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Random amplified polymorphic DNA (RAPD) finger prints evidencing high genetic variability among marine angiosperms of India

Published online by Cambridge University Press:  19 May 2016

Elangovan Dilipan ,
Jutta Papenbrock  and
Thirunavakkarasu Thangaradjou
Elangovan Dilipan
Affiliation:
Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai – 608 502, Cuddalore Dt., Tamilnadu, India
Jutta Papenbrock
Affiliation:
Institute of Botany, Leibniz University Hannover, Herrenhäuserstr. 2, D-30419 Hannover, Germany
Thirunavakkarasu Thangaradjou*
Affiliation:
Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai – 608 502, Cuddalore Dt., Tamilnadu, India
*
Correspondence should be addressed to:T. Thangaradjou, Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai – 608 502, Cuddalore Dt., Tamilnadu, India email: umaradjou@yahoo.com
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Abstract

In India 14 seagrass species can be found with monospecific genera (Enhalus, Thalassia and Syringodium), Cymodocea with two species and Halophila and Halodule represented by more than two taxonomically complex species. Considering this, the present study was made to understand the level and pattern of genetic variability among these species collected from Tamilnadu coast, India. Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the level of polymorphism existing between the species. Out of the 12 primers tested, 10 primers amplified 415 DNA fragments with an average of 41.5 fragments per primer. Of the total 415 amplified fragments only 123 (29.7%) were monomorphic and the remaining 292 (70.3%) were polymorphic for Indian seagrass species. Among the 10 primers used four are identified as the key primers capable of distinguishing all the Indian seagrasses with a high degree of polymorphism and bringing representative polymorphic alleles in all the tested seagrasses. From the present investigation, this study shows that the RAPD marker technique can be used not only as a tool to analyse genetic diversity but also to resolve the taxonomic uncertainties existing in the Indian seagrasses. The efficiency of these primers in bringing out the genetic polymorphism or homogeneity among different populations of the Halophila and Halodule complex still has to be tested before recommending these primers as an identification tool for Indian seagrasses.

Keywords

Marine angiospermgenetic variabilityRAPDIndia
Type
Research Article
Information
Journal of the Marine Biological Association of the United Kingdom , Volume 97 , Issue 6 , September 2017 , pp. 1307 - 1315
Copyright
Copyright © Marine Biological Association of the United Kingdom 2016 

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Footnotes

*

Present address: Science and Engineering Research Board, New Delhi 110070.

References

REFERENCES

Alberto, F., Mata, L. and Santos, R. (2001) Genetic homogeneity in the seagrass Cymodocea nodosa at its northern Atlantic limit revealed through RAPD. Marine Ecological Progress Series 221, 299–301.CrossRefGoogle Scholar
Angel, R. (2002) Genetic diversity in Halodule wrightii using Random Amplified Polymorphic DNA. Aquatic Botany 74, 165–174.Google Scholar
Avise, J.C. (1994) Molecular markers, natural history, and evolution. New York: Chapman and Hall, 511 pp.Google Scholar
Bai, Y., Huang, C.C., Hulst, R.V., Meijer Dekens, F., Bonnema, G. and Lindhout, P. (2003) QTLs for tomato powdery mildew resistance (Oidium lycopersici) in Lycopersicon parviflorum G1.1601 co-localize with two qualitative powdery mildew resistance genes. Molecular Plant-Microbe Interactions 16, 169–176.Google Scholar
Callejas, C., Luskova, V. and Ochando, M.D. (2004) A contribution to the genetic characterization of some species of the genus Gobia (Cyprinidae). Folia Zoology 53, 433–436.Google Scholar
Capiomont, A., Sandmeier, M., Caye, G. and Meinesz, A. (1996) Enzyme polymorphism in Posidonia oceanica, a seagrass endemic to the Mediterranean. Aquatic Botany 54, 265–277.Google Scholar
Chalmers, K.J., Cambell, A.W., Kretschmer, J., Karakousis, A., Henschke, P.H., Pierens, S., Harker, N., Pallotta, M., Cornish, G.B., Shariflou, M.R., Rampling, L.R., McLauchlan, A., Daggard, G., Sharp, P.J., Holton, T.A., Sutherland, M.W., Appels, R. and Langridge, P. (2001) Construction of three linkage maps in bread wheat, Triticum aestivium . Australian Journal of Agricultural Research 52, 1089–1119.Google Scholar
Clark, A.G. and Lanigan, C.M.S. (1993) Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution 10, 1096–1111.Google Scholar
Das, B.K., Jena, R.C. and Samal, K.C. (2009) Optimization of DNA isolation and PCR protocol for RAPD analysis of banana/plantain (Musa spp.). International Journal of Agricultural Sciences 1, 21–25.Google Scholar
Davis, J.L., Childers, D.L. and Kuhn, D.N. (1999) Clonal variation in a Florida Bay Thalassia testudinum meadow: molecular genetic assessment of population structure. Marine Ecological Progress Series 186, 127–136.CrossRefGoogle Scholar
De Heij, H. and Nienhuis, P.H. (1992) Intraspecific variation on isozyme patterns of phenotypically separated populations of Zostera marina L. in the south-western Netherlands. Journal of Experimental Marine Biology and Ecology 161, 1–14.Google Scholar
den Hartog, C. (1970) The seagrasses of the world. Amsterdam: North-Holland Publishing, 275 pp.Google Scholar
Dong, Y.H., Gituru, R.W. and Wang, Q.F. (2010) Genetic variation and gene flow in the endangered aquatic fern Ceratopteris pteridoides in China and conservation implications. Annales Botanici Fennici 47, 34–44.CrossRefGoogle Scholar
Eiseman, N.J. and McMillan, C. (1980) A new species of seagrass, Halophila johnsonii, from the Atlantic coast of Florida. Aquatic Botany 9, 15–19.Google Scholar
Grosberg, R.K., Levitan, D.R. and Cameron, B.B. (1996) Characterization of genetic structure and genealogies using RAPD-PCR markers: a random primer for the novice and nervous. In Ferraris, J.D. and Palumbi, S.R. (eds) Molecular zoology: advances, strategies and protocols. New York, NY: John Wiley and Sons, pp. 67–100.Google Scholar
Jones, C.T., Gemmil, C.E.C. and Pilditch, C.A. (2008) Genetic variability of New Zealand seagrass (Zostera muelleri) assessed at multiple spatial scales. Aquatic Botany 88, 39–46.Google Scholar
Jover, M.A., Del Castillo-Agudo, L., Garcia-Carrascosa, M. and Segura, J. (2003) Random amplified polymorphic DNA assessment of diversity in western Mediterranean populations of the seagrass Posidonia oceanica . American Journal of Botany 90, 364–369.Google Scholar
Kannan, L. and Thangaradjou, T. (2006) Identification and assessment of biomass and productivity of seagrasses. In Proceedings of the national training workshop on marine and coastal biodiversity assessment for conservation and sustainable utilization, SDMRI Publication. pp. 9–15.Google Scholar
Kirsten, J.H., Dawes, C.J. and Cochrane, B.J. (1998) Randomly amplified polymorphism detection (RAPD) reveals high genetic diversity in Thalassia testudinum Banks ex König (Turtlegrass). Aquatic Botany 61, 269–287.Google Scholar
Lambert, D.M. and Millar, C.D. (1995) DNA science and conservation. Pacific Conservation Biology 2, 21–38.CrossRefGoogle Scholar
Laushman, R.H. (1993) Population genetics of hydrophilous angiosperms. Aquatic Botany 44, 147–158.Google Scholar
Lim, S.H., Teng, P.C.P. and Lee, Y.H. (1999) RAPD analysis of some species in the genus Vanda (Orchidaceae). Annals of Botany 83, 193–196.CrossRefGoogle Scholar
Lucas, C., Thangaradjou, T. and Papenbrock, J. (2012) Development of a DNA barcoding system for seagrasses: successful but not simple. PLoS ONE 7, 1–12.CrossRefGoogle Scholar
Mahmood, T., Iqbal, A., Nazar, N., Naveed, I., Abbasi, B.H. and Naqvi, S.M.S. (2011) Assessment of genetic variability among selected species of Apocynaceae. Biologia 66, 64–67.Google Scholar
Mariette, S., Le Corre, V., Austerlitz, F. and Kremer, A. (2002) Sampling within the genome for measuring within-population diversity: trade-offs between markers. Molecular Ecology 11, 1145–1156.Google Scholar
Martin, J.P. and Hernandez, B.J.E. (2000) Genetic variation in the endemic and endangered Rosmarinus tomentosus Huber-Morath and Maire (Labiatae) using RAPD markers. Heredity 85, 434–443.Google Scholar
McMillan, C. (1981) Morphological variation and isozymes under laboratory conditions in Cymodocea serrulata . Aquatic Botany 10, 356–370.Google Scholar
McMillan, C. (1982) Isozymes in seagrasses. Aquatic Botany 14, 231–243.Google Scholar
McMillan, C. and Williams, S.C. (1980) Systematic implications of isozymes in Halophila section Halophila . Aquatic Botany 9, 21–31.Google Scholar
Micheli, C., Paganin, P., Peirano, A., Caye, G., Meinesz, A. and Bianchi, C.N. (2005) Genetic variability of Posidonia oceanica (L.) Delile in relation to local factors and biogeographic patterns. Aquatic Botany 82, 210–221.Google Scholar
Nei, M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590.CrossRefGoogle ScholarPubMed
Nei, M. (1987) Molecular evolutionary genetics. New York, NY: Columbia University Press, pp. 361–364.Google Scholar
Nei, M. and Li, W. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences USA 76, 5269–5273.Google Scholar
Nguyen, X.V., Thangaradjou, T. and Papenbrock, J. (2013) Genetic variation among Halophila ovalis (Hydrocharitaceae) and closely related seagrass species from the coast of Tamil Nadu, India – an AFLP fingerprint approach. Systematics and Biodiversity 11, 467–476.Google Scholar
Nguyen, X.V., Detcharoen, M., Tuntiprapas, P., Soe-Htun, U., Sidik, B.J., Harah, Z.M., Prathep, A. and Papenbrock, J. (2014) Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean. BMC Evolutionary Biology 14, 92.Google Scholar
Page, R.D. (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12, 357–358.Google Scholar
Pau, M.S. and Othman, A.S. (2002) Randomly amplified polymorphic DNA analysis of seagrass, Halophila ovalis. In Proceedings of the 4th IMT-GT UNINET Conference, Penang, Malaysia, pp. 1–5.Google Scholar
Procaccini, G. and Mazzella, L. (1996) Genetic variability and reproduction in two Mediterranean seagrasses. In Kuo, J., Phillips, R.C., Walker, D.I. and Kirkman, H. (eds) Seagrass biology: proceedings of an international workshop, Rottnest Island, Western Australia. SCIENCES UWA, pp. 85–92.Google Scholar
Procaccini, G., Mazzella, L., Alberte, R.S. and Les, D.H. (1999) Chloroplast tRNA Leu (UAA) intron sequences provide phylogenetic resolution of seagrass relationships. Aquatic Botany 62, 269–283.Google Scholar
Ramamurthy, K., Balakrishnan, N.P., Ravikumar, K. and Ganesan, R. (1992) Seagrasses of Coromandel coast, India. Flora of India – Series 4, Botanical Survey of India, 80 pp.Google Scholar
Randall, S.A., Suba, G.K., Procaccini, G., Zimmerman, R.C. and Fain, S.R. (1994) Assessment of genetic diversity of seagrass population using DNA fingerprinting: implication for population stability and management. Proceedings of the National Academy of Sciences USA 91, 1049–1053.Google Scholar
Reusch, T.B.H. (2001) Fitness-consequences of geitonogamous selfing in a clonal marine angiosperm (Zostera marina). Journal of Evolutionary Biology 14, 129–138.Google Scholar
Reusch, T.B.H. (2002) Microsatellites reveal high population connectivity in eelgrass (Zostera marina) in two contrasting coastal areas. Limnology and Oceanography 47, 78–85.CrossRefGoogle Scholar
Reynolds, L.K., Waycott, M., McGlathery, K.J., Orth, R.J. and Zieman, J.C. (2012) Eelgrass restoration by seed maintains genetic diversity: case study from a coastal bay system. Marine Ecological Progress Series 448, 223–233.Google Scholar
Rohlf, F.J. (2000) NTSYSpc . Numerical taxonomy and multivariate analysis system. Version 2.01. Setauket, NY: Exeter software.Google Scholar
Rotini, A., Micheli, C., Valiante, L. and Migliore, L. (2011) Assessment of Posidonia oceanica (L.) Delile conservation status by standard and putative approaches: the case study of Santa Marinella meadow (Italy, W Mediterranean). Open Journal of Ecology 1, 48–56.Google Scholar
Schaal, B.A., Hayworth, D.A., Olsen, K.M., Rauscher, J.T. and Smith, W.A. (1998) Phylogenetic studies in plants: problems and prospects. Molecular Ecology 7, 465–474.Google Scholar
Slatkin, M. (1987) Gene flow and the geographic structure of populations. Science 236, 787–792.Google Scholar
Smith, J.J., McMillan, C., Kenworthy, W.J. and Bird, K. (1997) Flowering and genetic banding patterns of Halophila johnsonii and conspecifics. Aquatic Botany 59, 323–331.CrossRefGoogle Scholar
Storchova, H., Hrdlickova, R., Chrtek, J., Tetera, M. and Fitze, D. (2000) An improved method of DNA isolation from plants collected in the field and conserved in saturated NaCl/CTAB solution. Taxon 49, 79–84.Google Scholar
Viccini, L.F., Souza da Costa, D.C., Machado, M.A. and Campos, A.L. (2004) Genetic diversity among nine species of Lippia (Verbenaceae) based on RAPD markers. Plant Systematics and Evolution 246, 1–8.Google Scholar
Waycott, M. (1995) Assessment of genetic variation and clonality in the seagrass Posidonia australis using RAPD and allozyme analysis. Marine Ecological Progress Series 116, 289–295.CrossRefGoogle Scholar
Waycott, M. (1998) Genetic variation, its assessment and implications to the conservation of seagrasses. Molecular Ecology 7, 793–800.Google Scholar
Waycott, M. and Barnes, P.A.G. (2001) AFLP diversity within and between populations of the Caribbean seagrass Thalassia testudinum (Hydrocharitaceae). Marine Biology 139, 1021–1028.Google Scholar