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First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora.
Molecular Biology Reports ( IF 2.6 ) Pub Date : 2020-09-15 , DOI: 10.1007/s11033-020-05758-z
Maneesh S Bhandari 1 , Rajendra K Meena 1 , Arzoo Shamoon 1 , Shanti Saroj 1 , Rama Kant 1 , Shailesh Pandey 2
Affiliation  

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.



中文翻译:

Salvadora属中的第一个从头基因组特异性开发,表征和验证简单序列重复(SSR)标记。

Salvadoraceae构成了3个属的生态必需沙漠家庭:AzimaDoberaSalvadora。在该家族的Salvadora属下,油橄榄S. oleoides是具有社会经济和医学价值的重要物种。该物种在干旱地区自然生长,但由于土地用途的变化和再生的减少,目前正遭受严重的破坏,这可能导致遗传多样性的消耗。因此,开发用于研究油橄榄的种群遗传学的基因组资源至关重要。这项研究旨在开发健壮的微卫星标记,Salvodora属尚未报道由于缺乏基因组序列信息。我们使用Illumina的配对末端测序技术开发了S. oleoides中的新型微卫星标记。根据在13 Gb原始序列数据中检测到的21,055个微卫星重复序列,成功设计了14,552个简单序列重复序列(SSR)标记。之后,随机选择并验证了101个SSR的子集,成功扩增了94个引物,并显示了34个多态性。这些SSR被用来估计拉贾斯坦邦和古吉拉特邦三个自然种群的遗传多样性。重要的是,平均等位基因数(N a),观察到的杂合度(H o),预期杂合度(H e)和多态信息含量(PIC)分别记录为2.4、0.529、0.357和0.326。此外,在波斯菊中评价了15种引物的交叉转移性,所有引物均被成功扩增,但是只有八种表现出多态性。这项研究是首次针对油橄榄和印度干旱地区的本地物种的先驱者进行的。

更新日期:2020-09-15
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