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

doi:10.1270/jsbbs.63.246

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 journal › Article › peer-review

38 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 language	English (US)
Pages (from-to)	246-254
Number of pages	9
Journal	Breeding Science
Volume	63
Issue number	3
DOIs	https://doi.org/10.1270/jsbbs.63.246
State	Published - Oct 8 2013
Externally published	Yes

Keywords

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

ASJC Scopus subject areas

Agronomy and Crop Science
Genetics
Plant Science

Access to Document

10.1270/jsbbs.63.246

Cite this

@article{d30d372a169d451e8a13333a9aa1491d,

title = "Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza",

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.",

keywords = "Genetic resource, Genome type, Genus Oryza, Insertion/deletion marker, Rice, Wild species",

author = "Shinichiro Yamaki and Hajime Ohyanagi and Masanori Yamasaki and Mitsugu Eiguchi and Toshie Miyabayashi and Takahiko Kubo and Nori Kurata and Nonomura, {Ken Ichi}",

year = "2013",

month = oct,

day = "8",

doi = "10.1270/jsbbs.63.246",

language = "English (US)",

volume = "63",

pages = "246--254",

journal = "Breeding Science",

issn = "1344-7610",

publisher = "Japanese Society of Breeding",

number = "3",

}

TY - JOUR

T1 - Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza

AU - Yamaki, Shinichiro

AU - Ohyanagi, Hajime

AU - Yamasaki, Masanori

AU - Eiguchi, Mitsugu

AU - Miyabayashi, Toshie

AU - Kubo, Takahiko

AU - Kurata, Nori

AU - Nonomura, Ken Ichi

PY - 2013/10/8

Y1 - 2013/10/8

N2 - 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.

AB - 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.

KW - Genetic resource

KW - Genome type

KW - Genus Oryza

KW - Insertion/deletion marker

KW - Rice

KW - Wild species

UR - http://www.scopus.com/inward/record.url?scp=84885163809&partnerID=8YFLogxK

U2 - 10.1270/jsbbs.63.246

DO - 10.1270/jsbbs.63.246

M3 - Article

AN - SCOPUS:84885163809

SN - 1344-7610

VL - 63

SP - 246

EP - 254

JO - Breeding Science

JF - Breeding Science

IS - 3

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this