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Tree Genetics & Genomes

, 13:110 | Cite as

Retrotransposon-based insertion polymorphism markers in mango

  • Kenji Nashima
  • Shingo Terakami
  • Miyuki Kunihisa
  • Chikako Nishitani
  • Moriyuki Shoda
  • Masato Matsumura
  • Yuko Onoue-Makishi
  • Naoya Urasaki
  • Kazuhiko Tarora
  • Tatsushi Ogata
  • Toshiya YamamotoEmail author
Original Article
Part of the following topical collections:
  1. Genome Biology

Abstract

Retrotransposons are major components of eukaryotic genomes and are present in high copy numbers. We developed retrotransposon-based insertion polymorphism (RBIP) markers based on long terminal repeat (LTR) sequences and flanking genome regions by using shotgun genome sequence data of mango (Mangifera indica L.). Three novel LTR sequences were identified based on two LTR retrotransposon structural features; a 5′ LTR located upstream of the primer binding site and a 3′ LTR showing high sequence similarity to the 5′ LTR. Starting with 377 unique sequences containing both 3′ LTR and downstream genome region sequences, we developed 82 RBIP markers that were applied to DNA fingerprinting of 16 mango accession. Five RBIP markers were enough to distinguish all 16 accessions. Our result showed that LTR identification from shotgun genome sequences was effective for development of retrotransposon-based DNA markers without whole-genome sequence information. We discuss application of the developed RBIP markers for identification of genetic diversity and construction of a genetic linkage map.

Keywords

DNA marker LTR retrotransposon Mangifera indica RBIP marker 

Notes

Acknowledgements

We thank Mss. F. Hosaka, H. Oshino, N. Shigeta, and N. Yagihashi for their technical help. This study was partially supported by an Okinawa special promotion grant.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

All sequences obtained by 454 GS FLX Plus sequencing are available in the DDBJ Sequence Read Archive (http://trace.ddbj.nig.ac.jp/dra/index.shtml) under the following accession numbers (Submission, DRA004360; BioProject, PRJDB4532; BioSample, SAMD00046318; experiment, DRX049157; and runs, DRR054307 and DRR054308). Nucleotide sequences of 82 retroratnsposon-based insertion polymorphism markers in mango are available in the DDBJ (http://www.ddbj.nig.ac.jp) under the following accession nos. LC089767–LC089848.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Kenji Nashima
    • 1
    • 2
  • Shingo Terakami
    • 1
  • Miyuki Kunihisa
    • 1
  • Chikako Nishitani
    • 1
  • Moriyuki Shoda
    • 3
  • Masato Matsumura
    • 4
  • Yuko Onoue-Makishi
    • 4
  • Naoya Urasaki
    • 3
  • Kazuhiko Tarora
    • 3
  • Tatsushi Ogata
    • 5
  • Toshiya Yamamoto
    • 1
    Email author
  1. 1.Institute of Fruit Tree and Tea ScienceNAROTsukubaJapan
  2. 2.College of Bioresource SciencesNihon UniversityFujisawaJapan
  3. 3.Okinawa Prefectural Agricultural Research CenterItomanJapan
  4. 4.Okinawa Prefectural Agricultural Research Center Nago BranchNagoJapan
  5. 5.Tropical Agricultuer Research FrontJapan International Research Center for Agricultural SciencesIshigakiJapan

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