SpringerLink
Log in

Evaluating genetic diversity of geographically diverse populations of Embelia ribes Burm f., a highly medicinal woody liana from the Western Ghats of India, using random amplified polymorphic DNA (RAPD) and intersimple sequence repeats (ISSR) markers

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Background

Embelia ribes Burm f. (Primulaceae) is a medicinal and vulnerable woody liana distributed throughout India. Embelin, a well-recognized active phytoconstituents in berries, is commonly used in ayurvedic formulations. Due to over-exploitation, the status of the plant is vulnerable. Previous studies on this species mainly focused on its phytochemical analysis, which led to overexploitation and loss of the germplasm.

Methods and results

In the present study, 20 RAPD and 18 ISSR markers were employed to assess genetic divergence in 40 genotypes of E. ribes collected from different parts of the Western Ghats of India. In RAPD analysis, all 40 accessions with 20 RAPD primers amplified 282 fragments, with 83.91% average polymorphism and with an average of 14.10 bands per primer. The size of amplicons varied from 200 to 2500 bp. While, ISSR primers produced 203 fragments of which 161 were polymorphic with an average of 11.28 bands per primer with 73.25% average polymorphism. The size of amplicons ranges from 200 to 2500 bp. RAPD and ISSR markers were also assessed by calculating polymorphic information content (PIC) to discriminate the genotypes; the average PIC value for RAPD, ISSR, and combined RAPD + ISSR markers obtained was more than 0.50 suggesting the informativeness of markers. UPGMA analysis based on Jaccard’s similarity coefficient for RAPD, ISSR, and RAPD + ISSR data reveals that 40 accessions of E. ribes were depicted in four clusters. The clustering pattern of all individuals in PCoA analysis agreed with the UPGMA dendrograms, which further confirms the genetic relationships explained by cluster analysis. AMOVA analysis of RAPD, ISSR, and combined marker system revealed variation within the population, ranging from 41 to 44%, and among the population, it ranged from 56 to 59%.

Conclusion

The present study provides an optimized method for evaluating the genetic diversity of Embelia ribes using RAPD and ISSR markers which are useful for further sustainable utilization and conservation of natural populations in the Western Ghats of India.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price includes VAT (Germany)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Angiosperm Phylogeny Group IV (APG IV) (2016) An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc 181:1–20. https://doi.org/10.1111/boj.12385

    Article  Google Scholar 

  2. Kamble V, Attar U, Umdale S, Nimbalkar M, Ghane S, Gaikwad N (2020) Phytochemical analysis, antioxidant activities and optimized extraction of embelin from different genotypes of Embelia ribes Burm f.: a woody medicinal climber from Western Ghats of India. Physiol Mol Biol Plants 26(9):1855–1865

    Article  CAS  Google Scholar 

  3. Chitra M, Sukumar E, Suja V, Devi S (1994) Antitumor, anti-inflammatory and analgesic property of embelin, a plant product. Chemotherapy 40:109–113

    Article  CAS  Google Scholar 

  4. Khan S, Balick MJ (2001) Therapeutic plants of Ayurveda: a review of selected clinical and other studies for 166 species. J Altern Complement Med 7:405–515

    Article  CAS  Google Scholar 

  5. Bhandari U, Kanojia R, Pillai KK (2002) Effect of ethanolic extract of Embelia ribes on dyslipidemia in diabetic rats. Int J Exp Diabetes Res 3:159–162

    Article  Google Scholar 

  6. Xu M, Cui J, Fu H et al (2005) Embelin derivatives and their anticancer activity through microtubule disassembly. Planta Med 71:944–948

    Article  CAS  Google Scholar 

  7. Ansari MN, Bhandari U (2008) Antihyperhomocysteinemic activity of an Ethanol Extract from Embelia ribes. albino Rats Pharm Biol 46:283–287

    Article  Google Scholar 

  8. Ansari MN, Bhandari U (2008) Effect of an ethanol extract of Embelia ribes fruits on isoproterenol-induced myocardial infarction in albino rats. Pharm Biol 46:928–932

    Article  Google Scholar 

  9. Singh D, Singh R, Singh P, Gupta RS (2009) Effects of embelin on lipid peroxidation and free radical scavenging activity against liver damage in rats. Basic Clin Pharmacol Toxicol 105:243–248

    Article  CAS  Google Scholar 

  10. Chaudhari HS, Bhandari U, Khanna G (2012) Preventive effect of embelin from embelia ribes on lipid metabolism and oxidative stress in high-fat diet-induced obesity in rats. Planta Med 78:651–657

    Article  CAS  Google Scholar 

  11. Durg S, Veerapur VP, Neelima S, Dhadde SB (2017) Antidiabetic activity of Embelia ribes, embelin and its derivatives: A systematic review and meta-analysis. Biomed Pharmacother 86:195–204

    Article  CAS  Google Scholar 

  12. Ravikumar K, Ved DK, Vijaya Sankar R, Udayan PS (2000) 100 Red listed medicinal plants of conservation concern in Southern India

  13. Rajashekaran PE (2001) Biodiversity of threatened species of medicinal plants in India. Trends Wildl Biodivers Conserv Manag 2:104–125

    Google Scholar 

  14. Myers N (1988) Threatened biotas:“ hot spots” in tropical forests. Environmentalist 8:187–208

    Article  CAS  Google Scholar 

  15. Grover A, Sharma PC (2016) Development and use of molecular markers: past and present. Crit Rev Biotechnol 362:290–302

    Article  Google Scholar 

  16. Petit RJ, Hampe A (2006) Some evolutionary consequences of being a tree. Annu Rev Ecol Evol Syst 37:187–214. https://doi.org/10.1146/annurev.ecolsys.37.091305.110215

    Article  Google Scholar 

  17. Devaiah KM, Venkatasubramanian P (2008) Genetic characterization and authentication of Embelia ribes using RAPD-PCR and SCAR marker. Planta Med 74:194–196

    Article  CAS  Google Scholar 

  18. Nagamani V, Rani AS Development of RAPD Markers for Identification and Authentification of Embelia ribes ARed Listed Indian Medicinal Plant

  19. Gowda B, Chandrika K, Prasanna K, Kirana V (2010) AFLP authentication of Embelia ribes Burm. f. and Embelia tsjeriam-cottam A. DC. Int J Sci Nat 1(1):58–60

    Google Scholar 

  20. Chrungoo NK, Rout GR, Balasubramani SP et al (2018) Establishing taxonomic identity and selecting genetically diverse populations for conservation of threatened plants using molecular markers.Curr Sci539–553

  21. Prajapat P, Sasidharan N, Ballani A (2015) Assessment of genetic diversity in four brassica species using randomly amplifed polymorphic DNA markers. Int J Agric Environ Biotechnol 84:831–836

    Article  Google Scholar 

  22. Bhattacharyya P, Kumaria S (2015) Molecular characterization of Dendrobium nobile Lindl., an endangered medicinal orchid, based on randomly amplifed polymorphic DNA. Plant Syst Evol 3011:201–210

    Article  Google Scholar 

  23. Salazar-Laureles ME, Pérez López DDJ, González- Huerta A, Vázquez-García LM, Valadez-Moctezuma E (2015) Genetic variability analysis of faba bean accessions using Inter-simple sequence repeat (ISSR) markers. Chil J Agric Res https://doi.org/10.4067/S0718-58392015000100017

    Article  Google Scholar 

  24. Asfaw BM, Dagne K, Keneni G, Kemal S, Kassahu T (2018) Genetic diversity study of Ethiopian Faba bean (Vicia faba L.) varieties based on phenotypic traits and inter simple sequence repeat (ISSR) markers. Afr J Biotechnol. https://doi.org/10.5897/AJB2017.16331

    Article  Google Scholar 

  25. Kapteyn J, Goldsbrough P, Simon J (2002) Genetic relationships and diversity of commercially relevant Echinacea species. Theor Appl Genet 105:369–376

    Article  CAS  Google Scholar 

  26. Moghaieb REA, Abdelhadi AA, El-Sadawy HA et al (2017) Molecular identification and genetic diversity among Photorhabdus and Xenorhabdus isolates. 3 Biotech 7:1–9

  27. Verma KS, Kachhwaha S, Kothari SL (2013) In vitro plant regeneration of Citrullus colocynthis (L.) Schard. and assessment of genetic fidelity using ISSR and RAPD markers. Indian J Biotech 12:409–414

    CAS  Google Scholar 

  28. Khurana-Kaul V, Kachhwaha S, Kothari SL (2012) Characterization of genetic diversity in Jatropha curcas L. germplasm using RAPD and ISSR markers. Indian J Biotech 11:54–61

    CAS  Google Scholar 

  29. Velasco-Ramírez AP, Torres-Morán MI, Molina-Moret S et al (2014) Efficiency of RAPD, ISSR, AFLP and ISTR markers for the detection of polymorphisms and genetic relationships in camote de cerro (Dioscorea spp.). Electron J Biotechnol 17:65–71

    Article  Google Scholar 

  30. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bull 19:11–15

    Google Scholar 

  31. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA (1990) Nucleic Acids, DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nuc Res 18:6531–6535

    Article  CAS  Google Scholar 

  32. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    Article  CAS  Google Scholar 

  33. Rohlf FJ (1998) NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. Exeter Software, Setauket, New York

    Google Scholar 

  34. Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. San Francisco: Freeman, 1973. 573 p

  35. Hammer O, Harper D, Ryan PD (2001) Past: paleontological statistics software package for education and data analysis. palaeontol electron 4:9

    Google Scholar 

  36. Liu K, Muse SV (2005) Power marker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. doi:https://doi.org/10.1093/bioinformatics/bti282

    Article  CAS  Google Scholar 

  37. Smith JSC, Chin ECL, Shu H et al (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor Appl Genet 95:163–173

    Article  CAS  Google Scholar 

  38. Prevost A, Wilkinson M (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112

    Article  CAS  Google Scholar 

  39. Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173:638–649

    Article  CAS  Google Scholar 

  40. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in excel, Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539

    Article  CAS  Google Scholar 

  41. Tamboli AS, Yadav PB, Gothe AA, Yadav SR, Govindwar SP (2018) Molecular phylogeny and genetic diversity of genus Capparis (Capparaceae) based on plastid DNA sequences and ISSR markers. Plant Syst Evol 304(2):205–217. https://doi.org/10.1007/s00606-017-1466-z

    Article  CAS  Google Scholar 

  42. Vinceti B, Loo J, Gaisberger H, Van Zonneveld MJ, Schueler S, Konrad H (2013) Conservation priorities for Prunus africana defned with the aid of spatial analysis of genetic data and climatic variables. PLoS ONE 8(3):e59987

    Article  CAS  Google Scholar 

  43. Stevens L, Salomon B, Sun G (2007) Microsatellite variability and heterozygote excess in Elymus trachycaulus populations from British Columbia in Canada. Biochem Syst Ecol 35:725–736. doi:https://doi.org/10.1016/j.bse.2007.05.017

    Article  CAS  Google Scholar 

  44. Shrisha NB, Kigga KSK, Ramachandra KK (2018) Genetic diversity of Embelia species, Maesa indica and Ardisia solanacea sampled from Western Ghats of Karnataka using DNA markers Res J Life Sci Bioinform. Pharma Chem Sci 4(6):457–467

    Google Scholar 

  45. Jayaram K, Prasad MNV (2008) Genetic diversity in Oroxylum indicum L. Vent. Bignoniaceae, a vulnerable medicinal plant by random amplifed polymorphic DNA marker. Afr J Biotech 7:254–26265

    CAS  Google Scholar 

  46. Pei YL, Zou YP, Yin Z, Wang XQ, Zhang ZX, Hong DY (1995) Preliminary report of RAPD analysis in Paeonia sufruticosa subsp. spontanea and P. rockii. Acta Phys Sin 33:350–35666

    Google Scholar 

  47. Brauner S, Crawford DJ, Stuessy TF (1992) Ribosomal DNA and RAPD variation in the rare plant family Lactoridaceae. Am J Bot 79:1436–143967

    Article  CAS  Google Scholar 

  48. Abedian M, Talebi M, Golmohammdi HR, Sayed-Tabatabaei BE (2012) Genetic diversity and population structure of mahaleb cherry (Prunus mahaleb L.) and sweet cherry (Prunus avium L.) using SRAP markers. Biochem Syst Ecol 40:112–117. doi:https://doi.org/10.1016/j.bse.2011.10.005

    Article  CAS  Google Scholar 

  49. TilwariA, Sharma R (2021) Random amplifed polymorphic DNA and inter simple sequence repeat markers reveals genetic diversity between micro propagated, wild and feld cultivated genotypes of Gloriosa superba: an endangered medicinal plant. Mol Biology Rep 48:2437–2452

    Article  Google Scholar 

  50. Farajpour M, Ebrahimi M, Amiri R et al (2011) Study of genetic variation in yarrow using inter-simple sequence repeat (ISSR) and random amplifed polymorphic DNA (RAPD) markers. Afr J Biotechnol 10(54):11137–1114174

    CAS  Google Scholar 

  51. Patel DM, Fougat RS, Sakure AA, Kumar S, Kumar M, Mistry JG (2016) Detection of genetic variation in sandalwood using various DNA markers. 3 Biotech 61:55

    Article  Google Scholar 

  52. Velasco-Ramirez AP, Torres-Moran MI, Molina-Moret S et al (2014) Efciency of RAPD, ISSR, AFLP and ISTR markers for the detection of polymorphisms and genetic relationships in camote de cerro Dioscorea spp. Electron J Biotechnol 172:65–71. https://doi.org/10.1016/j.ejbt.2014.01.00

    Article  Google Scholar 

  53. Debajit S, Sukriti D, Sneha G, Mohan L et al (2015) RAPD and ISSR based Intra-specifc molecular genetic diversity analysis of Cymbopogon fexuosus L. Stapf with a distinct correlation of morpho-chemical observations. Res J Biotechnol 107:105–113

    Google Scholar 

Download references

Acknowledgements

The authors thank the Head, Department of Botany, Shivaji University, Kolhapur, for providing the necessary facilities. We also thank the Maharashtra and Karnataka State Biodiversity Board for providing the necessary permission. VVK is thankful to Mr. V. Y. Kamble, Ganga, Vinayak, and Sushant Sawant for the collections. VVK is thankful to UGC, New Delhi, for financial support under UGC-BSR Fellowship in Sciences for Students (No.F.25 − 1/2013-14 (BSR)/7-163/2007(BSR). Thanks are due to the Natural National Science Foundation of China (NSFC Grant Number 32250410305) awarded to SAR.

Author information

Author notes

    Authors and Affiliations

    1. Department of Botany, Shivaji University, Kolhapur, 416004, Maharashtra, India

      Vidya V. Kamble & Nikhil B. Gaikwad

    2. PG Department of Botany, Basavaprabhu Kore, Arts, Science, and Commerce College, Chikodi, 591201, Karnataka, India

      Vidya V. Kamble

    3. Department of Biochemistry, Shivaji University, Kolhapur, 416004, Maharashtra, India

      Asif S. Tamboli

    4. Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea

      Asif S. Tamboli

    5. Department of Botany, Jaysingpur College Jaysingpur, Kolhapur, 416101, Maharashtra, India

      Suraj D. Umdale

    6. Center for Integrative Conservation, **shuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China

      Shabir A. Rather & Hongmei Liu

    7. Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Jammu, Kashmir, India

      Shabir Hussain Wani

    Authors
    1. Vidya V. Kamble
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Asif S. Tamboli
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Suraj D. Umdale
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Shabir A. Rather
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Hongmei Liu
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Shabir Hussain Wani
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Nikhil B. Gaikwad
      View author publications

      You can also search for this author in PubMed Google Scholar

    Contributions

    VVK and NBG designed the study. NBG supervised the study. VVK, NBG, and SDU collected the samples. VVK conducted laboratory experiments. SAR, VVK, AST, and SDU conducted bioinformatics and statistical analyses. SAR, VVK, SHW, HL, and AST drafted and revised the manuscript.

    Corresponding author

    Correspondence to Nikhil B. Gaikwad.

    Ethics declarations

    Conflict of interest

    The authors declare that they have no conflict of interest.

    Ethical approval

    This article does not contain any studies with human participants performed by any of the authors.

    Additional information

    Publisher’s Note

    Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

    The authors Vidya V. Kamble and Shabir A. Rather have contributed equally to this work.

    Electronic supplementary material

    Rights and permissions

    Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Kamble, V.V., Tamboli, A.S., Umdale, S.D. et al. Evaluating genetic diversity of geographically diverse populations of Embelia ribes Burm f., a highly medicinal woody liana from the Western Ghats of India, using random amplified polymorphic DNA (RAPD) and intersimple sequence repeats (ISSR) markers. Mol Biol Rep 50, 1603–1615 (2023). https://doi.org/10.1007/s11033-022-08099-1

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s11033-022-08099-1

    Keywords

    Search

    Navigation