Estimation of genetic diversity and population structure inTinospora cordifoliausing SSR markers
Estimation of genetic diversity and population structure inTinospora cordifoliausing SSR markers
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DOI：
10.1007/s13205-020-02300-7
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发表时间：
2020-06-16
期刊：
影响因子：
2.8
通讯作者：
Yadav, Hemant Kumar
中科院分区：
文献类型：
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作者：
Lade, Suchita;Pande, Veena;Yadav, Hemant Kumar
利用从心叶青牛胆 RNA 测序中获得的 30 个多态性 SSR，对从印度 10 个不同地理区域收集的 96 个种质进行遗传多样性和群体结构评估。从 268149 个转录本中总共鉴定出 7611 个 SSR。在所有SSR位点中，69.07%是三核苷酸重复基序，其次是二核苷酸重复基序（12.82%）。 30个SSR共产生230个等位基因，平均每个位点产生7.67个等位基因，多态信息含量较高（平均0.68）。预期 (He) 和观察到 (Ho) 杂合度平均值分别为 0.71 和 0.12。所有位点均显示出与 Hardy-Weinberg 平衡 (HWE) 的显着偏差。基于杰卡德系数的邻接聚类将所有96份材料分为三个主要簇，这也与基于模型的结构图一致。分子方差（AMOVA）的结果显示群体内的遗传变异高于群体之间的遗传变异。结果反映了所收集的T. 材料中存在高水平的遗传多样性。心叶。发现材料 Tc131、Tc31、Tc129、Tc38、Tc16、Tc59、Tc60、Tc17、Tc106 和 Tc130 本质上具有潜力和多样性，SSR TCSSR-18、TCSSR-37、TCTSSR-59、TCTSSR-92、TCTSSR-123 和 TCTSSR-126作为潜在的标记。这些材料和新开发的 SSR 标记提供了宝贵的资源，可战略性地用于 T 的进一步遗传改良。心叶。
Thirty polymorphic SSRs, derived from RNA sequencing ofTinospora cordifolia(willd.), were utilized for genetic diversity and population structure evaluation among 96 accessions collected from ten different geographical regions of India. A total of 7611 SSRs were identified from 268149 transcripts. Of all SSR loci, 69.07% of them were tri-nucleotide repeat motifs, followed by di-nucleotide repeat motifs (12.82%). A total of 230 alleles were generated by 30 SSRs with an average of 7.67 alleles per locus with comparatively higher polymorphic information content (average 0.68). The expected (He) and observed (Ho) heterozygosity means were 0.71 and 0.12, respectively. All the loci showed significant deviation from Hardy-Weinberg Equilibrium (HWE). The neighbor joining clustering based on jaccard's coefficient grouped all the 96 accessions into three major cluster which was also in congruence with model-based structure plot. The result of molecular variance (AMOVA) revealed higher genetic variance within populations than among populations. The result reflects an existence of high level of genetic diversity in the collected accessions ofT. cordifolia. The accessions Tc131, Tc31, Tc129, Tc38, Tc16, Tc59, Tc60, Tc17, Tc106 and Tc130 was found to be potential and diverse in nature and the SSRs TCSSR-18, TCSSR-37, TCTSSR-59, TCTSSR-92, TCTSSR-123 and TCTSSR-126 as potential markers. These accessions and newly developed SSR markers provide valuable resource and could be strategically utilized for further genetic improvement ofT. cordifolia.