SSR marker information mining in blackberry from transcriptome sequences

A total of 63,632 unigenes derived from blackberry (Rubus L.) transcriptome sequencing data were used for development of functional expressed sequence tag-simple sequence repeat (EST-SSR) molecular markers. Overall, 3,393 single simple sequence repeat (SSR) markers were detected, accounting for 5.33% of all the unigenes. Among them, 3,205 markers contained simple SSR type and 188 were compound and comprised of at least two SSR types. The average length and distance between neighboring transcriptome-derived SSRs were 16 and 11.47 kb, respectively. Mononucleotide SSRs were the main motif type, accounting for the highest frequency of 43.38%, followed by trinucleotide and dinucleotide motifs, with similar frequencies. Furthermore, ten was the most frequent number of repeats, and accounted for 15.89% of all the SSRs. A total of 118 types of repeat motifs were identified in the blackberry transcriptome. A/T in mononucleotide and AG/CT in dinucleotide repeats were the most frequent motifs, accounting for 43.06 and 10.96% of all the SSRs, respectively. Of all the SSR repeat types, 338 SSRs (9.96% of motifs) were over 20 bp and are expected to be highly polymorphic. These transcriptomic SSRs will provide new tools for future genetic research and breeding use for blackberry.