Skip to main content
SpringerLink
Log in

Molecular Analysis of Potatoes from the Pacific Northwest Tri-State Variety Development Program and Selection of Markers for Practical DNA Fingerprinting Applications

  • Published:
American Journal of Potato Research Aims and scope Submit manuscript

Abstract

DNA fingerprinting is a valuable tool for plant cultivar discrimination and identification. Simple Sequence Repeat (SSR) markers represent an excellent option for obtaining DNA fingerprints of potatoes in an easy, fast, and reliable fashion. The highly polymorphic and co-dominant nature of SSRs gives them good discrimination power to declare the distinctiveness of new potato clones for Plant Variety Protection (PVP) and to properly identify existing cultivars. They are also useful for confirming origin and avoiding duplications and mixtures in breeding, foundation and certification programs, and also during growing and marketing stages. A total of 54 (50 tetraploid and 4 diploid) potato clones, including new cultivars released by the Pacific Northwest Tri-State Potato Variety Development Program and a set of common commercial cultivars, were analyzed using 25 SSR markers. Marketing classes (French fry processing, fresh market, and chip processing) were clearly separated using those markers. We have empirically selected a subset of six SSRs that differentiate all the potato varieties and clones present in the study. This subset of six SSR markers could be used for practical DNA fingerprinting. In order to declare distinctiveness, we recommend that common reference varieties always be genotyped together with the newly tested potato clones and that focus be placed on the relative allelic differences between the new clones and the reference varieties.

Resumen

La huella genética es una valiosa herramienta para identificar y diferenciar cultivares vegetales. Los marcadores basados en repeticiones de secuencias simples (SSR) son una excelente opción para obtener huellas genéticas en papas de una manera fácil, rápida y eficaz. La naturaleza co-dominante y el alto polimorfismo de los marcadores SSR permiten tener un alto poder discriminatorio para declarar la singularidad de los nuevos clones de papa para la Protección de Variedades Vegetales (PVP) e identificación de cultivares existentes. Son también útiles para confirmar el origen de los cultivares y evitar así duplicidades y mezclas en los programas de mejoramiento, fundación y certificación así como en las etapas posteriores de cultivo y comercialización. Un total de 54 clones de papa (cincuenta tetraploides y cuatro diploides), incluyendo los cultivares más recientes desarrollados por el Programa Tri-estatal de Desarrollo de Variedades de Papa de la Región del Pacífico Noroccidental y un conjunto de cultivares comerciales de uso común, fueron analizados usando 25 marcadores SSR. Usando estos marcadores, los cultivares fueron claramente diferenciados según su uso final (procesamiento para papas fritas, papa tipo chip y uso en fresco). Empíricamente se seleccionó un grupo de seis marcadores SSR que diferencian los 54 clones y variedades presentes en este estudio. Este subconjunto de seis marcadores podría usarse en la práctica para determinar la huella genética. Para declarar la singularidad de variedades y clones recomendamos incluir variedades conocidas de referencia en el proceso de genotipado junto con los clones nuevos que van a evaluarse con especial énfasis en las diferencias relativas de los alelos presentes entre las variedades de referencia y los nuevos clones.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Barandalla, L., J.I. Ruiz de Galarreta, D. Rios, and E. Ritter. 2006. Molecular analysis of local potato cultivars from Tenerife Island using microsatellite markers. Euphytica 152: 283–291.

    Article  CAS  Google Scholar 

  • Bonierbale, M.W., R.L. Plaisted, O. Pineda, and S.D. Tanksley. 1994. QTL analysis of trichome-mediated insect resistance in potato. Theoretical and Applied Genetics 87: 973–987.

    Article  CAS  PubMed  Google Scholar 

  • Bornet, B., G. Goraguer, G. Joly, and M. Branchard. 2002. Genetic diversity in European and Argentinean cultivated potatoes (Solanum tuberosum subsp. tuberosum) detected by inter-simple sequence repeats (ISSRs). Genome 45: 481–484.

    Article  CAS  PubMed  Google Scholar 

  • Brown, C.R., M.I. Vales, S. Yilma, S. James, B. Charlton, D. Culp, D. Hane, C. Shock, E. Feibert, M. Pavek, R. Knowles, R. Novy, J. Whitworth, J. Stark, J.C. Miller Jr., D. Holm, R. Quick and R. Navarre. 2012. “AmaRosa”, a red skinned, red fleshed fingerling with high phytonutrient value. American Journal of Potato Research 89:249–254.

    Google Scholar 

  • Braun, A., and G. Wenzel. 2005. Molecular analysis of genetic variation in potato (Solanum tuberosum L.). I. German cultivars and advanced clones. Potato Research 47: 81–92.

    Article  Google Scholar 

  • Cooke, R.J. 1999. New approaches to potato variety identification. Potato Research 42: 529–539.

    Article  Google Scholar 

  • Coombs, J.J., L.M. Frank, and D.S. Douches. 2004. An applied fingerprinting system for cultivated potato using simple sequence repeats. American Journal of Potato Research 81: 243–250.

    Article  CAS  Google Scholar 

  • Del Rio, A., J. Bamberg, and Z. Huamán. 2006. Genetic equivalence of putative duplicate germplasm collections held at CIP and US potato genebanks. American Journal of Potato Research 83: 279–285.

    Article  Google Scholar 

  • Feingold, S., J. Lloyd, N. Norero, M. Bonierbale, and J. Lorenzen. 2005. Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theoretical and Applied Genetics 111: 456–466.

    Article  CAS  PubMed  Google Scholar 

  • Felcher, K.J., J.J. Coombs, A.N. Massa, C.N. Hansey, J.P. Hamilton, R.E. Veilleux, C.R. Buell, and D.S. Douches. 2012. Integration of two diploid potato linkage maps with the potato genome sequence. PLoS ONE 7(4): E 36347.

    Article  CAS  Google Scholar 

  • Ford, R., and P.W.J. Taylor. 1997. The application of RAPD markers for potato (Solanum tuberosum L.) cultivar identification in the Australian potato industry. Australian Journal of Agricultural Research 48: 1213–1217.

    Article  CAS  Google Scholar 

  • Fu, Y.B., G.W. Peterson, K.W. Richards, T.R. Tarn, and J.E. Percy. 2009. Genetic diversity of Canadian and exotic potato germplasm revealed by simple sequence repeat markers. American Journal of Potato Research 86: 38–48.

    Article  CAS  Google Scholar 

  • Ghislain, M., D.M. Spooner, F. Rodríguez, F. Villamón, J. Núñez, C. Vásquez, R. Waugh, and M. Bonierbale. 2004. Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theoretical and Applied Genetics 108: 881–890.

    Article  CAS  PubMed  Google Scholar 

  • Ghislain, M., D. Andrade, F. Rodríguez, R.J. Hijmans, and D.M. Spooner. 2006. Genetic analysis of the cultivated potato Solanum tuberosum L. Phureja Group using RAPDs and nuclear SSRs. Theoretical and Applied Genetics 113: 1515–1527.

    Article  CAS  PubMed  Google Scholar 

  • Ghislain, M., J. Núñez, M. del Rosario Herrera, J. Pignataro, F. Guzman, M. Bonierbale, and D.M. Spooner. 2009a. Robust and highly informative microsatellite-based genetic identity kit for potato. Molecular Breeding 23: 377–388.

    Article  CAS  Google Scholar 

  • Ghislain, M., J. Núñez, M. del Rosario Herrera, and D.M. Spooner. 2009b. The single Andigenum origin of Neo-Tuberosum potato materials is not supported by microsatellite and plastid marker analyses. Theoretical and Applied Genetics 118: 963–969.

    Article  CAS  PubMed  Google Scholar 

  • Isenegger, D.A., P.W.J. Taylor, R. Ford, P. Franz, G.R. McGregor, and J.F. Hutchinson. 2001. DNA fingerprinting and genetic relationships of potato cultivars (Solanum tuberosum L.) commercially grown in Australia. Australian Journal of Agricultural Research 52: 911–918.

    Article  CAS  Google Scholar 

  • Ispizúa, V.N., I.R. Guma, S. Feingold, and A.M. Clausen. 2007. Genetic diversity of potato landraces from Northwestern Argentina assessed with simple sequence repeats (SSRs). Genetics Resources and Crop Evolution 54: 1833–1848.

    Article  Google Scholar 

  • Jaccard, P. 1901. Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bulletin de la Société Vaudoise des Sciences Naturelles 37: 547–579.

    Google Scholar 

  • Karaagac, E., S. Yilma, and M.I. Vales. 2010. SSR-Based DNA fingerprinting of potato clones from the Pacific Northwest potato variety development program. ISHS Acta Horticulturae 859: 121–127.

    Article  Google Scholar 

  • Kawchuk, L.M., D.R. Lynch, J. Thomas, B. Penner, D. Sillito, and F. Kulcsar. 1996. Characterization of Solanum tuberosum simple sequence repeats and application to potato cultivar identification. American Potato Journal 73: 325–335.

    Article  CAS  Google Scholar 

  • Kloosterman, B., M. Oortwijn, C. Celis-Gamboa, J. Uitdewilligen, T. America, R. de Vos, R.G.F. Visser, and C. Bachem. 2010. From QTL to candidate gene: A genetical genomics approach using a pooling strategy for simple and complex traits in potato. BMC Genomics 11: 158.

    Article  PubMed Central  PubMed  Google Scholar 

  • Li, L., M.J. Paulo, J. Strahwald, J. Lübeck, H.R. Hofferbert, E. Tacke, H. Junghans, J. Wunder, A. Draffehn, F. Van Eeuwijk, and C. Gebhardt. 2008. Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theoretical and Applied Genetics 116: 1167–1181.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mathias, M.R., B.D. Sagrado, and J.B. Kalazich. 2007. Use of SSR markers to identify potato germplasm in INIA Chile breeding program. Agricultura Técnica 67: 3–15.

    Article  Google Scholar 

  • McGregor, C.E., M.M. Greylin, C.A. Lambert, 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 

  • McGregor, C.E., R. van Treuren, R. Hoekstra, and T.J.L. van Hintum. 2002. Analysis of the wild potato germplasm of the series Acaulia with AFLPs: Implications for ex situ conservation. Theoretical and Applied Genetics 104: 146–156.

    Article  CAS  PubMed  Google Scholar 

  • Milbourne, D., R.C. Meyer, A.J. Collins, L.D. Ramsay, C. Gebhardt, and R. Waugh. 1998. Isolation, characterization and mapping of simple sequence repeat loci in potato. Molecular and General Genetics 259: 233–245.

    Article  CAS  PubMed  Google Scholar 

  • Moisan-Thiery, M., S. Marhadour, M.C. Kerlan, N. Dessenne, M. Perramant, T. Gokelaere, and Y. Le Hingrat. 2005. Potato cultivar identification using simple sequence repeats markers (SSR). Potato Research 48: 191–200.

    Article  Google Scholar 

  • Morell, M.K., R. Peakall, R. Appels, L.R. Preston, and H.L. Lloyd. 1995. DNA profiling techniques for plant variety identification. Australian Journal of Experimental Agriculture 35: 801–819.

    Article  Google Scholar 

  • Perrier, X., and J.P. Jacquemoud-Collet. 2006. DARwin (http://darwin.cirad.fr/darwin), Version 5.0.

  • 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 

  • Provan, J., W. Powell, and R. Waugh. 1996. Microsatellite analysis of relationship within cultivated potato (Solanum tuberosum L.). Theoretical and Applied Genetics 92: 1078–1084.

    Article  CAS  PubMed  Google Scholar 

  • Reid, A., and E.M. Kerr. 2007. A rapid simple sequence repeat (SSR)-based identification method for potato cultivars. Plant Genetic Resources: Characterization and Utilization 5(1): 7–13.

    Article  CAS  Google Scholar 

  • Reid, A., L. Hof, D. Esselink, and B. Vosman. 2009. Potato cultivar genome analysis. Methods in Molecular Biology, Plant Pathology 508: 295–308.

    CAS  Google Scholar 

  • Ríos, D., M. Ghislain, F. Rodríguez, and D.M. Spooner. 2007. What is the origin of the European potato? Evidence from Canary Island landraces. Crop Science 47: 1271–1280.

    Article  Google Scholar 

  • Ruiz de Galarreta, J.I., L. Barandalla, D.J. Ríos, R. Lopez, and E. Ritter. 2011. Genetic relationships among local potato cultivars from Spain using SSR markers. Genetic Research and Crop Evolution 58(3): 383–395.

    Article  Google Scholar 

  • Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–425.

    CAS  PubMed  Google Scholar 

  • Schneider, K., and D.S. Douches. 1997. Assessment of PCR-based simple sequence repeats to fingerprint North American potato cultivars. American Potato Journal 74: 149–160.

    Article  CAS  Google Scholar 

  • Smith, J.S.C., E.C.L. Chin, H. Shu, O.S. Smith, S.J. Wall, M.L. Senior, S.E. Mitchell, S. Kresovich, and J. Ziegle. 1997. 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 95: 163–173.

    Article  CAS  Google Scholar 

  • Song, Y.S., L. Hepting, G. Schweizer, L. Hartl, G. Wenzel, and A. Schwarzfischer. 2005. Mapping of extreme resistance to PVY (Ry sto) on chromosome XII using anther-culture-derived primary dihaploid potato lines. Theoretical and Applied Genetics 111: 879–887.

    Article  CAS  PubMed  Google Scholar 

  • Spooner, D.M., K. McLean, G. Ramsay, R. Waugh, and G.J. Bryan. 2005. A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. PNAS 102: 14694–14699.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Spooner, D.M., J. Núñez, G. Trujillo, M. del Rosario Herrera, F. Guzmán, and M. Ghislain. 2007. Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. PNAS 104: 19398–19403.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Steffens, D.L., S.L. Sutter, and S.C. Roerner. 1993. An alternate universal forward primer for improved automated DNA sequencing of M13. Biotechniques 15: 580–581.

    CAS  PubMed  Google Scholar 

  • Vales, M.I., C.R. Brown, S. Yilma, D.C. Hane, S.R. James, C.C. Shock, B.A. Charlton, et al. 2012. Purple pelisse: A specialty ‘fingerling’potato with purple skin and flesh and medium specific gravity. American Journal of Potato Research 89(4): 1–9.

    Article  Google Scholar 

  • van der Voort, J.R., P. Wolters, R. Folkertsma, R. Hutten, P. van Zandvoort, H. Vinke, K. Kanyuka, A. Bendahmane, E. Jacobsen, R. Jansen, and J. Bakker. 1997. Mapping of the cyst nematode resistance locus Gpa2 in potato using a strategy based on comigrating AFLP markers. Theoretical and Applied Genetics 95: 874–880.

    Article  Google Scholar 

  • Visser, R.G.F., C.W.B. Bachem, J.M. de Boer, G.J. Bryan, S.K. Chakrabati, S. Feingold, R. Gromadka, R.C.H.J. van Ham, S. Huang, J.M.E. Jacobs, B. Kuznetsov, P.E. de Melo, D. Milbourne, G. Orjeda, B. Sagredo, and X. Tang. 2009. Sequencing the potato genome: Outline and first results to come from the elucidation of the sequence of the world’s third most important food crop. American Journal of Potato Research 86: 417–429.

    Article  CAS  Google Scholar 

  • Yilma, S., M.I. Vales, B.A. Charlton, D.C. Hane, S.R. James, C.C. Shock, A.R. Mosley, et al. 2012. Owyhee Russet: A variety with high yields of US no. 1 tubers, excellent processing quality, and moderate resistance to Fusarium dry rot (Fusarium solani var. coeruleum). American Journal of Potato Research 89(3): 1–9.

    Article  Google Scholar 

  • Zhang, Y., C.S. Junk, and W.S. De Jong. 2009. Genetic analysis of pigmented tuber flesh in potato. Theoretical and Applied Genetics 119: 143–150.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The USDA-NIFA (United States Department of Agriculture National - Institute of Food and Agriculture) special potato grant ‘Potato Variety Development and Improvement in the Northwest’ provided financial support for this research. We thank the United States Potato Genebank, the Oregon and Idaho Potato Foundation Programs, Drs. Herman J. van Eck, Merideth Bonierbale and Julio Kalazich for providing potato clones for this study and Brigid Meints for editing and Dr. Jeff Leonard for reviewing the manuscript. Thanks are extended to graduate and undergraduate students from the Oregon Potato Breeding and Genetics Program for technical assistance.

Author information

Authors and Affiliations

  1. Department of Crop and Soil Science, Oregon State University, 109 Crop Science Bldg., Corvallis, OR, 97331, USA

    Eda Karaagac, Solomon Yilma, Alfonso Cuesta-Marcos & M. Isabel Vales

Authors
  1. Eda Karaagac
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Solomon Yilma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alfonso Cuesta-Marcos
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. M. Isabel Vales
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eda Karaagac.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Supplementary Table 1

Description of the 54 potato varieties and clones used in the present study (DOCX 24 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Karaagac, E., Yilma, S., Cuesta-Marcos, A. et al. Molecular Analysis of Potatoes from the Pacific Northwest Tri-State Variety Development Program and Selection of Markers for Practical DNA Fingerprinting Applications. Am. J. Potato Res. 91, 195–203 (2014). https://doi.org/10.1007/s12230-013-9338-8

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12230-013-9338-8

Keywords

Search

Navigation