Hostname: page-component-cd9895bd7-jn8rn Total loading time: 0 Render date: 2024-12-29T10:17:32.643Z Has data issue: false hasContentIssue false
  • English
  • Français

Assessment of genetic diversity among Sri Lankan rice varieties by AFLP markers

Published online by Cambridge University Press:  15 June 2011

Gowri Rajkumar ,
Jagathpriya Weerasena ,
Kumudu Fernando  and
Athula Liyanage
Gowri Rajkumar
Affiliation:
Institute of Biochemistry Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
Jagathpriya Weerasena*
Affiliation:
Institute of Biochemistry Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
Kumudu Fernando
Affiliation:
Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
Athula Liyanage
Affiliation:
Plant Genetic Resources Centre, Gannoruwa, Peradeniya, Sri Lanka
*
*Corresponding author. E-mail: jagath@ibmbb.cmb.ac.lk
Get access Rights & Permissions [Opens in a new window]

Abstract

Sri Lanka has a valuable repository of germplasm collection due to the availability of a large number of different traditional and improved rice varieties. Molecular techniques can increase the effectiveness of traditional technologies in assessing genetic diversity. Amplified fragment length polymorphism (AFLP) was used to evaluate the genetic diversity among rice varieties available in the germplasm collection of Plant Genetic Resources Centre, Sri Lanka. AFLP analysis of rice varieties using ten different primer combinations yielded a total of 772 polymorphic bands (98.4%). Genetic similarities were estimated using Jaccard's (J) similarity coefficient. Unweighted pair group method with arithmetic mean (UPGMA)-based dendrogram was constructed. Genetic similarities varied from 0.073 to 0.565. Cluster analysis by genetic similarity divided the accessions into four main groups. The Cophenetic correlation with r = 0.781 indicated high confidence of AFLP data to group the varieties in UPGMA clusters. Principal component analysis further confirmed the patterns obtained by the cluster analysis. The results revealed very high genetic diversity at molecular level among the Sri Lankan rice varieties used in this study.

Keywords

AFLPdendrogramgenetic diversityriceUPGMA
Type
Research Article
Information
Plant Genetic Resources , Volume 9 , Issue 2 , July 2011 , pp. 224 - 228
Copyright
Copyright © NIAB 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abhijit, SD, Kamlesh, J, José, MG, Vyankatesh, JP, Milind, SP, Dilip, RR and Yogesh, SS (2004) Comparison of 16S rRNA gene sequences of genus Methanobrevibacter. BMC Microbiology 4: 20.Google Scholar
Chen, DH and Ronald, PC (1999) A rapid DNA mini preparation method suitable for AFLP and other PCR applications. Plant Molecular Biology Reporter 17: 53–57.CrossRefGoogle Scholar
Gower, JC and Legendre, P (1986) Metric and Euclidean properties of dissimilarity coefficients. Journal of Classification 3: 5–48.CrossRefGoogle Scholar
Jaccard, P (1901) Étude comparative de la distribuition floraledans une portion des Alpes et des Jura. Bull Soc Vandoise Sci Nat 37: 547–579.Google Scholar
Kovach, W (1998) MVSP-A multivariate statistical package. Version 3.1. Pentraeth, Wales: Kovach Computing Services.Google Scholar
Loh, JP, Kiew, R, Kee, A, Gan, LH and Gan, YY (1999) Amplified fragment length polymorphism (AFLP) provides molecular markers for the identification of Caladium bicolor cultivars. Annals of Botany 84: 155–161.CrossRefGoogle Scholar
Mantel, NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Research. 27: 209–220.Google Scholar
Sneath, PHA and Sokal, RR (1973) Numerical Taxonomy: The Principles and Practice of Numerical Classification. San Francisco, CA: Freeman.Google Scholar
Vos, P, Hogers, R, Bleeker, M, Reijans, M, van de Lee, T, Hornes, M, Fritjers, A, Pot, J, Peleman, J, Kuiper, M and Zabeau, M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acid Research 23: 4407–4414.CrossRefGoogle ScholarPubMed