Abstract
Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (FST = 0.119), severe inbreeding (FIS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.
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Availability of data and materials
The additional data required to understand the manuscript is available in the supplementary information of this manuscript, and the raw sequence data are available in Sequence Read Archive (SRA) database of NCBI with accession number PRJNA708171.
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Acknowledgements
Authors are thankful to the Director, Forest Research Institute, Dehradun for providing field and laboratory facilities. We are also grateful the Director, Rain Forest Research Institute who allowed the team of researchers at Forest Research Centre for Bamboo and Rattan, Aizawl, for population sampling in Mizoram. We also extend our gratitude to Mr. Gaurav Pal for providing technical assistance in laboratory work.
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The work was financially supported by the Ministry of Environment, Forest and Climate Change, New Delhi under National Compensatory Afforestation Fund (NCAF) scheme on ‘Strengthening Forestry Research for Ecological Sustainability and Productivity Enhancement’ vide letter number 72(XVIII)/2018/ICFRE(R)/RP/Project Proposals/154.
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RKM, MSB, SB, and HSG involved in project conceptualization, execution, and manuscript writing; PK, AS, and PD conducted the laboratory work and data analysis; HS involved in sample collection for population genetic analysis.
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Meena, R.K., Kashyap, P., Shamoon, A. et al. Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus. Funct Integr Genomics 23, 103 (2023). https://doi.org/10.1007/s10142-023-01033-z
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DOI: https://doi.org/10.1007/s10142-023-01033-z