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First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora

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Abstract

Salvadoraceae constitutes ecologically imperative desert families of 3 genera—Azima, Dobera and Salvadora. Under genus Salvadora of this family, S. oleoides is a keystone species of socio-economic and medicinal value. This species naturally grows in the arid zones but currently experiencing severe fragmentation due to land use change and reduced regeneration, which may have resulted in the depletion of genetic diversity. Hence, it is up-most important to develop genomic resources for studying the population genetics in S. oleoides. This study aims to develop robust microsatellites markers, which were not yet reported in genus Salvodora due to lack of genome sequence information. We developed novel microsatellites markers in S. oleoides using Illumina paired-end sequencing technology. In total, 14,552 simple sequence repeat (SSR) markers were successfully designed from 21,055 microsatellite repeats detected in the 13 Gb raw sequence data. Afterwards, a subset of 101 SSRs were randomly selected and validated, 94 primers were successfully amplified and 34 showed polymorphisms. These SSRs were used to estimate the measures of genetic diversity in three natural populations of state Rajasthan and Gujarat. Importantly, average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were recorded as 2.4, 0.529, 0.357, and 0.326, respectively. Furthermore, 15 primers were evaluated in S. persica for cross-transferability, and all were successfully amplified but only eight showed polymorphisms. This study has been conducted first time for S. oleoides and pioneer among the native species of arid-zone in India.

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Acknowledgements

The financial support by the Ministry of Environment, Forest and Climate change (MoEF&CC), Government of India, New Delhi under Grant No. 14/8/2013-RE; dated 09th May, 2016 is gratefully acknowledged. The authors are thankful to the Director, FRI for providing the research facilities. The authors wish to thank the reviewer for constructive comments on the early version of the manuscript.

Funding

Ministry of Environment, Forest and Climate change (MoEF&CC), Government of India, New Delhi under Grant No. 14/8/2013-RE; dated 09th May, 2016.

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Authors and Affiliations

  1. Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India

    Maneesh S. Bhandari, Rajendra K. Meena, Arzoo Shamoon, Shanti Saroj & Rama Kant

  2. Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, Uttarakhand, 248 006, India

    Shailesh Pandey

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  1. Maneesh S. Bhandari
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Bhandari, M.S., Meena, R.K., Shamoon, A. et al. First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora. Mol Biol Rep 47, 6997–7008 (2020). https://doi.org/10.1007/s11033-020-05758-z

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