Preprint / Version 1

Estimation of genetic diversity and population structure in Tinospora cordifolia using SSR markers

Authors

  • Suchita Lade Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India
  • Veena Pande Department of Biotechnology, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand India
  • Tikam Rana Plant Diversity, Systematics and Herbarium Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh, 226001 India
  • Hemant Yadav Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India

Keywords:

Tinospora cordifolia, Simple sequence repeat (SSR), Genetic diversity, AMOVA

Abstract

Thirty polymorphic SSRs, derived from RNA sequencing of Tinospora 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 of T. 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 of T. cordifolia. Electronic supplementary material The online version of this article (10.1007/s13205-020-02300-7) contains supplementary material, which is available to authorized users. Keywords: Tinospora cordifolia, Simple sequence repeat (SSR), Genetic diversity, AMOVA

Author Biographies

Suchita Lade, Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India

Department of Biotechnology, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand India

Tikam Rana, Plant Diversity, Systematics and Herbarium Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh, 226001 India

Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India

Hemant Yadav, Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India

Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India