Skip to main content
SpringerLink
Log in

Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses

  • Published:
Journal of Zhejiang University SCIENCE B Aims and scope Submit manuscript

Abstract

Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs. This study employed amplified fragment length polymorphism (AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman. Using 12 primer combinations, a total of 1094 bands were scored, of which 1012 were polymorphic. Eighty-two unique markers were identified, which revealed the distinct separation of the seven cultivars. The results obtained show that AFLP can be used to differentiate the banana cultivars. Further classification by phylogenetic, hierarchical clustering and principal component analyses showed significant differences between the clusters found with molecular markers and those clusters created by previous studies using morphological analysis. Based on the analytical results, a consensus dendrogram of the banana cultivars is presented.

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

Similar content being viewed by others

References

  • Allaby, R.G., Brown, T.A., 2003. AFLP data and the origins of domesticated crops. Genome, 46(3):448–453. [doi:10.1139/g03-025]

    Article  CAS  PubMed  Google Scholar 

  • Bhat, K.V., Jarret, R.L., Rana, R.S., 1995. DNA profiling of banana and plantain cultivars using random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers. Electrophoresis, 16(1):1736–1745. [doi:10.1002/elps.11501601287]

    Article  CAS  PubMed  Google Scholar 

  • Bhat, K.V., Amaravathi, Y., Guatam, P.L., Velayudhan, K.C., 2004. AFLP characterization and genetic diversity analysis of Indian banana and plantain cultivars (Musa spp.). Plant Genetic Resources, 2(2):121–130. [doi:10.1079/PGR200440]

    Article  CAS  Google Scholar 

  • de Langhe, E., 2002. Banana Diversity in the Middle East (Jordan, Egypt and Oman). International Network for the Improvement of Banana and Plantain (INIBAP), Montpellier, France.

    Google Scholar 

  • Doyle, J.J., Doyle, J.L., 1990. A rapid total DNA preparation procedure for fresh plant tissue. Focus, 12:13–15.

    Google Scholar 

  • Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D., 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Nat. Acad. Sci., 95(25):14863–14868. [doi:10.1073/pnas.95.25.14863]

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein, J., 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics, 5(2):163–166. [doi:10.1111/j.1096-0031.1989.tb00562.x]

    Article  Google Scholar 

  • Gawel, N.J., Jarret, R.L., 1992. Restriction fragment length polymorphism (RFLP)-based phylogenetic analysis of Musa. Theor. Appl. Genet., 84(3–4):286–290. [doi:10.1007/BF00229484]

    Google Scholar 

  • Godwin, I.D., Aitken, E.A.B., Smith, L.W., 1997. Application of inter-simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis, 18(9):1524–1528. [doi:10.1002/elps.1150180906]

    Article  CAS  PubMed  Google Scholar 

  • Grapin, A., Noyer, J.L., Carrel, F., Dambler, D., Baurens, F.C., Lanaud, C., Lagoda, P.J.L., 1998. Diploid Musa acuminate genetic diversity assayed with sequence-tagged microsatellite sites. Electrophoresis, 19(8–9):1374–1380. [doi:10.1002/elps.1150190829]

    Article  CAS  PubMed  Google Scholar 

  • Jansen, J., van Hintum, T., 2007. Genetic distance sampling: a novel sampling method for obtaining core collections using genetic distances with an application to cultivated lettuce. Theor. Appl. Genet., 114(3):421–428. [doi:10.1007/s00122-006-0433-9]

    Article  CAS  PubMed  Google Scholar 

  • Jiang, H., Liao, B., Ren, X., Lei, Y., Mace, E., Fu, T., Crouch, J.H., 2007. Comparative assessment of genetic diversity of peanut (Arachis hypogaea L.) genotypes with various levels of resistance to bacterial wilt through SSR and AFLP analyses. J. Genet. Genomics, 34(6):544–554. [doi:10.1016/S1673-8527(07)60060-5]

    Article  CAS  PubMed  Google Scholar 

  • Loh, J.P., Kiew, R., Set, O., Gan, L.H., Gan, Y.Y., 2000. Amplified fragment length polymorphism fingerprinting of 16 banana cultivars (Musa cvs.). Mol. Phylogenetics Evol., 17(3):360–366. [doi:10.1006/mpev.2000.0848]

    Article  CAS  Google Scholar 

  • Lu, G., Cao, J.S., Chen, H., 2002. Genetic linkage map of Brassica campestris L. using AFLP and RAPD markers. J. Zhejiang Univ.-Sci. A, 3(5):600–605. [doi:10.1631/jzus.2002.0600]

    Article  CAS  Google Scholar 

  • Magnussen, L.S., Hauser, T.P., 2007. Hybrids between cultivated and wild carrots in natural populations in Denmark. Heredity, 99(2):185–192. [doi:10.1038/sj.hdy.6800982]

    Article  CAS  PubMed  Google Scholar 

  • Martens, H., Karstang, T., Næs, T., 1987. Improved selectivity in spectroscopy by multivariate calibration. J. Chemom., 1(4):201–219. [doi:10.1002/cem.1180010403]

    Article  CAS  Google Scholar 

  • Miller, A.J., Schaal, B.A., 2006. Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae). Mol. Ecol., 15(6):1467–1480. [doi:10.1111/j.1365-294X.2006.02834.x]

    Article  CAS  PubMed  Google Scholar 

  • Oraguzie, N.C., Iwanami, H., Soejima, J., Harada, T., Hall, A., 2004. Inheritance of the Md-ACS1 gene and its relationship to fruit softening in apple (Malus×domestica Borkh). Theor. Appl. Genet., 108(8):1526–1533. [doi:10.1007/s00122-003-1574-8]

    Article  CAS  PubMed  Google Scholar 

  • Oraguzie, N.C., Yamamoto, T., Soejima, J., Suzuki, T., de Silva, N., 2005. DNA fingerprinting of apple (Malus spp.) rootstocks using simple sequence repeats. Plant Breeding, 124(2):197–202. [doi:10.1111/j.1439-0523.2004.01064.x]

    Article  CAS  Google Scholar 

  • Oraguzie, N.C., Rikkerink, E.H.A., Gardiner, S., de Silva, N., 2007. Association Mapping in Plants. Springer, New York. [doi:10.1007/978-0-387-36011-9]

    Book  Google Scholar 

  • Pillay, M., Ogundiwin, E., Nwakanma, D.C., Ude, G., Tenkouano, A., 2001. Analysis of genetic diversity and relationships in east African banana germplasm. Theor. Appl. Genet., 102(6–7):965–970. [doi:10.1007/s001220000500]

    Article  CAS  Google Scholar 

  • Pillay, M., Dimpka, C., Ude, G.N., Makumbi, D., Tushemereirwe, W., 2003. Genetic variation in banana cultivar ’sukali Nidzi’ grown in different regions of Uganda. Afr. Crop Sci. J., 11(2):87–95.

    Google Scholar 

  • Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., Rafalski, A., 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed., 2(3):225–238. [doi:10.1007/BF00564200]

    Article  CAS  Google Scholar 

  • Simmonds, N.W., 1966. Bananas. Tropical Agriculture Series, 2nd Ed. Longmans, London.

    Google Scholar 

  • Tenkouano, A., Crouch, J.H., Crouch, H.K., Vuylsteke, D., Ortiz, R., 1999. Comparison of DNA marker and pedigree-based methods of genetic analysis in plantain and banana (Musa spp.) clones. I. Estimation of genetic relationships. Theor. Appl. Genet., 98(1):62–68. [doi:10.1007/s001220051040]

    Article  CAS  Google Scholar 

  • Toral Ibañez, M.T., Caru, M., Herrera, M.A., Gonzalez, L., Martin, L.M., Miranda, J., Navarro-Cerrillo, R.M., 2009. Clones identification of Sequoia sempervirens (D. Don) Endl. in Chile by using PCR-RAPDs technique. J. Zhejiang Univ.-Sci. B, 10(2):112–119. [doi:10.1631/jzus.B0820162]

    Article  PubMed  Google Scholar 

  • Ude, G., Pillay, M., Nwakanma, D., Tenkouano, A., 2002a. Analysis of genetic diversity and sectional relationships in Musa using AFLP markers. Theor. Appl. Genet., 104(8):1239–1245. [doi:10.1007/s00122-001-0802-3]

    Article  CAS  PubMed  Google Scholar 

  • Ude, G., Pillay, M., Nwakanma, D., Tenkouano, A., 2002b. Genetic diversity in Musa acuminata Colla and Musa balbisiana Colla and some of their natural hybrids using AFLP markers. Theor. Appl. Genet., 104(8):1246–1252. [doi:10.1007/s00122-002-0914-4]

    Article  CAS  PubMed  Google Scholar 

  • Ude, G., Ogundiwin, E., Pillay, M., Tenkouano, A., 2003. Genetic diversity in an African Plantain core collection using AFLP and RAPD markers. Theor. Appl. Genet., 107(2):248–255. [doi:10.1007/s00122-003-1246-8]

    Article  CAS  PubMed  Google Scholar 

  • Ude, G.N., Dimpka, C.O., Anegbeh, P.O., Saibu, A.A., Tenkouano, A., Pillay, M., Tchoundjeu, Z., 2006. Analysis of genetic diversity in accessions of Irvingia gabonensis (Aubry-Lecomte ex O’Rorke) Baill. Afr. J. Biotechnol., 5(3):219–223.

    CAS  Google Scholar 

  • Viswanath, P., Nadaf, S.K., Mazroui, Y., Al-Jabry, A.A., Bakry, A.N., Hussaein, O.K., 2000. Present Status of Banana Production in Oman. In: Bananas and Food Security. International Symposium, Douala, Cameroon, Nov. 10–14, 1998, p.237–250.

  • Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., Zabeau, M., 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res., 23(21):4407–4414. [doi:10.1093/nar/23.21.4407]

    Article  CAS  PubMed  Google Scholar 

  • Wang, X.L., Chiang, T.Y., Roux, N., Hao, G.X., 2007. Genetic diversity of wild banana (Musa balbisiana Colla) in China as revealed by AFLP markers. Genet. Resour. Crop Evol., 54(5):1125–1132. [doi:10.1007/s10722-006-9004-9]

    Article  Google Scholar 

  • Wong, C., Kiew, R., Set, O., Argent, G., Lee, S.K., Gan, Y.Y., 2002. Assessment of the validity of the sections in Musa (Musaceae) using AFLP. Ann. Bot., 90(2):231–238. [doi:10.1093/aob/mcf170]

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Horticultural Science, Faculty of AgricSciences, University of Stellenbosch, Stellenbosch, 7602, South Africa

    Umezuruike Linus Opara

  2. Department of Viticulture and Oenology, Institute of Wine Biotechnology, Faculty of AgricSciences, University of Stellenbosch, Stellenbosch, 7602, South Africa

    Dan Jacobson

  3. Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, 123, Sultanate of Oman

    Nadiya Abubakar Al-Saady

Authors
  1. Umezuruike Linus Opara
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dan Jacobson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nadiya Abubakar Al-Saady
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Umezuruike Linus Opara.

Additional information

Project supported by Programs of Sultan Qaboos University (Nos. SR/AGR/BIOR/05/01 and IG/AGR/PLANT/04/01), Sultanate of Oman, and the Research Chair in Postharvest Technology at the University of Stellenbosch, South Africa

Rights and permissions

Reprints and permissions

About this article

Cite this article

Opara, U.L., Jacobson, D. & Al-Saady, N.A. Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses. J. Zhejiang Univ. Sci. B 11, 332–341 (2010). https://doi.org/10.1631/jzus.B0900310

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1631/jzus.B0900310

Key words

CLC number

Search

Navigation