly effective to reduce background signals in dot-blot hybridization. All 100 tested genes (200 alleles) in rice having SNPs or insertions/deletions were detected in an allele-specific manner. Genotypes of 43 rice cultivars were identified by this technique, and eight SNP markers were found to be sufficient for distinguishing all the cultivars from each other. Dot-blot analysis was also applied to genotyping of Wx and Sd1 of F4 plants in a conventional breeding program. Since dot-blot analysis with competitive hybridization provides a highly reliable, simple, and cost-effective technique for SNP analysis of a large number of samples, this technique is expected to realize the practical use of a novel breeding method, in which plants or breeding lines are selected by SNP analyses of many genes in a laboratory.

Original languageEnglish
Pages (from-to)147-155
Number of pages9
JournalTheoretical and Applied Genetics
Volume113
Issue number1
DOIs
Publication statusPublished - 2006 Jun 1

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

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