Development of genic SSR marker resource from RNA-Seq data in Dendrocalamus latiflorus

Bamboo is one of the most essential forest resources. Microsatellites have important role in genome, and are preferred over other molecular markers. For the first time, we exploited public transcriptome data of Dendrocalamus latiflorusfor identification and characterization of microsatellite markers in the species. Frequency of SSRs was found to be 1 per 4 Kb. Tri-repeats were found to be the most abundant (47.7 %). Among them, GC rich repeat motifs namely, CCG/CGG (24.18 %) and AGG/CCT (22.29 %) were predominant. 12,028 potential genic SSR markers were identified, of which, 92 % were class II type. A set of 21 functionally relevant markers were successfully validated in 5 accessions of D. latiflorus. Twenty markers were found polymorphic, with number of alleles and polymorphism information content averaging 4.8 and 0.452, respectively. Interestingly, 100 % markers showed cross transferability across 14 related bamboo species, and were utilized for establishing phylogenetic relationships. Genic SSR markers developed herein would assist in genetic diversity, evolutionary and association mapping studies in bamboo.