American Journal of Potato Research

, Volume 75, Issue 2, pp 107–112 | Cite as

Estimation of genetic variation and relationship in potato (Solanum Tuberosum L.) cultivars using AFLP markers

  • J. H. Kim
  • H. Joung
  • H. Y. Kim
  • Y. P. Lim
Article
Accepted:

Abstract

Amplified fragment length polymorphism (AFLP) markers were used to distinguish commercial cultivars and to assess the level of polymorphism in potato. AFLP analysis templates were made using Eco RI and Mse I as described in the Gibco BRL AFLP kit protocol. Seven primer combinations with three selective nucleotides on both primers were screened individually with 12 potato cultivars. Multiple polymorphisms could be detected in a single reaction to the extent that all 12 commercial potatoes tested could be distinguished using any one primer combination. Up to 84 polymorphic bands were detected with a single primer combination among 12 accessions. The seven primer combinations generated a total of 466 bands, of which 409 (88%) were clearly polymorphic among the cultivars. The presence or absence of each AFLP markers was scored and then phylogenetic and genetic distance analyses were used to generate dendrograms showing genetic relationships among the cultivars evaluated. The analyses based on amplified DNA fragments did not always reflect the known genetic relationships among the cultivars. These results demonstrate that AFLP DNA markers can be of great value in identification and measurement of variation, but should be treated with caution for purposes of estimating true measures of genetic similarity in potato.

Additional key words

Potato AFLP identification relationships fingerprinting 

Resumen

Marcadores del polimorfismo en la longitud de los fragmentos amplificados (AFLP) fueron empleados para distinguir los cultivares comerciales y para evaluar el nivel de polimorfismo en la papa. Se hicieron los modelos de análisis de AFLP usando Eco RI y Mse I como se describen en el kit de protocolo de AFLP de Gibco BRL. Las siete combinaciones de iniciadores con très nucleótidos selectivos en ambos iniciadores fueron evaluadas en forma individual con 12 cultivares de papa. Se pudieron detectar polimorfismos múltiples en una sola reacción hasta el punto que las 12 papas comerciales analizadas pudieron distinguirse empleando cualquier combinación única de iniciadores. Se detectaron hasta 84 bandas polimórficas con una sola combinación de iniciadores entre las doce entradas. Las siete combinaciones de iniciadores generaron un total de 466 bandas, de las cuales 409 (88%) fueron claramente polimórficas entre los cultivares. Se midió la presencia o ausencia de cada marcador de AFLP y se emplearon los análisis filogeneticos y de distancia genética para generar dendrogramas que mostraran his relaciones genéticas entre los cultivares evaluados. El análisis basado en fragmentos de ADN amplificados no siempre reflejó las relaciones genéticas conocidas entre los cultivares. Estos resultados demuestran que los marcadores de ADN del AFLP pueden tener un gran valor en la identificación y medida de la variatión pero deberían usarse con cautela para estimar las medidas reaies de la similitud genética en la papa.

This is a preview of subscription content, log in to check access.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Literature Cited

  1. Albert, V.A., B.D. Mishler, and M.W. Chase. 1992. Character state weighting for restriction site data in phylogenic reconstruction, with an example from chloroplast DNA.In: Soltis P.S., Soltis D.M., Doyle J.J. (eds) Molecular systematics of plants. Chapman & Hall, New York, pp. 369–401.Google Scholar
  2. Bassam, B.J., G. Caetano-Anolles, and P.M. Gresshoff, 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83.PubMedCrossRefGoogle Scholar
  3. Blum, H., H. Beier, and H.J. Gross. 1987. Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 8:93–99.CrossRefGoogle Scholar
  4. Chen, J. and S. Dellaporta. 1994. Urea-based plant DNA miniprep.In: Freeling M., Walbot V. (eds.) The maize handbook. Springer, Berlin Heidelberg New York, pp. 526–527.Google Scholar
  5. Demeke, T., L.M. Kawchuk, and D.R. Lynch. 1993. Identification of potato cultivars and clonal variants by random amplified polymorphic DNA analysis. Am Potato J 70:561–570.CrossRefGoogle Scholar
  6. Donoghue, M.J., R.G. Olmstead, J.F. Smith, and J.D. Palmer. 1992. Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann Miss Bot Gard 79:333–345.CrossRefGoogle Scholar
  7. Farris, J.S. 1970. Methods for computing Wagner trees. Syst Zool 19:110–104.Google Scholar
  8. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.CrossRefGoogle Scholar
  9. Gustafsson, M.H.G. and K. Bremer. 1995. Morphology and phylogenetic interrelationships of the Asteraceae, Calvceraceac, Campanulaceae, Goodeniaceae,, and related faceilties (Asterales). Am J Bot 82: 250–205.CrossRefGoogle Scholar
  10. Goldman, D. and C.R. Merril. 1982. Silver staining of DNA in polyacrylamide gels: linearity and effect of fragment size. Electrophoresis 3:24–26.CrossRefGoogle Scholar
  11. Hadrys, H., M. Balick, and B. Schierwater. 1992. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol 1:55–63.PubMedGoogle Scholar
  12. Hosaka, K., M. Mori, and K. Ogawa 1994. Genetic relationships of Japanese potato cultivars assayed by RAPD analysis. Am Potato J 71:535–546.CrossRefGoogle Scholar
  13. Innis, M.A., D.H. Gelfand, J.J. Sninsky, and T.J. White. 1990. PCR Protocols. Academic Press, San Diego.Google Scholar
  14. Johnson, L.A. and D.E. Soltis. 1994. MatK DNA sequencing and phylogenetic reconstruction in Saxifragaceae sensu stricto. Syst Bot 19:143–156.CrossRefGoogle Scholar
  15. Kawchuk, L.M., D.R. Lynch, J. Thomas, B. Penner, D. Sillito, and F. Kulcsar. 1996. Characterization of theSolanum tuberosum simple sequence repeats and application to potato cultivar identification. Am Potato J 73:325–335.CrossRefGoogle Scholar
  16. Hein-Lankhorst, R.M., A. Vermunt, R. Weide, T. Liharska, and P. Zabel. 1991. Isolation of molecular markers for tomato (Lycopersicom esculentum) using random amplified polymorphic DNA (RAPD). Theor Appl Genet 83:108–114.CrossRefGoogle Scholar
  17. Kumar, S., K. Tamura, and M. Nei. 1993. Molecular Evolutionary Genetics Analysis (MEGA), version 1.0. The Pennsylvania State University, University Park, PA 16802.Google Scholar
  18. Maughan, P.J., M.A. Saghai Maroof, G.R. Buss, and G.M. Huestis. 1996. Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis. Theor Appl Genet 93:392–401.CrossRefGoogle Scholar
  19. Milbourne, D., R. Meyer, J.E. Bradshaw, E. Baird, N. Bonar, J. Provan, W. Powell, R. Waugh. 1997. Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136.CrossRefGoogle Scholar
  20. Mori, M., K. Hosaka, Y. Umemura, and C. Kaneda, 1993. Rapid identification of Japanese potato cultivars by RAPDs. Jpn J Genet 68:167–174.CrossRefGoogle Scholar
  21. NIVAA. 1991. Niederlandischer katalog der kartoffelsorten. NIVAA, Den Haag, The Netherlands, p. 230.Google Scholar
  22. Pavek, J.J., D.L. Corsini, J.G. Garner, S. Michener, W.C. Sparks, G.F. Carnahan, C.E. Stanger, A.R. Mosley, M.J. Johnson, G.E. Carter, R.E. Voss, M.W. Martin, and R.H. Johansen. 1981. Lemhi Russet: A new high yielding potato variety with wide adaptation, attractive tubers, and high internal quality. Am Potato J 58:619–625.CrossRefGoogle Scholar
  23. PFSF. 1977. Potato Seed in Japan. Potato Foundation Seed Farm (PFSF), Japanese Agriculture and Fisheries Department, p. 156.Google Scholar
  24. Provan, J., W. Powell, and R. Waugh. 1996. Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92:1078–1084.CrossRefGoogle Scholar
  25. Rieman, G.H. 1962. Superior. Anew white, medium-maturing, scab-resistant potato variety with high chipping quality. Amer Potato J 39:19–28.CrossRefGoogle Scholar
  26. Saitou, N. and M. Nei 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425.PubMedGoogle Scholar
  27. Smith, O.S., J.S.C. Smith, S.L. Bowen, R.A. Tenborg, and S.J. Wall. 1990. Similarities among a group of elite maize inbreds as measured by pedigree, F1 grain yield, grain yield, heterosis, and RFLPs. Theor Appl Genet 80:833–840.CrossRefGoogle Scholar
  28. Swofford, D.L. 1993. PAUP: Phylogenetic Analysis Using Parsimonony, version 3.1.1. Computer program distributed by the Illinois Natural History Survey. Champaign, Illinois.Google Scholar
  29. Thornton, R.E. and J.B. Sieczka. 1980. Commercial potato production in North America, (Supplement to Vol. 57 of The Am Potato J). Potato Association of America Handbook. pp. 12–15.Google Scholar
  30. Van Buren, R., K.T. Harper, W.R. Andersen, D.J. Stanton, S. Seyoum, and J.L. England. 1994. Evaluating the relationship of autumn buttercup (Ranunculus acrifomis var.aestivalis) to some close congers using random amplified polymorphic DNA. Am J Bot 81:514–519.CrossRefGoogle Scholar
  31. Van Eck, H.J., J.R. van der Voort, J. Draaistra, P. van Zandvoort, E. van Enckevort, B. Segers, J. Peleman, E. Jacobsen, J. Helder, and J. Bakker. 1995. The inheritance and chromosomal localization of AFLP markers in a non-inbred potato offspring. Mol Breed 1:397–410.CrossRefGoogle Scholar
  32. Vos, P., R. Hogers, M. Bleeker, M. Reyans, T. van de Lee, M. Hornes, A. Freijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23:4407–4414.PubMedCrossRefGoogle Scholar
  33. Williams, J.G.K., A.R. Kubelik, K.J. Livak, J.A Rafalski., and S.V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531–6535.PubMedCrossRefGoogle Scholar
  34. Zabeau, M. and P. Vos. 1993. European Patent Application, publication number EP 0534858.Google Scholar

Copyright information

© Springer 1998

Authors and Affiliations

  • J. H. Kim
    • 1
  • H. Joung
    • 2
  • H. Y. Kim
    • 3
  • Y. P. Lim
    • 4
  1. 1.Department of HorticultureChungnam National UniversityYuspog-Gu, TaejonKorea
  2. 2.Plant Tissue Culture Research UnitKRIBB, KISTTaejonKorea
  3. 3.Department of HorticultureKangnung National UniversityKangnung, Kangwon-DoKorea
  4. 4.Department of HorticultureChungnam National UniversityYusong-Gu, TaejonKorea

Personalised recommendations