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Retrotransposon-based insertion polymorphism markers in mango

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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.

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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.

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Authors and Affiliations

  1. Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki, 305-8605, Japan

    Kenji Nashima, Shingo Terakami, Miyuki Kunihisa, Chikako Nishitani & Toshiya Yamamoto

  2. College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan

    Kenji Nashima

  3. Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa, 901-0336, Japan

    Moriyuki Shoda, Naoya Urasaki & Kazuhiko Tarora

  4. Okinawa Prefectural Agricultural Research Center Nago Branch, Nago, Okinawa, 905-0012, Japan

    Masato Matsumura & Yuko Onoue-Makishi

  5. Tropical Agricultuer Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Okinawa, 907-0002, Japan

    Tatsushi Ogata

Authors
  1. Kenji Nashima
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  2. Shingo Terakami
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Corresponding author

Correspondence to Toshiya Yamamoto.

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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.

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Communicated by L. A. Meisel

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Nashima, K., Terakami, S., Kunihisa, M. et al. Retrotransposon-based insertion polymorphism markers in mango. Tree Genetics & Genomes 13, 110 (2017). https://doi.org/10.1007/s11295-017-1192-2

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