Genome-wide discovery of single- and multi-locus simple sequence repeat markers and their characterization in Dendrocalamus strictus: a commercial polyploid bamboo species of India

Dendrocalamus strictus, popularly known as lathi baans, is a multipurpose bamboo species known for its manifold domestic and industrial applications. In the current scenario, the extraction of raw material (culms) has surpassed the available growing stock, which puts the accessible genetic resource under pressure. Despite the commercial significance and overexploitation, population genetics of this valuable species is poorly studied, mainly due to the paucity of genomic information and marker resources. Moreover, polyploid genome structure obstructs the usage of robust codominant markers like simple sequence repeats (SSRs) for genetic analysis. Hence, the present study was conducted to develop genome sequence information as well as de novo SSRs in D. strictus. About 15 Gb sequence data was generated by sequencing 103.95 million reads using the Illumina protocol, which were further assembled into 902,453 contigs with 47.15% GC content and a 712 bp N50 value. A total of 39,473 microsatellite repeats were identified, wherein di-nucleotides were the most abundant (64.42%), followed by tri (29.66%), tetra (4.53%), penta (1.16%), and hexa-repeats (0.24%). Primer pairs were developed for 20,606 SSRs, and 250 of these were selected for validation. Through PCR amplification in 20 individuals, 69 SSRs displayed polymorphic banding pattern, of which 43 were single-locus and 26 were multi-locus SSRs. By comparison, both primer sets were reliable, giving similar results in analysed individuals. The available sequence data and unique single-locus SSR markers have the potential to improve our understanding towards D. strictus genomic background. The study also highlights the usability of identified SSRs in polyploids.

Automated summary

The study developed genome sequence information and novel SSRs for D. strictus, identified a large number of microsatellite repeats, and validated polymorphic SSR markers through PCR amplification. The reliable results from the analysed individuals suggest the potential of these SSRs in improving our understanding of the genomic background of D. strictus.