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

被引:0
|
作者
Maneesh S. Bhandari
Rajendra K. Meena
Arzoo Shamoon
Shanti Saroj
Rama Kant
Shailesh Pandey
机构
[1] Forest Research Institute,Division of Genetics & Tree Improvement
[2] Forest Research Institute,Forest Pathology Discipline, Division of Forest Protection
来源
Molecular Biology Reports | 2020年 / 47卷
关键词
Salvadoraceae; Genome sequencing; Microsatellite markers; Genetic diversity;
D O I
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中图分类号
学科分类号
摘要
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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页码:6997 / 7008
页数:11
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