Chloroplast Microsatellite Based Molecular and Computational Studies in Selected Bamboo Species

Abstract

Bamboo is a tribe of flowering perennial evergreen plants in the grass family Poaceae. Chloroplast microsatellites (cpSSRs) are generally short mononucleotide tandem repeats, usually located in the noncoding regions of the chloroplast genome that commonly show intraspecific variation. Hence they act as a high resolution tool for examining levels and patterns of cytoplasmic variation in a wide range of plant species. The present study comprises of an in silico as well as a wet lab based approach to characterize microsatellites. The in silico approach is used for cpSSR mining across six chloroplast genomes available in NCBI-Organellar Genome resource. Due to the unavailability of any completely sequenced chloroplast genome from Bamboo species native to Gujarat, a further wet lab based approach was designed to find the potential of cpSSR to distinguish the selected bamboo species. Five chloroplastic SSR loci were used for the present study viz. trnK intron, psbK/psbI, rpoC2/rps2, atpI/atpH and atpB/rbcL across four Bamboo species. The PCR amplification was conducted, where the forward primer was 5´- labeled with one of the three fluorochromes 6-FAM, NED and VIC. Capillary electrophoresis with a semi-automated system: ABI PRISM 3130 Genetic Analyser was used to separate amplified PCR products; which were detected using a molecular sizing standard. The obtained results are discussed.