Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza

Shinichiro Yamaki, Hajime Ohyanagi, Masanori Yamasaki, Mitsugu Eiguchi, Toshie Miyabayashi, Takahiko Kubo, Nori Kurata, Ken Ichi Nonomura*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

Abstract

The wild Oryza species are rich in genetic diversity and are good resources for modern breeding of rice varieties. The reliable ex situ conservation of various genetic resources supports both basic and applied rice research. For this purpose, we developed PCR-based and co-dominant insertion/deletion (INDEL) markers which enable the discrimination of the genome types or species in the genus Oryza. First, 12,107 INDEL candidate sequences were found in the BAC end sequences for 12 Oryza species available in public databases. Next, we designed PCR primers for INDEL-flanking sequences to match the characteristics of each INDEL, based on an assessment of their likelihood to give rise to a single or few PCR products in all 102 wild accessions, covering most Oryza genome types. Then, we selected 22 INDEL markers to discriminate all genome types in the genus Oryza. A phylogenetic tree of 102 wild accessions and two cultivars according to amplicon polymorphisms for the 22 INDEL markers corresponded well to those in previous studies, indicating that the INDEL markers developed in this study were a useful tool to improve the reliability of identification of wild Oryza species in the germplasm stocks.

Original languageEnglish (US)
Pages (from-to)246-254
Number of pages9
JournalBreeding Science
Volume63
Issue number3
DOIs
StatePublished - Oct 8 2013

Keywords

  • Genetic resource
  • Genome type
  • Genus Oryza
  • Insertion/deletion marker
  • Rice
  • Wild species

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

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