Breeding Science
Online ISSN : 1347-3735
Print ISSN : 1344-7610
Research Papers
Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza
Shinichiro YamakiHajime OhyanagiMasanori YamasakiMitsugu EiguchiToshie MiyabayashiTakahiko KuboNori KurataKen-Ichi Nonomura
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2013 Volume 63 Issue 3 Pages 246-254

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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.

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© 2013 by JAPANESE SOCIETY OF BREEDING
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