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SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr.

Authors
  • Nashima, Kenji1
  • Hosaka, Fumiko2
  • Terakami, Shingo2
  • Kunihisa, Miyuki2
  • Nishitani, Chikako2
  • Moromizato, Chie3
  • Takeuchi, Makoto3
  • Shoda, Moriyuki4
  • Tarora, Kazuhiko4
  • Urasaki, Naoya4
  • Yamamoto, Toshiya2
  • 1 College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan. , (Japan)
  • 2 Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-0852, Japan. , (Japan)
  • 3 Okinawa Prefectural Agricultural Research Center Nago Branch, 4605-3 Nago, Nago, Okinawa 905-0012, Japan. , (Japan)
  • 4 Okinawa Prefectural Agricultural Research Center, 820 Makabe, Itoman, Okinawa 901-0336, Japan. , (Japan)
Type
Published Article
Journal
Breeding science
Publication Date
Jun 01, 2020
Volume
70
Issue
3
Pages
415–421
Identifiers
DOI: 10.1270/jsbbs.19158
PMID: 32714066
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Simple sequence repeat (SSR) markers provide a reliable tool for the identification of accessions and the construction of genetic linkage maps because of their co-dominant inheritance. In the present study, we developed new SSR markers with next-generation sequencing using the Roche 454 GS FLX+ platform. Five hundred SSR primer sets were tested for the genetic identification of pineapple, including 100 each for the di-, tri-, tetra-, penta-, and hexa-nucleotide motif SSRs. In total, 160 SSR markers successfully amplified fragments and exhibited polymorphism among accessions. The SSR markers revealed the number of alleles per locus (ranging from 2 to 13), the expected heterozygosity (ranging from 0.041 to 0.823), and the observed heterozygosity (ranging from 0 to 0.875). A total of 117 SSR markers with tri- or greater nucleotide motifs were shown to be effective at facilitating accurate genotyping. Using the SSR markers, 25 accessions were distinguished genetically, with the exception of accessions 'MD-2' and 'Yonekura'. The developed SSR markers could facilitate the establishment of efficient and accurate genetic identification systems and the construction of genetic linkage maps in the future. Copyright © 2020 by JAPANESE SOCIETY OF BREEDING.

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