Next Generation Global Transcriptome Sequencing to Expedite Genetic Characterization Efforts in Bamboo

In the recent past, various next generation sequencing platforms are witness for paradigm shift in genomics of model as well as non-model species. Bamboo (family: Poaceae) is one the most important forest resources worldwide.  Infrequent flowering followed by death, however limits its genetic improvement through conventional breeding. Genome wide association mapping, an alternative approach for dissection of complex traits is limited due non-availability of species wise genomic resource. Among the various sequence based markers, microsatellite are derisible due to their hypervaribility, ubiquitous abundance, co-dominance, reproducibility and cross transferability across distant genera of bamboo. Such markers derived from the transcribed genome gives more opportunities for establishing their functional relevance to desirable traits. Further, genomic resources are unavailable in many of the commercially important sub-tropical bamboos including Dendrocalamus hamiltonii (DH).  We generated 56.9 million high quality reads through transcriptomic sequencing of multiple libraries of DH. After assembly, 2,968 sequences containing 3,198 SSRs were identified. Frequency of SSRs was found to be 1 per 12.1 kb of assembled sequences. Tri-repeats were most predominant (55.8%) followed by di-repeats 39.6%. Among tri-repeats, CCG/CGG were maximum (23.6%) and AG/CT were predominant (65.5%) among di-repeats. 906 SSR containing sequences were matched against various protein databases namely, Swissprot, TAIR, TF, KEGG and Gene Ontology. 2,064 primer pairs could be successfully designed, and 48 gene specific primers were synthesized for validation in the species. These marker resource would assist in diversity and future genetic mapping studies of bamboo.