First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Ge
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ORIGINAL ARTICLE
First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora Maneesh S. Bhandari1 · Rajendra K. Meena1 · Arzoo Shamoon1 · Shanti Saroj1 · Rama Kant1 · Shailesh Pandey2 Received: 16 April 2020 / Accepted: 28 August 2020 © Springer Nature B.V. 2020
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. Keywords Salvadoraceae · Salvadora oleoides · Genome sequencing · Microsatellite markers · Genetic diversity · Salvadora persica
Introduction Salvadora oleoides Decne. is a small bushy evergreen tree, indigenous to tropical Africa and South Asia, and dispersed in the arid tracts of state Punjab, Haryana, Rajasthan, Gujarat, Madhya Pradesh and southwestern parts of Uttar Pradesh in India [1]. The tree attains a height of 6–9 m under
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-020-05758-z) contains supplementary material, which is available to authorized users. Accession No.: PRJNA608853. * Maneesh S. Bhandari [email protected]; [email protected] Extended author information available on the last page of the article
favorable conditions, and has huge ecological, cultural, aesthetic, socio-economic, and medicinal importance to the desert community [2]. Adversely, the species is declining very rapidly due to overutilization, indisc
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