Application of iPBS in high-throughput sequencing for thedevelopment of retrotransposon-based molecular markers

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Application of iPBS in high-throughput sequencing for thedevelopment of retrotransposon-based molecular markers

Yuki Monden [et al.] - Nama Orang;

Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retro-transposons are especially predominant. Thus, numerous LTR retrotransposon families with high copynumbers exist in most plant genomes. As the integrated copies of these retrotransposons are geneticallyinherited, their insertion polymorphisms among crop cultivars have been used as functional molecularmarkers such as inter-retrotransposon amplification polymorphism (IRAP), retrotransposon microsatel-lite amplification polymorphism (REMAP), retrotransposon-based insertion polymorphism (RBIP) andsequence-specific amplification polymorphism (S-SAP). However, the effective use of these methodsrequires suitable LTR sequences showing high insertion polymorphism among crop cultivars. Recently,we conducted an efficient screening of LTR retrotransposon families that showed high insertion poly-morphism among closely related strawberry cultivars using a next-generation sequencing platform. Thismethod focuses on the primer binding site (PBS), which is adjacent to the 5LTR sequence and is conservedamong different LTR retrotransposon families. Construction of a sequencing library using the PBS motifallowed 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 relatedstrawberry cultivars, and these families should thus be useful in the development of molecular mark-ers for phylogenetic and genetic diversity studies. This article briefly describes the general aspects ofretrotransposon-based molecular markers and also outlines our method for screening LTR sequencessuitable for genetic analyses.

Keywords:RetrotransposonNext-generation sequencingPolymorphismMolecular markerStrawberry

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Judul Seri: Current Plant Biology
No. Panggil: -
Penerbit: : Elsevier., 2014
Deskripsi Fisik: Current Plant Biology 1 (2014) 40–44
Bahasa: English
ISBN/ISSN: -
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Edisi: -
Subjek: KIMIA
Info Detail Spesifik: -
Pernyataan Tanggungjawab: Wati/Agus

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FULL TEXT:Application of iPBS in high-throughput sequencing for thedevelopment of retrotransposon-based molecular markers

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