Development of novel SSR markers from the genome sequence of pineapple

K. Nashima, F. Hosaka, S. Terakami, C. Nishitani, M. Kunihisa, T. Yamamoto, M. Shoda, M. Takeuchi, C. Moromizato, K. Yonamine, N. Urasaki, K. Tarora

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Citation (Scopus)


Molecular markers combined with high-density genetic linkage maps are useful for fundamental and applied genetic research and for breeding programs. Simple sequence repeat (SSR) markers provide a reliable method for genetic map construction and evaluation of genetic diversity because of their co-dominant inheritance and the abundance of alleles per locus. However, very few SSR markers have been developed in pineapple. In this study, we performed random shotgun sequencing to obtain the pineapple genome sequence, and then identified candidate SSR sequences. We analyzed the genomic DNA of pineapple cultivar 'N67-10' by using the Roche 454 GS FLX+ platform and used RepeatMasker software to identify repeated sequences, which included long terminal repeat (LTR) elements, short and long interspersed elements (SINE and LINE), DNA transposons, small RNAs and simple repeats; together, these accounted for 8.84% of the total sequence length. We performed de novo assembly and found SSRs in the obtained contigs and singletons by using MIcroSAtellite search tool analysis. A total of 55,621 SSRs were found with di-, tri-, tetra-, penta-, or hexanucleotide motifs. SSR markers designed from the newly obtained genome sequence was evaluated for alleles per locus and genetic diversity, and used to construct a genetic linkage map in pineapple. This information will help us to develop genome-wide markers and to perform marker-assisted selection in pineapple breeding programs.

Original languageEnglish
Title of host publication29th International Horticultural Congress on Horticulture
Subtitle of host publicationSustaining Lives, Livelihoods and Landscapes (IHC 2014): 4th International Symposium on Papaya, 8th International Pineapple Symposium, and International Symposium on Mango
EditorsJ. Zhu, M. Fitch, R. Drew
PublisherInternational Society for Horticultural Science
Number of pages6
ISBN (Electronic)9789462611054
Publication statusPublished - 29 Feb 2016
Externally publishedYes

Publication series

NameActa Horticulturae
ISSN (Print)0567-7572


  • Ananas comosus
  • DNA marker
  • Genome DNA
  • Next-generation sequencing
  • Simple sequence repeat


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