Skip to main content

Analysis of intraspecific genetic variation in Musa balbisiana Colla from Meghalaya as revealed by Single Primer Amplification Reaction approach


The Indian subcontinent is considered to be the major centre of hybridization of the wild Musa progenies, as it forms the centre of secondary origin of the taxa and therefore expected to exhibit a high degree of diversity. Musa balbisiana Colla is known to be one of the wild progenitors of cultivated bananas and plantains. Knowledge of genetic variability is very important for contemplating any conservation and management programmes. Single Primer Amplification Reaction (SPAR) approach i.e., a combination of random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and directed amplification of minisatellites DNA (DAMD) markers function as important tools for analyzing genetic variation in plants. They collectively provide a comprehensive description of the nature and the extent of existing natural genetic diversity, as the primers target different regions of the genome. A total of 47 SPAR primers (RAPD-25, ISSR-12 and DAMD-10) with high reproducibility were used for analysis of intraspecific genetic variation of the 12 genotypes of M. balbisiana, which yielded 331 polymorphic bands. The RAPD, ISSR and DAMD markers revealed 82.63 %, 90.36 % and 84.72 % of polymorphic bands respectively. The polymorphic information content (PIC) values were almost identical for each marker system while the resolving power (Rp) was found to be highest in DAMD (4.10). The dendrogram obtained showed the presence of two main clusters in all the analyses, with some genotypes (MB10-MB11 and MB5-MB7) always maintaining and manifesting their strong genetic relationship by clustering together in almost all the analyses. Combinations of such markers can be considered as more effective and promising tool for assessing genetic variation in other Musa species as well.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


  1. 1.

    Arnaud-Haond S, Teixeira S, Massa S, Billot C, Saenger P, Coupland G, et al. Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations. Mol Ecol. 2006;15:3515–25.

    CAS  Article  PubMed  Google Scholar 

  2. 2.

    Bhat KV, Jarret RL. Random Amplified Polymorphic DNA and genetic diversity in Indian Musa germplasm. Genet Resour Crop Evol. 1995;42:107–18.

    Article  Google Scholar 

  3. 3.

    Cheesman EE. Classification of the bananas. III. Critical notes on species. a. M. balbisiana. Kew Bull. 1948;3:11–6.

    Article  Google Scholar 

  4. 4.

    Creste S, Tulmann-Neto A, Silva SO, Figueira A. Genetic characterization of banana cultivars (Musa spp.) from Brazil using microsatellite markers. Euphytica. 2003;132:259–68.

    CAS  Article  Google Scholar 

  5. 5.

    Crouch JH, Crouch HK, Constandt H, Van Gysel A, Breyne P, Van Montagu M, et al. Comparison of PCR-based molecular marker analyses of Musa breeding populations. Mol Breed. 1999;5:233–44.

    CAS  Article  Google Scholar 

  6. 6.

    Daniells JW, Jenny C, Karamura DA, Tomekpe K, Arnaud E, Sharrock S. Musalogue: a catalogue of Musa germplasm diversity in the genus Musa. France: INIBAP; 2001.

    Google Scholar 

  7. 7.

    Dickinson A. Recommended Intakes of Vitamins and Essential minerals. In: CRN (Council for responsible Nutrition). The benefits of Nutritional Supplements; 2000.

  8. 8.

    Drew RA. The application of biotechnology to the conservation and improvement of tropical and subtropical fruit species. FAO: Rome; 1997 p. 1–77.

    Google Scholar 

  9. 9.

    Francisco-Ortega J, Santos-Guerra A, Kim SC, Crawford DJ. Plant genetic diversity in the Canaries: a conservation perspective. Am J Bot. 2000;87:909–19.

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Frankham R Genetics and conservation biology. C R Biol. 2003;326:22–9.

    Article  Google Scholar 

  11. 11.

    Frison EA, Escalant JV, Sharrock S. The Global Musa Genomic Consortium: A boost for banana improvement. In: Jain SM, Swennen R, editors. Banana Improvement: Cellular, Molecular Biology, and Induced Mutations. Science Publishers, Enfield, New Hampshire: USA; 2004. p. 341–9.

    Google Scholar 

  12. 12.

    Gawel NJ, Jarret RL. A modified CTAB DNA extraction procedure for Musa and Ipomoea. Plant Mol Biol Rep. 1991;9:262–6.

    CAS  Article  Google Scholar 

  13. 13.

    Ge XJ, Liu MH, Wang WK, Schaal BA, Chiang TY. Population structure of wild bananas, Musa balbisiana, in China determined by SSR fingerprinting and cpDNA-RFLP. Mol Ecol. 2005;14:933–44.

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Grajal-Martin M, Siverio-Grillo G, Marrero-Dominguez A. The use of randomly amplified polymorphic DNA (RAPD) for the study of genetic diversity and somaclonal variation in Musa. Acta Hortic. 1998;490:445–54.

    CAS  Article  Google Scholar 

  15. 15.

    Grapin A, Noyer JL, Carreel F, Dambier D, Baurens FC, Lanaud C, et al. Diploid Musa acuminata genetic diversity assayed with sequence tagged microsatellite sites. Electrophoresis. 1998;19:1374–80.

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    Heath DD, Iwana GK, Delvin RH. PCR primed with VNTR core sequences yields species specific patterns and hypervariable probes. Nucleic Acids Res. 1993;21:5782–5.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. 17.

    IPGRI, INIBAP, CIRAD. Descriptors for Banana (Musa spp.). IPGRI, Rome, Italy; INIBAP, Montpellier, France; CIRAD, France; 1996.

  18. 18.

    Jaccard P. Étude comparative de la distribuition florale dans une portion des Alpes et des Jura. 1901. p. 547–79.

  19. 19.

    Jamieson IG. Has the debate over genetics and extinction of island endemics truly been resolved? Anim Conserv. 2007;10:139–44.

    Article  Google Scholar 

  20. 20.

    Juan C, Emerson BC. Oromı́ P, Hewitt GM. Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands. Trends Ecol Evol. 2000;15:104–9.

    Article  PubMed  Google Scholar 

  21. 21.

    Jussieu AL. Ordo I. Musae. Genera plantarum: secundum ordines naturals disposita, juxta methodum in Horto regio parisiensi exaratam, anno M.DCC.LXXIV., Paris; 1789. p. 61–62.

  22. 22.

    Kaemmer D, Afza R, Weising K, Kahl G, Novak FJ. Oligonucleotide and amplification fingerprinting of wild species and cultivars of banana (Musa spp.). Biotechnology (NY). 1992;10:1030–5.

    CAS  Article  Google Scholar 

  23. 23.

    Kumar A, Mishra P, Singh SC, Sundaresan V. Efficiency of ISSR and RAPD markers in genetic divergence analysis and conservation management of Justicia adhatoda L., a medicinal plant. Plant Syst Evol. 2014;300:1409–20.

    Article  Google Scholar 

  24. 24.

    Lamare A, Rao SR. Efficacy of RAPD, ISSR and DAMD markers in assessment of genetic variability and population structure of wild Musa acuminata Colla. Physiol Mol Biol Plants. 2015;3:349–58.

    Article  Google Scholar 

  25. 25.

    Liu YF, Xing M, Zhao W, Fan RJ, Luo S, Chen X. Genetic diversity analysis of Rhododendron aureum Georgi (Ericaceae) located on Changbai Mountain using ISSR and RAPD markers. Plant Syst Evol. 2012;298:921–30.

    CAS  Article  Google Scholar 

  26. 26.

    Loh JP, Kiew R, Set O, Gan LH, Gan YY. Amplified fragment length polymorphism (AFLP) fingerprinting of 16 banana cultivars (Musa spp.). Mol Phylogenet Evol. 2000;17:360–6.

    CAS  Article  PubMed  Google Scholar 

  27. 27.

    Milligan BG, Leebens-Mack J, Strand AE. Conservation genetics: beyond the maintenance of marker diversity. Mol Ecol. 1994:423–35.

  28. 28.

    Newton AC, Allnutt TR, Gillies ACM, Lowe AJ, Ennos RA. Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends Ecol Evol. 1999;14:140–5.

    Article  PubMed  Google Scholar 

  29. 29.

    Noyer JL, Causse S, Tomekpe K, Bouet A, Baurens FC. A new image of plantain diversity assessed by SSR. AFLP and MSAP markers Genetica. 2005;124:61–9.

    CAS  PubMed  Google Scholar 

  30. 30.

    Nwakanma DC, Pillay M, Okoli BE, Tenkouano A. Sectional relationships in the genus Musa L. inferred from the PCR-RFLP of organelle DNA sequences. Theor Appl Genet. 2003;107:850–6.

    CAS  Article  PubMed  Google Scholar 

  31. 31.

    Onguso JM, Kahangi EM, Ndiritu DW, Mizutani F. Genetic characterization of cultivated bananas and plantains in Kenya by RAPD markers. Sci Hort. 2004;99:9–20.

    CAS  Article  Google Scholar 

  32. 32.

    Prevost A, Wilkinson MJ. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor App Genet. 1999;98:107–12.

    CAS  Article  Google Scholar 

  33. 33.

    Rohlf FJ. Applied Biostatistics Inc.; Setauket, New York. NTSYSpc Numerical Taxonomy and Multivariate Analysis System Version 2.0 User Guide. 1998.

  34. 34.

    Sehgal D, Rajpal VR, Raina SN, Sasanuma T, Sasakuma T. Assaying polymorphism at DNA level for genetic diversity diagnostics of the safflower (Carthamus tinctorius L.) world germplasm resources. Genetica. 2009;135:457–70.

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    Silva L, Elias RB, Moura M, Meimberg H, Dias E. Genetic variability and differentiation among populations of the Azorean endemic gymnosperm Juniperus brevifolia: baseline information for a conservation and restoration perspective. Biochem Genet. 2011;49:715–34.

    CAS  Article  PubMed  Google Scholar 

  36. 36.

    Simmonds NW. Botanical results of the banana collecting expedition, 1954–1955. Kew Bull. 1956. p. 463–90.

  37. 37.

    Simmonds NW. Bananas Musa (Musaceae). In: Smartt J, Simmonds NW, editors. Evolution of Crop Plants. 2nd ed. Essex, UK.: Longmans Scientific and Technical; 1995. p. 370–5.

    Google Scholar 

  38. 38.

    Simmonds NW, Shepherd K. The taxonomy and origins of cultivated bananas. Bot J Linn Soc. 1955;55:302–12.

    Article  Google Scholar 

  39. 39.

    Ude G, Pillay M, Nwakanma D, Tenkouano A. Analysing of genetic diversity and sectional relationships in Musa using AFLP markers. Theor Appl Genet. 2002a;104:1239–45.

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Ude G, Pillay M, Nwakanma D, Tenkouano A. Genetic diversity in Musa acuminata Colla and Musa balbisiana Colla and some of their natural hybrids using AFLP markers. Theor Appl Genet. 2002b;104:1246–52.

    CAS  Article  PubMed  Google Scholar 

  41. 41.

    Ude G, Pillay M, Nwakanma D, Tenkouano A. Genetic diversity in an African plantain core collection using AFLP and RAPD markers. Theor Appl Genet. 2003;107:248–55.

    CAS  Article  PubMed  Google Scholar 

  42. 42.

    Uma S, Siva SA, Saraswathi MS, Durai P, Sharma TV, Singh DB, et al. Studies on the origin and diversification of Indian wild banana (Musa balbisiana) using arbitrarily amplified DNA markers. J Hortic Sc Biotech. 2005;80(5):575–80.

    CAS  Article  Google Scholar 

  43. 43.

    Uma S, Siva SA, Saraswathi MS, Manickavasagam M, Durai P, Selvarajan R, Sathiamoorthy. Variation and intraspecific relationships in Indian wild Musa balbisiana (BB) population as evidenced by random amplified polymorphic DNA. Genet Resour Crop Ev. 2006;53:349–55.

    CAS  Article  Google Scholar 

  44. 44.

    Venkatachalam LR, Sreedhar V, Bhagyalakshmi N. The use of genetic markers for detecting DNA polymorphism, genotype identification and phylogenetic relationships among banana cultivars. Mol Phylogenet Evol. 2008;47(3):974–85.

    CAS  Article  PubMed  Google Scholar 

  45. 45.

    Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, et al. AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res. 1995;21:4407–14.

    Article  Google Scholar 

  46. 46.

    Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990;18:6531–5.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Wong C, Kiew R, Argent G, Set O, Lee SK, Gan YY. Assessment of the validity of the sections in Musa (Musaceae) using AFLP. Ann Bot. 2002;90:231–8.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Zhou Z, Bebeli PJ, Somers DJ, Gustafson JP. Direct amplification of minisatellite-region DNA with VNTR core sequences in the genus Oryza. Theor Appl Genet. 1997;95:942–9.

    CAS  Article  Google Scholar 

  49. 49.

    Zietkiewicz E, Rafalski A, Labuda D. Genome fingerprinting by simple sequence repeat (SSR) – anchored polymerase chain reaction amplification. Genomics. 1994;20(2):176–83.

    CAS  Article  PubMed  Google Scholar 

Download references


The authors wish to thank the Head, Department of Biotechnology and Bioinformatics, North-Eastern Hill University for providing the facilities and support to carry out this research. Sincere thanks are also given to all the members of Plant Biotechnology Laboratory for their constant encouragement and support.

Author information



Corresponding author

Correspondence to Satyawada Rama Rao.

Electronic Supplementary Material


(DOCX 19 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Lamare, A., Baruah, I., Borah, N. et al. Analysis of intraspecific genetic variation in Musa balbisiana Colla from Meghalaya as revealed by Single Primer Amplification Reaction approach. Nucleus 59, 25–34 (2016).

Download citation


  • Wild species
  • Musa balbisiana
  • SPAR
  • Genetic variation