Abstract
The correct identification of potato varieties is crucial to maintaining the quality level of seeds produced under the Canadian Seed Potato Certification Program. During inspection of in vitro potato plant propagation centres or seed potato production field lots, morphological characteristics may not be sufficient for the identification of plantlets or tubers and therefore molecular identification is sought by inspectors for variety confirmation. With international harmonization of testing methods in mind, we proposed to evaluate further the microsatellite (SSR) markers established successfully by Reid et al. (2009, Euphytica 182: 239–249, 2011), using the reference potato variety DNA collection at the Canadian Food Inspection Agency (CFIA) established and currently used for Amplified Fragment Length Polymorphism (AFLP) genotyping. The SSR markers developed by the European community laboratories were successfully validated by and established within the CFIA laboratory. Most genotypes generated for a set of 34 varieties were identical between the 2 laboratories with only 3 discrepancies due to the different interpretation of the presence/absence of the alleles. When used with potato reference DNAs of the CFIA collection, the method successfully differentiated 217 varieties apart but 10 groups, which are most likely clonal variants, were not discriminated. The SSR markers were successfully used to address 5 potato variety verification requests from CFIA inspectors during field inspections for seed potato certification. The markers successfully confirmed the presence of rogue varieties in 4 of these requests, therefore fulfilling the CFIA’s mandate towards stakeholders of the Canadian potato industry in preserving the quality of certified seeds.
Resumen
La identificación correcta de variedades de papa es crucial para el mantenimiento del nivel de calidad de las semillas producidas bajo el Programa Canadiense de Certificación de Semilla de Papa. Durante la inspección de los centros de propagación de plantas de papa in vitro o de los lotes de campo de producción de semilla de papa, las características morfológicas pudieran ser insuficientes para la identificación de plántulas o tubérculos, y en consecuencia, se busca la identificación molecular por los inspectores para confirmación de la variedad. Con la armonización internacional de los métodos de prueba en mente, proponemos evaluar más adelante los marcadores de microsatélites (SSR) establecidos con éxito por Reid et al. (2009, Euphytica 182: 239–249, 2011), usando la referencia de la colección de ADN de variedades de papa en la Agencia Canadiense de Inspección de Alimentos (CFIA) establecida y actualmente en uso para el genotipo por Polimorfismo de Longitudes de Fragmentos Amplificados (AFLP). Los marcadores SSR desarrollados por los laboratorios de la comunidad Europea se validaron con éxito por y establecidos dentro del laboratorio de la CFIA. La mayoría de los genotipos generados para un juego de 34 variedades fue idéntico entre los dos laboratorios con solo tres discrepancias debido a la interpretación diferente de la presencia/ausencia de los alelos. Cuando se usaron con ADN’s de referencia de papa de la colección de la CFIA, el método diferenció exitosamente 217 variedades, excepto 10 grupos, que lo más probable es que sean variantes clonales, que no fueron discriminados. Los marcadores SSR se usaron con éxito para atender solicitudes de verificación de cinco variedades de papa, de inspectores de la CFIA durante inspecciones de campo para certificación de semilla de papa. Los marcadores confirmaron exitosamente la presencia de falsas variedades en cuatro de estas solicitudes, satisfaciendo entonces el mandato de la CFIA hacia participantes de la industria de papa en Canadá en la preservación de la calidad de semillas certificadas.
Similar content being viewed by others
References
Cho, K.-S., H.-S. Won, H.-J. Jeong, J.-H. Cho, Y.-E. Park, and S.-Y. Hong. 2011. Development of multiplex microsatellite marker set for identification of Korean potato cultivars. Korean Journal of Horticultural Science & Technology 29: 366–373.
Cooke, R.J. 1999. New approaches to potato variety identification. Potato Research 42: 529–539.
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.
de Galarreta, J.I.R., L. Barandalla, D.J. Rios, R. Lopez, and E. Ritter. 2011. Genetic relationships among local potato cultivars from Spain using SSR markers. Genetic Resources and Crop Evolution 58: 383–395.
De Jong, H., and A.M. Murphy. 2003. Congo: A versatile blue-fleshed heritage potato variety with many names. Potato Gene Resources Newsletter 10: 1–3.
Doyle, J.J., and J.L. Doyle. 1990. Focus 12 #1.
Duan, Y.-F., J. Liu, C.-S. Bian, S.-G. Duan, J.-F. Xu, and L.-P. Jin. 2009. Construction of fingerprinting and analysis of genetic diversity with SSR markers for eighty-eight approved potato cultivars (Solanum tuberosum) in China. Acta Agronomica Sinica 35: 1451–1457.
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.
Ghislain, M., J. Núñez, M. Del Rosario Herrera, J. Pignataro, F. Guzman, M. Bonierbale, and D.M. Spooner. 2009. Robust and highly informative microsatellite-based genetic identity kit for potato. Molecular Breeding 23: 377–388.
Jones, H., A. Bernole, L. Bach Jensen, R.A. Horsnell, J.R. Law, R.J. Cooke, and C.E. Norris. 2008. Minimising inter-laboratory variation when constructing a unified molecular database of plant varieties in an allogamous crop. Theoretical and Applied Genetics 117: 1335–1344.
Karaagac, E., S. Yilma, and M.I. Vales. 2010. SSR-based DNA fingerprinting of potato clones from the Pacific Northwest potato variety development program. Acta Horticulturae 859: 121–127.
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.
Li, L.-Q., M. Haroon, S.E. Coleman, A. Sullivan, M. Singh, L. Ward, S.H. DeBoer, T. Zhang, and D.J. Donnelly. 2008. A simplified procedure for verigying and identifying potato cultivars using multiplex PCR. Canadian Journal of Plant Science 88: 583–592.
Lung’aho, C., G.N. Chemining’wa, Y.-B. Fu, S.I. Shibairo, M.J. Hutchinson, and H.G. Paniagua. 2011. Genetic deversity of Kenyan potato germplasm revealed by simple sequence repeat markers. American Journal of Potato Research 88: 424–434.
Milbourne, D., R.C. Meyer, A.J. Collins, L.D. Ramsay, C. Gebhardt, and R. Waugh. 1998. Isolation, characterisation and mapping of simple sequence repeat loci in potato. Molecular and General Genetics 259: 233–245.
Moisan-Thiery, M., S. Marhadour, M.C. Kerlan, N. Dessenne, M. Perramant, T. Gokelaere, and Y. Le Hingrat. 2005. Potato cultivars identification using simple sequence repeats markers (SSR). Potato Research 48: 191–200.
Norero, N., J. Malleville, M. Huarte, and S. Feingold. 2002. Cost efficient potato (Solanum tuberosum L.) cultivar identification by microsatellite amplification. Potato Research 45: 131–138.
Nováková, A., K. Šimáčková, J. Bárta, and V. Čurn. 2010. Utilization of DNA markers based on microsatellite polymorphism for identification of potato varieties cultivated in the Czech Republic. Journal of Central European Agriculture 11: 415–422.
Reid, A., L. Hof, D. Esselink, and B. Vosman. 2009. Potato cultivar genome analysis. In Methods in molecular biology, plant pathology, vol.508, ed. R. Burns, 295–308. New York: Springer.
Reid, A., L. Hof, G. Felix, B. Rücker, S. Tams, E. Milczynska, D. Esselink, G. Uenk, B. Vosman, and A. Weitz. 2011. Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue. Euphytica 182: 239–249.
Acknowledgments
We thank the CFIA inspection staff, PhytoDiagnostics Company (British Columbia, Canada) and the Plant Propagation Centre in Fredericton (New Brunswick, Canada) for providing us with reference material. A special thanks to C. Dollard and S. Nadin-Davis for reviewing the manuscript. We are grateful to Plant Breeders rights Office (CFIA) for providing the opportunity to do this project. Funding support was provided by CFIA.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Côté, MJ., Leduc, L. & Reid, A. Evaluation of Simple Sequence Repeat (SSR) Markers Established in Europe as a Method for the Identification of Potato Varieties Grown in Canada. Am. J. Potato Res. 90, 340–350 (2013). https://doi.org/10.1007/s12230-013-9310-7
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12230-013-9310-7