Share This Article:

Assessment of EST-SSR Markers for Evaluating Genetic Diversity in Watermelon Accessions from Zimbabwe

Full-Text HTML Download Download as PDF (Size:429KB) PP. 1448-1456
DOI: 10.4236/ajps.2013.47177    3,332 Downloads   5,541 Views   Citations


Fifteen expressed sequence tag (EST)-derived simple sequence repeats (EST-SSRs) were used to investigate genetic diversity in 139 plants obtained from seeds of 35 watermelon accessions collected from all the geographical provinces of Zimbabwe. In addition, 15 plants representing three commercial varieties developed in the United States (USA) were analyzed for comparison. A total of 65 alleles were detected among all the watermelon accessions. For the 13 polymorphic EST-SSR loci, number of alleles per locus varied from 2 to 13, with an average of 5 alleles per locus. Values for the polymorphic information content increased as the number of alleles increased, and varied from 0.15 to 0.77 with an average of 0.54 suggesting sufficient discriminatory power. Both cluster analysis and principal coordinate analysis (PCA) produced two major clusters; one with the 22 cow-melon accessions and the other with the 16 sweet watermelon accessions. Within the sweet watermelon group, two distinct sub-clusters formed, one of which contained only two of the commercial varieties from USA. Partitioning of genetic variation in the Zimbabwean material using analysis of molecular variation (AMOVA) revealed that 64% of the total variation resides between the two major forms, i.e. sweet watermelons and cow-melons, 28% between accessions within forms and 8% within accessions. The EST-SSR markers revealed a somewhat higher diversity in sweet watermelon accessions compared to that of cow-melons. This finding is contrary to previous reports using other markers (genomic SSR loci or RAPD) and/or a plant material that is likely to have experienced more stringent selection procedures compared to the landraces analyzed in our study.

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

C. Mujaju, J. Sehic and H. Nybom, "Assessment of EST-SSR Markers for Evaluating Genetic Diversity in Watermelon Accessions from Zimbabwe," American Journal of Plant Sciences, Vol. 4 No. 7, 2013, pp. 1448-1456. doi: 10.4236/ajps.2013.47177.


[1] C. Mujaju, J. Sehic, G. Werlemark, L. Garkava-Gustavsson, M. Fatih and H. Nybom, “Genetic Diversity in Watermelon (Citrullus lanatus) Landraces from Zimbabwe Revealed by RAPD and SSR Markers,” Hereditas, Vol. 147, No. 4, 2010, pp. 142-153. doi:10.1111/j.1601-5223.2010.02165.x
[2] A. Levi, C. E. Thomas, M. Newman, O. U. K. Reddy, X. Zhang and Y. Xu, “ISSR and AFLP Markers Differ among American Watermelon Cultivars with Limited Genetic Diversity,” Journal of the American Society for Horticultural Science, Vol. 129, No. 4, 2004, pp. 553-558.
[3] C. Mujaju, A. Zborowska, G. Werlemark, L. Garkava-Gustavsson, S. B. Andersen and H. Nybom, “Genetic Diversity among and within Watermelon (Citrullus lanatus) Landraces in Southern Africa,” The Journal of Horticultural Science & Biotechnology, Vol. 86, No. 4, 2011, pp. 353-358.
[4] P. Munisse, “Diversity and Traditional Uses of Watermelon (Citrullus lanatus) Landraces in Mozambique,” Ph.D. Thesis, Faculty of Life Sciences, University of Copenhagen, Copenhagen, 2011, pp. 1-64.
[5] N. Navot and D. Zamir, “Isozyme and Seed Protein Phylogeny of the Genus Citrullus (Cucurbitaceae),” Plant Systematics and Evolution, Vol. 156, No. 1-2, 1987, pp. 61-67. doi:10.1007/BF00937202
[6] A. Levi, C. E. Thomas, T. C. Wehner and X. P. Zhang, “Low Genetic Diversity Indicates the Need to Broaden the Genetic Base of Cultivated Watermelon,” Hortscience, Vol. 36, No. 6, 2001, pp. 1096-1101.
[7] A. Levi, W. P. Wechter, K. R. Harris, A. R. Davis and Z. Fei, “High-Frequency Oligonucleotides in Watermelon Expressed Sequenced Tags-Unigenes Are Useful in Producing Polymorphic Polymerase Chain Reaction Markers among Watermelon Genotypes,” Journal of American Society of Horticultural Science, Vol. 135, No. 4, 2010, pp. 369-378.
[8] A. Levi, P. Wechter and A. Davis, “EST-PCR Markers Representing Watermelon Fruit Genes Are Polymorphic among Watermelon Heirloom Cultivars Sharing a Narrow Genetic Base,” Plant Genetic Resources Characterization and Utilization, Vol. 7, No. 1, 2009, pp. 16-32. doi:10.1017/S1479262108014366
[9] K. F. Salem, R. K. Varshney, M. S. Roder and A. Borner, “EST-SSR Based Estimates on Functional Genetic Variation in a Barley (Hordeum vulgare L.) Collection from Egypt,” Genetic Resources and Crop Evolution, Vol. 57, No. 4, 2010, pp. 515-521. doi:10.1007/s10722-009-9489-0
[10] R. K. Varshney, A. Graner and M. E. Sorrells, “Genic Microsatellite Markers in Plants: Features and Applications,” Trends in Biotechnology, Vol. 23, No. 1, 2005, pp. 48-55. doi:10.1016/j.tibtech.2004.11.005
[11] A. Levi, A. Davis, P. Wechter, A. Hernandez and J. Thimmapuram, “Developing Expressed Sequenced Tags (ESTs) for Watermelon Fruit,” Hortscience, Vol. 41, No. 3, 2006, pp. 518-519.
[12] J. S. C. Smith, E. C. L. Chin, H. Shu, O. S. Smith, S. J. Wall, M. L. Senior, S. E. Mitchell, S. Kresovich and J. Ziegle, “An Evaluation of the Utility of SSR Loci as Molecular Markers in Maize (Zea mays L.): Comparisons with Data from RFLPs and Pedigree,” Theoretical and Applied Genetics, Vol. 95, No. 1-2, 1997, pp. 163-173. doi:10.1007/s001220050544
[13] R. Peakall and P. E. Smouse, “Genalex 6: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research,” Molecular Ecology Notes, Vol. 6, 2006, pp. 288-295. doi:10.1111/j.1471-8286.2005.01155.x
[14] M. Nei, “F-Statistics and Analysis of Gene Diversity in Subdivided Populations,” Annals of Human Genetics, Vol. 41, 1977, pp. 225-233. doi:10.1111/j.1469-1809.1977.tb01918.x
[15] L. Excoffier, G. Laval and S. Schneider, “Arlequin ver. 3.0: An Integrated Software Package for Population Genetics Data Analysis,” Evolutionary Bioinformatics, 2005, pp. 47-50 (Online).
[16] F. J. Rohlf, “NTSYS-pc Numerical Taxonomy and Multivariate Analysis System: Version 2.1 (ed.),” Setauket, Exeter Publishing Ltd., New York, 1993.
[17] S. Rudd, “Expressed Sequence Tags: Alternative or Complement to Whole Genome Sequences?” Trends in Plant Science, Vol. 8, No. 7, 2003, pp. 321-329. doi:10.1016/S1360-1385
[18] A. Martin, C. Mattioni, M. Cherubini, D. Taurchini and F. Villani, “Genetic Diversity in European Chestnut Populations by Means of Genomic and Genic Microsatellite Markers,” Tree Genetics & Genomics, Vol. 6, No. 5, 2010, pp. 735-744. doi:10.1007/s11295-010-0287-9
[19] J. Hu, L. Wang and J. Li, “Comparison of Genomic SSR and EST-SSR Markers for Estimating Genetic Diversity in Cucumber,” Biologia Plantarum, Vol. 55, No. 3, 2011, pp. 577-580. doi:10.1007/s10535-011-0129-0
[20] J. E. Munoz-Falcón, S. Vilanova, M. Plazas and J. Prohens, “Diversity, Relationships, and Genetic Fingerprinting of the Listada de Gandía Eggplant Landrace Using Genomic SSRs and EST-SSRs,” Scientia Horticulturae, Vol. 129, No. 2, 2011, pp. 238-246. doi:10.1016/j.scienta.2011.03.034
[21] Y-B. Fu, G. W. Peterson, K. W. Richards, T. R. Tarn and J. E. Percy, “Genetic Diversity of Canadian and Exotic Potato Germplasm Revealed by Simple Sequence Repeat Markers,” American Journal of Potato Research, Vol. 86, No. 1, 2009, pp. 38-48. doi:10.1007/s12230-008-9059-6
[22] O. Tahan, Y. Geng, L. Zeng, S. Dong, F. Chen, J. Chen, Z. Song and Y. Zhong, “Assessment of Genetic Diversity and Population Structure of Chinese Wild Almond, Amygdalus nana, Using EST and Genomic SSRs,” Biochemical Systematics and Ecology, Vol. 37, No. 3, 2009, pp. 146-153. doi:10.1016/j.bse.2009.02.006
[23] M. Verma and L. Arya, “Development of EST-SSRs in Watermelon (Citrullus lanatus var. Lanatus) and Their Transferability to Cucumis spp.,” Journal of Horticultural Science and Biotechnology, Vol. 83, No. 6, 2008, pp. 732-736.
[24] J. H. Whang, S. G. Ahn, J. Y. Oh, Y. W. Choi, J. S. Kang and Y. H. Park, “Functional Characterization of Watermelon (Citrullus lanatus L.) EST-SSR by Gel Electrophoresis and High Resolution Melting Analysis,” Scientia Horticulturae, Vol. 130, No. 4, 2011, pp. 715-724. doi:10.1016/j.scienta.2011.08.014
[25] H. Zhang, H. Wang, S. Guo, Y. Ren, G. Gong, Y. Weng and Y. Xu, “ Identification and Validation of a Core Set of Microsatellite Markers for Genetic Diversity Analysis in Watermelon, Citrullus lanatus Thunb. Matsum. & Nakai,” Euphytica, Vol. 186, No. 2, 2012, pp. 329-342. doi:10.1007/s10681-011-0574-z
[26] Y. S. Kwon, E. K. Park, W. S. Lee, S. I. Yi, K. M. Bae, J. S. An and H. Y. Kim, “Genetic Assessment of Watermelon (Citrullus lanatus) Varieties Using SSR Markers Developed from Cucurbit Species,” Korean Journal of Genetics, Vol. 29, No. 2, 2007, pp. 137-146.
[27] D. Struss and J. Plieske, “The Use of Microsatellite Markers for Detection of Genetic Diversity in Barley Populations,” Theoretical and Applied Genetics, Vol. 97, No. 1-2, 1998, pp. 308-315. doi:10.1007/s001220050900
[28] R. L. Jarret, L. C. Merrick, T. Holms, J. Evans and M. K. Aradhya, “Simple Sequence Repeats in Watermelon (Citrullus lanatus (Thunb) Matsum & Nakai),” Genome, Vol. 40, No. 4, 1997, pp. 433-441. doi:10.1139/g97-058
[29] A. Levi, C. E. Thomas, A. P. Keinath and T. C. Wehner, “Estimation of Genetic Diversity among Citrullus Accessions Using RAPD Markers,” Proceedings of the 7th EUCARPIA Meeting on Cucurbit Breeding and Genetics, Ma’ale Ha Hamisha, Israel, 19-23 March 2000, pp. 385-390.
[30] A. Levi and C. E. Thomas, “Low Genetic Diversity Indicates the Need to Broaden the Genetic Base of Cultivated watermeLon,” Hortscience, Vol. 36, No. 6, 2001, pp. 1096-1101.
[31] A. Levi, C. E. Thomas, A. P. Keinath and T. C. Wehner, “Genetic Diversity among Watermelon (Citrullus lanatus and Citrullus colocynthis) Accessions,” Genetic Resources and Crop Evolution, Vol. 48, No. 6, 2001, pp. 559-566. doi:10.1023/A:1013888418442
[32] A. Levi, C. E. Thomas, A. M. Simmons and J. A. Thies, “Analysis Based on RAPD and ISSR Markers Reveals Closer Similarities among Citrullus and Cucumis Species than with Praecitrullus fistulosus (stocks) Pangalo,” Genetic Resources and Crop Evolution, Vol. 52, No. 4, 2005, pp. 465-472. doi:10.1007/s10722-005-2260-2
[33] A. Levi, J. A. Thies, W. P. Wechter, H. F. Harrison, A. M. Simmons, U. K. Reddy, P. Nimmakayala and Z. Fei, “High Frequency Oligonucleotides: Targeting Active Gene (HFO-Tag) Markers Revealed Wide Genetic Diversity among Citrullus spp. Accessions Useful for Enhancing Disease or Pest Resistance in Watermelon Cultivars,” Genetic Resource and Crop Evolution, Vol. 60, No. 2, 2013, pp. 427-440. doi:10.1007/s10722-012-9845-3
[34] H. Nybom, “Comparison of Different Nuclear DNA Markers for Estimating Intraspecific Genetic Diversity in plants,” Molecular Ecology, Vol. 13, No. 5, 2004, pp. 1143-1155. doi:10.1111/j.1365-294X.2004.02141.x
[35] L. A. Minsart, I. A. Zoro bi, Y. Djé, J. P. Baudoin, A. L. Jacquemart and P. Bertin, “Set up of Simple Sequence Repeat Markers and First Investigation of the Genetic Diversity of West-African Watermelon (Citrullus lanatus ssp. Vulgaris Oleaginous Type),” Genetic Resources and Crop Evolution, Vol. 1, No. 1, 2009, pp. 1-10.
[36] H. Nybom and I. V. Bartish, “Effects of Life History Traits and Sampling Strategies on Genetic Diversity Estimates Obtained from RAPD Markers in Plants,” Perspectives in Plant Ecology, Evolution and Systematics, Vol. 3, No. 2, 2000, pp. 93-114. doi:10.1078/1433-8319-00006.

comments powered by Disqus

Copyright © 2018 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.