Abstract
Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retrotransposons are especially predominant. Thus, numerous LTR retrotransposon families with high copy numbers exist in most plant genomes. As the integrated copies of these retrotransposons are genetically inherited, their insertion polymorphisms among crop cultivars have been used as functional molecular markers such as inter-retrotransposon amplification polymorphism (IRAP), retrotransposon microsatellite amplification polymorphism (REMAP), retrotransposon-based insertion polymorphism (RBIP) and sequence-specific amplification polymorphism (S-SAP). However, the effective use of these methods requires suitable LTR sequences showing high insertion polymorphism among crop cultivars. Recently, we conducted an efficient screening of LTR retrotransposon families that showed high insertion polymorphism among closely related strawberry cultivars using a next-generation sequencing platform. This method focuses on the primer binding site (PBS), which is adjacent to the 5' LTR sequence and is conserved among different LTR retrotransposon families. Construction of a sequencing library using the PBS motif allowed us to identify a large number of LTR sequences and their insertion sites throughout the genome. The LTR sequences identified by our method showed high insertion polymorphism among closely related strawberry cultivars, and these families should thus be useful in the development of molecular markers for phylogenetic and genetic diversity studies. This article briefly describes the general aspects of retrotransposon-based molecular markers and also outlines our method for screening LTR sequences suitable for genetic analyses.(. http://www.ddbj.nig.ac.jp/).
| Original language | English |
|---|---|
| Pages (from-to) | 40-44 |
| Number of pages | 5 |
| Journal | Current Plant Biology |
| Volume | 1 |
| DOIs | |
| Publication status | Published - Aug 1 2014 |
Fingerprint
Keywords
- Molecular marker
- Next-generation sequencing
- Polymorphism
- Retrotransposon
- Strawberry
ASJC Scopus subject areas
- Plant Science
- Genetics
- Biochemistry
- Cell Biology
- Developmental Biology
Cite this
Application of iPBS in high-throughput sequencing for the development of retrotransposon-based molecular markers. / Monden, Yuki; Yamaguchi, Kentaro; Tahara, Makoto.
In: Current Plant Biology, Vol. 1, 01.08.2014, p. 40-44.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Application of iPBS in high-throughput sequencing for the development of retrotransposon-based molecular markers
AU - Monden, Yuki
AU - Yamaguchi, Kentaro
AU - Tahara, Makoto
PY - 2014/8/1
Y1 - 2014/8/1
N2 - Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retrotransposons are especially predominant. Thus, numerous LTR retrotransposon families with high copy numbers exist in most plant genomes. As the integrated copies of these retrotransposons are genetically inherited, their insertion polymorphisms among crop cultivars have been used as functional molecular markers such as inter-retrotransposon amplification polymorphism (IRAP), retrotransposon microsatellite amplification polymorphism (REMAP), retrotransposon-based insertion polymorphism (RBIP) and sequence-specific amplification polymorphism (S-SAP). However, the effective use of these methods requires suitable LTR sequences showing high insertion polymorphism among crop cultivars. Recently, we conducted an efficient screening of LTR retrotransposon families that showed high insertion polymorphism among closely related strawberry cultivars using a next-generation sequencing platform. This method focuses on the primer binding site (PBS), which is adjacent to the 5' LTR sequence and is conserved among different LTR retrotransposon families. Construction of a sequencing library using the PBS motif allowed us to identify a large number of LTR sequences and their insertion sites throughout the genome. The LTR sequences identified by our method showed high insertion polymorphism among closely related strawberry cultivars, and these families should thus be useful in the development of molecular markers for phylogenetic and genetic diversity studies. This article briefly describes the general aspects of retrotransposon-based molecular markers and also outlines our method for screening LTR sequences suitable for genetic analyses.(. http://www.ddbj.nig.ac.jp/).
AB - Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retrotransposons are especially predominant. Thus, numerous LTR retrotransposon families with high copy numbers exist in most plant genomes. As the integrated copies of these retrotransposons are genetically inherited, their insertion polymorphisms among crop cultivars have been used as functional molecular markers such as inter-retrotransposon amplification polymorphism (IRAP), retrotransposon microsatellite amplification polymorphism (REMAP), retrotransposon-based insertion polymorphism (RBIP) and sequence-specific amplification polymorphism (S-SAP). However, the effective use of these methods requires suitable LTR sequences showing high insertion polymorphism among crop cultivars. Recently, we conducted an efficient screening of LTR retrotransposon families that showed high insertion polymorphism among closely related strawberry cultivars using a next-generation sequencing platform. This method focuses on the primer binding site (PBS), which is adjacent to the 5' LTR sequence and is conserved among different LTR retrotransposon families. Construction of a sequencing library using the PBS motif allowed us to identify a large number of LTR sequences and their insertion sites throughout the genome. The LTR sequences identified by our method showed high insertion polymorphism among closely related strawberry cultivars, and these families should thus be useful in the development of molecular markers for phylogenetic and genetic diversity studies. This article briefly describes the general aspects of retrotransposon-based molecular markers and also outlines our method for screening LTR sequences suitable for genetic analyses.(. http://www.ddbj.nig.ac.jp/).
KW - Molecular marker
KW - Next-generation sequencing
KW - Polymorphism
KW - Retrotransposon
KW - Strawberry
UR - http://www.scopus.com/inward/record.url?scp=84919414860&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84919414860&partnerID=8YFLogxK
U2 - 10.1016/j.cpb.2014.09.001
DO - 10.1016/j.cpb.2014.09.001
M3 - Article
AN - SCOPUS:84919414860
VL - 1
SP - 40
EP - 44
JO - Current Plant Biology
JF - Current Plant Biology
SN - 2214-6628
ER -