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
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.
Nashima, K., Hosaka, F., Terakami, S., Nishitani, C., Kunihisa, M., Yamamoto, T., Shoda, M., Takeuchi, M., Moromizato, C., Yonamine, K., Urasaki, N. and Tarora, K. (2016). Development of novel SSR markers from the genome sequence of pineapple. Acta Hortic. 1111, 189-194
DOI: 10.17660/ActaHortic.2016.1111.28
Ananas comosus, next-generation sequencing, genome DNA, simple sequence repeat, DNA marker

Acta Horticulturae