Skip to main content
SpringerLink
Log in

Efficiency of RAPD, ISSR and ITS markers in detecting genetic variability among Salacia species sampled from the Western Ghats of Karnataka

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

Abstract

Diversity and phylogenetic relationship between four closely related Salacia species, i.e., Salacia chinensis, Salacia macrosperma, Salacia fruticosa and Salacia oblonga, collected from the Western Ghats of Karnataka, India, was assessed. Ten each of RAPD and ISSR primers generated a total of 76 and 68 loci, generating polymorphisms of 92.21 and 89.71%, respectively. Maximum likelihood analysis of the ITS sequences revealed three clades. Dendrogram analyses of RAPD and ISSR revealed two and four clusters, respectively. Overall polymorphism revealed by RAPD was 41.45 ± 10%, ISSR was 33.58 ± 6.52%, and ITS was 25.50 ± 17.25%. Molecular variance revealed significant variance within and among the Salacia species. Tajima’s D neutrality test and Fu’s Fs were negative for all four species, implying presences of rare alleles and population expansion. Comparative study of RAPD, ISSR and ITS for Salacia species has given an insight into the efficiency of each technique in detecting diversity within and among the population sampled in the Western Ghats of Karnataka.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Salunkhe V, Wachasundar N (2009) Clinical evaluation of antidiabetic polyherbal Ayurvedic formulation-Madhujeevan Churna using Stevia rebaudiana. Indian J Pharm Pract 2(2):58–65

    Google Scholar 

  2. Rajalakshmy M, Maniyan AK, Sruthi C, Sindhu A (2014) Standardisation of a polyherbal anti-diabetic Ayurvedic medicine Diajith. Ayurpharm Int J Ayur Alli Sci 3(7):186–194

    Google Scholar 

  3. Yoshikawa M, Nishida N, Shimoda H, Takada M, Kawahara Y, Matsuda H (2001) Polyphenol constituents from Salacia species: quantitative analysis of mangiferin with alpha-glucosidase and aldose reductase inhibitory activities. Yakugaku zasshi: J Pharm Soc Jpn 121(5):371–378

    Article  CAS  Google Scholar 

  4. Yoshimi N, Matsunaga K, Katayama M, Yamada Y, Kuno T, Qiao Z, Hara A, Yamahara J, Mori H (2001) The inhibitory effects of mangiferin, a naturally occurring glucosylxanthone, in bowel carcinogenesis of male F344 rats. Cancer Lett 163(2):163–170

    Article  CAS  PubMed  Google Scholar 

  5. Zheng M, Lu Z (1990) Antiviral effect of mangiferin and isomangiferin on Herpes simplex virus. Chin Med J 103(2):160–165

    CAS  PubMed  Google Scholar 

  6. Guha S, Ghosal S, Chattopadhyay U (1996) Antitumor, immunomodulatory and anti-HIV effect of mangiferin, a naturally occurring glucosylxanthone. Chemotherapy 42(6):443–451

    Article  CAS  PubMed  Google Scholar 

  7. Xie W, Tanabe G, Matsuoka K, Amer MF, Minematsu T, Wu X, Yoshikawa M, Muraoka O (2011) Role of the side chain stereochemistry in the α-glucosidase inhibitory activity of kotalanol, a potent natural α-glucosidase inhibitor. Bioorganic Med Chem 19(7):2252–2262

    Article  CAS  Google Scholar 

  8. Udayan P, Yohannan R, Devipriya M, Devipriya V, Pradeep A (2012) A new species of Salacia (Hippocrateaceae) from South India. Edinburgh J Bot 69(02):255–258

    Article  Google Scholar 

  9. Udayan PS, Yohannan R, Devipriya MS, Pradeep AK (2013) Salacia Vellaniana Udayan, Yohannan & Pradeep (Celastraceae), a new species from India. Candollea 68(1):147–149

    Article  Google Scholar 

  10. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20(2):176–183

    Article  CAS  PubMed  Google Scholar 

  11. Alvarez I, Wendel J (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phyl Evol 29(3):417–434

    Article  CAS  Google Scholar 

  12. Stange C, Prehn D, Arce-Johnson P (1998) Isolation of Pinus radiata genomic DNA suitable for RAPD analysis. Plant Mol Biol Rep 16(4):366–366

    Article  Google Scholar 

  13. White T (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR-Protocols: A guide to methods and applications

    Google Scholar 

  14. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. https://doi.org/10.1093/molbev/msr121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Thompson JD, Gibson T, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinform 2:2.3. 1–2.3. 22

    Google Scholar 

  16. Roldàn-Ruiz I, Dendauw J, Van Bockstaele E, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed 6(2):125–134

    Article  Google Scholar 

  17. 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(6):638–649

    Article  CAS  Google Scholar 

  18. Prevost A, Wilkinson M (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. TAG Theor Appl Genet 98(1):107–112

    Article  CAS  Google Scholar 

  19. Yeh FC, Yang R-C, Boyle T (1999) POPGENE version 1.31. Microsoft window-based freeware for population genetic analysis University of Alberta, Edmonton, Canada

  20. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Resour 6(1):288–295

    Article  Google Scholar 

  21. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452

    Article  CAS  PubMed  Google Scholar 

  22. Stöver BC, Müller KF (2010) TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinform 11(1):7. https://doi.org/10.1186/1471-2105-11-7

    Article  Google Scholar 

  23. Priya G, Gopalakrishnan M, Sekar T (2016) RAPD–PCR Analysis of various species of Salacia collected from Wayanad to study its genetic fidelity. World J Pharm Pharm Sci 5(9):1227–1242

    CAS  Google Scholar 

  24. Fernandez M, Figueiras A, Benito C (2002) The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. TAG Theor Appl Genet 104(5):845–851

    Article  CAS  PubMed  Google Scholar 

  25. Loarce Y, Gallego R, Ferrer E (1996) A comparative analysis of the genetic relationships between rye cultivars using RFLP and RAPD markers. Euphytica 88(2):107–115

    Article  Google Scholar 

  26. Ramasetty BT, Bajpe SN, Kadappa SKK, Saini RK, Basavaraju SN, Ramachandra KK, Sripathy PH (2016) Identification and genetic diversity analysis of Memecylon species using ISSR, RAPD and Gene-based DNA barcoding tools. Electron J Biotechnol 24(Supplement C):1–8. https://doi.org/10.1016/j.ejbt.2016.09.001

    Article  CAS  Google Scholar 

  27. Anerao JS, Jha V, Korgaonkar L, Devi SP, Desai N (2017) Dissecting genetic diversity in Garcinia xanthochymus using ISSR and RAPD markers. J Plant Breed Genet 4(3):69–76

    Google Scholar 

  28. Dev SA, Anoop B, Anoja K, Udayan P, Muralidharan E (2015) Species discrimination through DNA barcoding in the genus Salacia of the Western Ghats in India. Nord J Bot 33(6):722–728

    Article  Google Scholar 

  29. Udayan P, Raghu A, Sreekumar V, Muraleedaran E, District T (2014) A new variety of Salacia (Celastraceae) from the Western Ghats of Kerala, South India. Int J Plant Animal Environ Sci 4(3, July-Sep):3

    Google Scholar 

Download references

Acknowledgements

The authors acknowledge the support from the Institution of Excellence Program of University of Mysore awarded by the Ministry of Human Resource Development and University Grants Commission, Government of India.

Author information

Authors and Affiliations

  1. Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore, Karnataka, 570006, India

    Shrisha Naik Bajpe, Tumkur Ramasetty Bharathi, Kuppur Mallikarjunaiah Marulasiddaswamy, Harishchandra Sripathy Prakash & Ramachandra Kukkundoor Kini

  2. Government Pre-University College, Davengere, India

    Kigga Kadappa Sampath Kumara

Authors
  1. Shrisha Naik Bajpe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tumkur Ramasetty Bharathi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kuppur Mallikarjunaiah Marulasiddaswamy
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kigga Kadappa Sampath Kumara
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Harishchandra Sripathy Prakash
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ramachandra Kukkundoor Kini
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ramachandra Kukkundoor Kini.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies conducted on human or animal subjects.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bajpe, S.N., Bharathi, T.R., Marulasiddaswamy, K.M. et al. Efficiency of RAPD, ISSR and ITS markers in detecting genetic variability among Salacia species sampled from the Western Ghats of Karnataka. Mol Biol Rep 45, 931–941 (2018). https://doi.org/10.1007/s11033-018-4248-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-018-4248-y

Keywords

Search

Navigation