Dna markers based on retrotransposon insertion polymorphisms can detect short dna fragments for strawberry cultivar identification

Chiharu Hirata, Takamitsu Waki, Katsumi Shimomura, Takuya Wada, Seiya Tanaka, Hidetoshi Ikegami, Yousuke Uchimura, Keita Hirashima, Yoshiko Nakazawa, Kaori Okada, Kiyoshi Namai, Makoto Tahara, Yuki Monden

Research output: Contribution to journalArticle

Abstract

In this study, DNA markers were developed for discrimination of strawberry (Fragaria × ananassa L.) cultivars based on retrotransposon insertion polymorphisms. We performed a comprehensive genomic search to identify retrotransposon insertion sites and subsequently selected one retrotransposon family, designated CL3, which provided reliable discrimination among strawberry cultivars. Through analyses of 75 strawberry cultivars, we developed eight cultivar-specific markers based on CL3 retrotransposon insertion sites. Used in combination with 10 additional polymorphic markers, we differentiated 35 strawberry cultivars commonly cultivated in Japan. In addition, we demonstrated that the retrotransposon-based markers were effective for PCR detection of DNA extracted from processed food materials, whereas a SSR marker was ineffective. These results indicated that the retrotransposon-based markers are useful for cultivar discrimination for processed food products, such as jams, in which DNA may be fragmented or degraded.

Original languageEnglish
Pages (from-to)231-240
Number of pages10
JournalBreeding Science
Volume70
Issue number2
DOIs
Publication statusPublished - Jan 1 2020

Keywords

  • Fragaria × ananassa
  • High-throughput sequencing
  • PCR product
  • Processed foods
  • Retrotransposon insertion polymorphisms

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

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    Hirata, C., Waki, T., Shimomura, K., Wada, T., Tanaka, S., Ikegami, H., Uchimura, Y., Hirashima, K., Nakazawa, Y., Okada, K., Namai, K., Tahara, M., & Monden, Y. (2020). Dna markers based on retrotransposon insertion polymorphisms can detect short dna fragments for strawberry cultivar identification. Breeding Science, 70(2), 231-240. https://doi.org/10.1270/jsbbs.19116