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Efficiency of Arbitrarily Amplified Dominant Markers (SCOT, ISSR and RAPD) for Diagnostic Fingerprinting in Tetraploid Potato

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Abstract

Three molecular markering techniques: start codon targeted (SCOT), inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers were compared for fingerprinting of 24 varieties and a segregating population of tetraploid potato. The number of scoreable and polymorphic bands produced using the SCOT, ISSR and RAPD primers for varieties was more than that of genotypes. SCOTs markers were more informative, followed by ISSRs marker, than other markers for the assessment of varieties based on polymorphism information content (PIC). There were no significant differences among these markers in terms of the evaluation of genotypes. All marker techniques individually illustrated that Diversity Index and Marker Index for varieties were higher than that of genotypes, and SCOT had superiority to other markers. The resolving power (Rp) of the SCOT, ISSR and RAPD techniques was 71.25, 46.62 and 30.63 for varieties and 21.38, 18.83 and 18.87 for genotypes, respectively. Standard Jaccard’s similarity coefficient of each marker technique revealed that similarity among varieties was less than that of the genotypes. Overall the Shannon index showed that relative genetic diversity of the varieties was high when SCOT markers were used but it was fairly similar when ISSR and RAPD markers were applied. The results of Analysis of Molecular Variance (AMOVA) revealed that variation within groups of varieties of a country was significantly higher than among groups. These results suggest that efficiency of SCOT, ISSR and RAPD markers was relatively the same in fingerprinting of genotypes but SCOT analysis is more effective in fingerprinting of potato varieties. Overall, our results indicate that SCOT, ISSR and RAPD fingerprinting could be used to detect polymorphism for genotypes and for varieties of potato.

Resumen

Se compararon tres técnicas de marcadores moleculares para caracterizar molecularmente 24 variedades y a una población segregante de papa tetraploide: enfocado a codón de inicio (SCOT), repetición de secuencia inter-simple (ISSR) y amplificación al azar de ADN polimórfico (RAPD). El número de bandas polimórficas registrables producidas usando iniciadores para SCOT, ISSR y RAPD, fue mayor para las variedades que el de los genotipos. Los marcadores SCOT fueron más informativos, seguidos por los de ISSR, más que otros marcadores para el análisis de variedades con base al contenido de información del polimorfismo (PIC). No hubo diferencias significativas entre estos marcadores en términos de la evaluación de genotipos. Todas las técnicas de marcación ilustraron individualmente que el Índice de Diversidad y el índice de marcador para las variedades fue mayor que el de los genotipos, y SCOT tuvo superioridad sobre otros marcadores. El poder de resolución (Rp) de las técnicas SCOT, ISSR y RAPD fue de 71.25, 46.62 y 30.63 para las variedades y de 21.38, 18.83 y 18.87 para los genotipos, respectivamente. El coeficiente estándar de similitud de Jaccard de cada técnica de marcador reveló que la similitud entre variedades era menor que la de los genotipos. En general, el índice Shannon mostró que la diversidad genética relativa de las variedades era alta cuando se usaban los marcadores SCOT, pero era muy similar cuando se aplicaban los marcadores ISSR y RAPD. Los resultados del Análisis de Varianza Molecular (AMOVA) revelaron que la variación dentro de grupos de variedades de un país era significativamente más alta que entre grupos. Estos resultados sugieren que la eficiencia de los marcadores SCOT, ISSR y RAPD fue relativamente la misma en la caracterización de los genotipos, pero el análisis SCOT es más efectivo en la caracterización molecular de las variedades. En general, nuestros resultados indican que la caracterización SCOT, ISSR y RAPD puede usarse para detectar el polimorfismo para genotipos y para variedades de papa.

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References

  • Albert, V.A. 2005. Parsimony and phylogenetics in the genomic age. In Parsimony, phylogeny and genomics, ed. V.A. Albert, 1–11. Oxford: Oxford University Press.

    Google Scholar 

  • Andersen, J.R., and T. Lubberstedt. 2003. Functional markers in plants. Trends in Plant Science 8: 554–560.

    Article  PubMed  CAS  Google Scholar 

  • Arif, M., N.W. Zaidi, and Y.P. Singh. 2009. A comparative analysis of ISSR and RAPD markers for study of genetic diversity in Shisham (Dalbergia sissoo). Plant Molecular Biology Reporter 27: 488–495.

    Article  CAS  Google Scholar 

  • Bowman, K.O., K. Hutcheson, E.P. Odum, and L.R. Shenton. 1969. Comments on the distribution of indices of diversity. Proceedings of the International Symposium on Statistical Ecology 3: 315–359.

    Google Scholar 

  • Bussell, J.D., M. Waycott, and J.A. Chappill. 2005. Arbitrarily amplified DNA markers as characters for phylogenetic inference. Perspectives in Plant Ecology, Evolution and Systematics 7: 3–26.

    Article  Google Scholar 

  • Chen, J.M., W.R. Citura, Y.H. Wang, and Q.F. Wang. 2006. The extent of clonality and genetic diversity in the rare Cladesia grandis (Alismataceae): Comparative results for RAPD and ISSR markers. Aquatic Botany 84: 301–307.

    Article  CAS  Google Scholar 

  • Collard, B.C.Y., and D.J. Mackill. 2009. Start Codon Targeted (SCOT) polymorphism: A simple novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology 27: 86–93.

    Article  CAS  Google Scholar 

  • Demeke, T., L.M. Kawchuk, and D.R. Lynch. 1993. Identification of potato cultivars and clonal variants by random amplified polymorphic ANA analysis. American Potato Journal 70: 461–470.

    Article  Google Scholar 

  • Ghislain, M., D. Zhang, D. Fajardo, Z. Huamann, and R.H. Hijmans. 1999. Marker-assisted sampling of the cultivated Andean potato Solanum phureja collections using RAPD markers. Genetic Resources and Crop Evolution 46: 547–555.

    Article  Google Scholar 

  • Gupta, P.K., and S. Rustgi. 2004. Molecular markers from the transcribe/expressed region of the genome in higher plants. Functional & Integrative Genomics 4: 139–162.

    Article  CAS  Google Scholar 

  • Gupta, P.K., Y.S. Chyi, J. Romero-Severson, and J.L. Owen. 1994. Amplification of DNA markers from evolutionary diverse genomes using single primers of simple-sequence repeats. Theoretical and Applied Genetics 89: 998–1006.

    Article  CAS  Google Scholar 

  • Gupta, P.K., R.K. Varshney, P.C. Sharma, and B. Ramesh. 1999. Molecular markers and their application in wheat breeding. Plant Breeding 118: 369–390.

    Article  CAS  Google Scholar 

  • Hallden, C., M. Hansen, N.O. Nilsson, A. Hjerdin, and T. Sall. 1996. Competition as a source of errors in RAPD analysis. Theoretical and Applied Genetics 93: 1185–1192.

    Article  CAS  Google Scholar 

  • Huson, D.H., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23(2): 254–267.

    Article  PubMed  CAS  Google Scholar 

  • Ikegami, H., H. Nogata, K. Hirashima, M. Awamura, and T. Nakahara. 2009. Analysis of genetic diversity among European and Asian fig varieties (Ficus carica L.) using ISSR, RAPD, and SSR markers. Genetic Resources and Crop Evolution 56: 201–209.

    Article  CAS  Google Scholar 

  • Jondle, R.J. 1992. Legal aspects of varietal protection using molecular markers. In Applications of RAPD technology to plant breeding, 50–52. Joint Plant Breeding symposia series.

  • Kalinowski, S.T. 2005. Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity 94: 33–36.

    Article  PubMed  CAS  Google Scholar 

  • Karp, A., O. Seberg, and M. Buiatti. 1996. Molecular techniques in the assessment of botanical diversity. Annals of Botany 78: 143–149.

    Article  CAS  Google Scholar 

  • Kumar, J., R.J. Nelson, and R.S. Zeigler. 1999. Population structure and dynamics of M. grisea in the Indian Himalayas. Genetics 152: 971–984.

    PubMed  CAS  Google Scholar 

  • Mark, P.S., Z. Li-Bing, T.W. Colleen, and M. Kai. 2007. A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. Molecular Phylogenetics and Evolution 42: 528–542.

    Article  Google Scholar 

  • McGregor, C.E., C.A. Lambert, M.M. Greyling, J.H. Louw, and L. Warnich. 2000. A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113: 135–144.

    Article  CAS  Google Scholar 

  • Norero, N., J. Malleville, M. Huarte, and S. Feingold. 2003. Cost efficient potato (Solanum tuberosum L.) cultivar identification by microsatellite amplification. Potato Research 45: 131–138.

    Article  Google Scholar 

  • Prevost, A., and M.J. Wilkinson. 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics 98: 107–112.

    Article  CAS  Google Scholar 

  • Salhi-Hannachi, A., K. Chatti, M. Mars, M. Marrakchi, and M. Trifi. 2005. Comparative analysis of genetic diversity in two Tunisian collections of fig cultivars based on random amplified polymorphic DNA and inter simple sequence repeats fingerprints. Genetic Resources and Crop Evolution 52: 563–573.

    Article  Google Scholar 

  • Sanderson, M.J., and M.F. Wojciechowski. 2005. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Systematic Biology 149: 671–685.

    Google Scholar 

  • Schluter, P.M., and S.A. Harris. 2006. Analysis of multilucous fingerprinting data sets containing missing data. Molecular Ecology Notes 6: 569–572.

    Article  Google Scholar 

  • Semagen, K., A. Bjornstad, and M.N. Ndjiondjop. 2006. An overview of molecular marker methods for plants. African Journal of Biotechnology 5: 2540–2568.

    Google Scholar 

  • Smith, S. 1998. Cultivar identification and varietal protection. In DNA markers: Protocols, applications and overviews, ed. G. Caetano-Annolés and P.M. Gresshoff, 383–400. New York: Wiley-VCH.

    Google Scholar 

  • Smith, J.S.C., and J.G.K. Williams. 1994. Arbitrary primer mediated fingerprinting in plants: Case studies in plant breeding, taxonomy and phylogeny. In Molecular ecology and evolution: Approaches and applications, ed. B. Schierwater, B. Streit, G.P. Wagner, and R. DeSalle, 5–15. Basel: Birkhauser Verlag.

    Google Scholar 

  • Sonia, C., and T. Gopalakrishna. 2007. Comparative assessment of REMAP and ISSR marker assays for genetic polymorphism studies in Magnaporthe grisea. Current Science 93: 688–692.

    Google Scholar 

  • Sosinski, B., and D.S. Douches. 1996. Using polymerase chain reaction-based DNA amplification to fingerprint North American potato cultivars. HortScience 31(1): 130–133.

    Google Scholar 

  • Souframanien, J., and T. Gopalakrishna. 2004. Acomparative analysis of genetic diversity in black gram genotypes using RAPD and ISSR markers. Theoretical and Applied Genetics 109: 1687–1693.

    Article  PubMed  CAS  Google Scholar 

  • Strong, E.E., and D. Lipscomb. 1999. Character coding and inapplicable data. Cladistics 15: 363–372.

    Article  Google Scholar 

  • Walbot, V., and C. Warren. 1998. Regulation of Mu element copy number in maize line with an active or inactive mutator transposonable element system. Molecular & General Genetics 211: 27–34.

    Article  Google Scholar 

  • Williams, J.G.K., M.K. Hanafey, J.A. Rafalski, and S.V. Tingey. 1993. Genetic analysis using random amplified polymorphic DNA markers. Methods in Enzymology 218: 704–740.

    Article  PubMed  CAS  Google Scholar 

  • Wolfe, A.D., and A. Liston. 1998. Contribution of PCR based methods to plant systematic and evolutionary biology. In Molecular systematic of plants II, ed. P.S. Soltis, D.E. Soltis, and J.J. Doyle, 43–86. New York: Chapman and Hall.

    Google Scholar 

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Acknowledgement

We are grateful to Kinga Mátyás for maintaining the genotypes which have been used in this study, Dr. Kawchuk and three anonymous reviewers for their valuable comments on the manuscript.

This work was partially supported by the Hungarian National Office for Research and Technology (NKTH) grant of TECH-09-A3-2009-0210.

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Authors and Affiliations

  1. Potato Research Centre, Centre of Agricultural Sciences, University of Pannonia, Deak F. u. 16, H-8360, Keszthely, Hungary

    Ahmad Mousapour Gorji & Zsolt Polgar

  2. Department of Plant Science and Biotechnology, Georgikon Faculty, University of Pannonia, Deak F. u. 16, H-8360, Keszthely, Hungary

    Peter Poczai & Janos Taller

  3. Seed and Plant Improvement Institute (SPII), Karaj, Iran

    Ahmad Mousapour Gorji

Authors
  1. Ahmad Mousapour Gorji
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  2. Peter Poczai
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  3. Zsolt Polgar
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  4. Janos Taller
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Correspondence to Zsolt Polgar.

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Gorji, A.M., Poczai, P., Polgar, Z. et al. Efficiency of Arbitrarily Amplified Dominant Markers (SCOT, ISSR and RAPD) for Diagnostic Fingerprinting in Tetraploid Potato. Am. J. Pot Res 88, 226–237 (2011). https://doi.org/10.1007/s12230-011-9187-2

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