A Core Subset of the ex situ  Collection of S. demissum at the US Potato Genebank


Useful genetic diversity found in wild potato germplasm is important for progress in potato breeding and science. An effective way to maximize its utilization is through characterization of ex situ collections. For example, marker-based core subsets from large collections are an effective strategy to accelerate evaluation, utilize germplasm, and enhance cost-effectiveness. This project used AFLP markers to create a core subset for the US Potato Genebank’s collection of S. demissum. This species from Mexico and Guatemala is known for excellent levels of late blight resistance and frost tolerance. A total of 149 accessions with diverse geographic origin were characterized with 1403 AFLP markers; these markers were effective on determining genetic associations among the accessions. For the core subset, the AFLP loci were considered as traits, with the presence of the marker as the required state to include in a core. The results of the analyses identified that 10 of the accessions of S. demissum captured 83% of all the markers detected in the whole collection. The inclusion of 28 additional accessions, which had between 1 to 5 unique markers, resulted in a core set of 38 accessions that captured 96% of all the marker diversity. We expect this can benefit the genebank and the potato community by opening opportunities for research, trait screenings, and marker association studies.


La diversidad genética útil que se encuentra en el germoplasma de la papa silvestre es importante para el progreso en el mejoramiento de la papa y de la ciencia. Una manera efectiva de maximizar su utilización es a través de la caracterización de las colecciones ex situ. Por ejemplo, sub grupos o core subsets de colecciones grandes, basados en marcadores moleculares, son una estrategia efectiva para acelerar la evaluación, uso del germoplásma, y mejorar costo-efectividad. Este proyecto utilizó marcadores AFLP para crear un sub grupo para la colección de S. demissum del banco de germoplasma de papa de los Estados Unidos . Esta especie de México y Guatemala es conocida por sus excelentes niveles de resistencia al tizón tardío y tolerancia al frío. Se caracterizaron un total de 149 accesiones de diverso origen geográfico con 1403 marcadores AFLP; estos marcadores fueron efectivos en la determinación de asociaciones genéticas entre las accesiones. Para el sub grupo o core, los loci AFLP se consideraron como los caracteres utiles, con la presencia del marcador como el estado requerido para incluirse en un grupo. Los resultados de estos análisis identificaron que 10 de las accesiones de Sdemissum capturaron 83% de todos los marcadores detectados en la colección completa. La inclusión de 28 accesiones adicionales, que tenían de 1 a 5 marcadores únicos, resultaron en un sub grupo final de 38 accesiones que capturaron 96% de toda la diversidad encontrada en los marcadores. Esperamos que esto pueda beneficiar al banco de germoplasma y a la comunidad de la papa mediante la apertura de oportunidades para investigación, detección de caracteres, y de estudios de asociación s a marcadores.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4



Amplified Fragment Length Polymorphism


Genetic Similarity


US Potato Genebank


  1. Balfourier, F., Prosperi, J.M., Charmet, G., Goulard, M., and P. Monastiez. 1999. Using spatial patterns of diversity to develop core collections. In: Johnson, R.C., Hodgkin, T., (eds). Core Collections for Today and Tomorrow. Rome, IPGRI, p. 81.

  2. Bamberg, J.B., and A.H. del Rio. 2004. Genetic heterogeneity estimated by RAPD polymorphism of four tuber-bearing potato species differing by breeding system. American Journal of Potato Research 81: 377–383.

    CAS  Article  Google Scholar 

  3. Bamberg, J.B. and A.H. del Rio. 2005. Conservation of potato genetic resources. In: Razdan, M.K. and Mattoo, a.K. (eds.) genetic improvement of Solanaceous crops. Volume I: Potato. Science publishers, Inc. Plymouth, p. 476.

  4. Bamberg, J.B., and A.H. del Rio. 2011. Diversity relationships among wild potato collections from seven “Sky Island” mountain ranges in the Southwest USA. American Journal of Potato Research 88: 493–499.

    Article  Google Scholar 

  5. Bamberg, J.B., and A.H. del Rio. 2014. Selection and validation of an AFLP marker Core collection for the wild potato Solanum microdontum. American Journal of Potato Research 91: 368–375.

    CAS  Article  Google Scholar 

  6. Bamberg, J.B., A. del Rio, J. Coombs, and D. Douches. 2015. Assessing SNPs versus RAPDs for predicting heterogeneity in wild potato species. American Journal of Potato Research 92: 276–283.

    CAS  Article  Google Scholar 

  7. Bamberg, J.B., A.H. del Rio, D. Kinder, L. Louderback, B. Pavlik, and C. Fernandez. 2016. Core collections of potato (Solanum) species native to the USA. American Journal of Potato Research 93 (6): 564–571.

    Article  Google Scholar 

  8. Bamberg, J.B., A. del Rio, S. Jansky, and D. Ellis. 2018. Ensuring the genetic diversity of potatoes. In: Achieving sustainable cultivation of potatoes no. 26, Vol.1 (Ed. prof. Gefu Wang-Pruski). Burleigh-Dodds science publishers. Chapter 3: 57–80.

    Google Scholar 

  9. Bidot Martínez, I., M. Valdés de la Cruz, N. Riera, M. Nelson, and P. Bertin. 2017. Establishment of a core collection of traditional Cuban Theobroma cacao plants for conservation and utilization purposes. Plant Molecular Biology Reporter 35 (1): 47–60.

    Article  Google Scholar 

  10. Bryan, G.J., K. McLean, R. Waugh, and D.M. Spooner. 2017. Levels of intra-specific AFLP diversity in tuber-bearing potato species with different breeding systems and Ploidy levels. Frontiers in Genetics 8: 119.

    Article  Google Scholar 

  11. Chandra, S., Z. Huaman, S. Hari Krishna, and R. Ortiz. 2002. Optimal sampling strategy and core collection size of Andean tetraploid potato based on isozyme data - a simulation study. Theoretical and Applied Genetics 104: 1325–1334.

    CAS  Article  Google Scholar 

  12. del Rio, A.H., J.B. Bamberg, and Z. Huaman. 1997. Assessing changes in the genetic diversity of potato genebanks. 1. Effects of seed increase. Theoretical and Applied Genetics 95: 191–198.

  13. del Rio, A.H., J. Bamberg, Z. Huaman, A. Salas, and S. Vega. 2001. Association of eco-geographical variables and RAPD marker variation in wild potato populations of the USA. Crop Science 41 (3): 870–878.

    Article  Google Scholar 

  14. del Rio, A.H., and J.B. Bamberg. 2002. Lack of association between genetic and geographic origin characteristics for the wild potato Solanum sucrense Hawkes. American Journal of Potato Research 79: 335–338.

  15. Frankel, O.H. 1984. Genetic perspectives of germplasm conservation. In Genetic manipulation: Impact on man and society, ed. W.K. Arber, K. Llimensee, W.J. Peacock, and P. Starlinger, 161–170. Cambridge: Cambridge University Press.

    Google Scholar 

  16. Hawkes, J.G. 1958. Significance of wild species and primitive forms of potato breeding. Euphytica 7: 257–270.

    Google Scholar 

  17. Hanneman, R.E. 1989. The potato germplasm resource. American Potato Journal 66: 655–667.

    Article  Google Scholar 

  18. Hardigan, M., J. Bamberg, C. Robin Buell, and D. Douches. 2015. Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota. The Plant Genome 8: 1–16.

    CAS  Article  Google Scholar 

  19. Hijmans, R.J., M. Jacobs, J. Bamberg, and D. Spooner. 2003. Frost tolerance in wild potato species: Assessing the predictivity of taxonomic, geographic, and ecological factors. Euphytica 130: 47–59.

    Article  Google Scholar 

  20. JMP®, Version 15.0.0. SAS Institute Inc., Cary, NC, 1989–2019.

  21. Jo, K., M. Arens, T. Kim, M.A. Jongsma, R. Visser, E. Jacobsen, and J. Vossen. 2011. Mapping of the S. demissum late blight resistance gene R8 to a new locus on chromosome IX. Theoretical and Applied Genetics 123: 1331–1340.

    CAS  Article  Google Scholar 

  22. Kramer, L.J., and J. Bamberg. 2019. Comparing methods of Ploidy estimation in potato (Solanum) species. American Journal of Potato Reserach 96: 419–426.

    Article  Google Scholar 

  23. Perrier, X., Jacquemoud-Collet, J.P. 2006. DARwin software. http://darwin.cirad.fr/

  24. Reed, D.H., and R. Frankham. 2001. How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 55: 1095–1103.

    CAS  Article  Google Scholar 

  25. Rohlf, F.J. (2000) NTSYS-pc: Numerical taxonomy and multivariate analysis system version 2.1. Exeter publishing Setauket, New York.

  26. Spooner, D.M., R.G. Van den Berg, and J.B. Bamberg. 1995. Examination of species boundaries of Solanum series Demissa and potentially related species in series Acaulia and series Tuberosa (sect. Petota). Systematic Botany 20: 295–314.

    Article  Google Scholar 

  27. Spooner, D.M., R.R. van Treuren, M.C. de Vicente. 2005. Molecular markers for germplasm and genebank management. Technical bulletin 10. International Plant Genetic Resources Institute (IPGR), Rome, Italy.

  28. Vega, S.E., and J.B. Bamberg. 1995. Screening the U.S. potato collection for frost hardiness. American Potato Journal 72: 13–21.

    Article  Google Scholar 

  29. Vleeshouwers, V.G., R. Finkers, D. Budding, M. Visser, M.M. Jacobs, R. van Berloo, M. Pel, N. Champouret, E. Bakker, P. Krenek, H. Rietman, D. Huigen, R. Hoekstra, A. Goverse, B. Vosman, E. Jacobsen, and R.G. Visser. 2011. SolRgene: An online database to explore disease resistance genes in tuber-bearing Solanum species. Biomed Central Plant Biology 11: 1–8.

    Google Scholar 

  30. Vossen, J.H., G. van Arkel, M. Bergervoet, K. Jo, E. Jacobsen, and R.G. Visser. 2016. The Solanum demissum R8 late blight resistance gene is an sw-5 homologue that has been deployed worldwide in late blight resistant varieties. Theoretical and Applied Genetics 129 (9): 1785–1796.

    CAS  Article  Google Scholar 

  31. Zhang, C.Y., X.S. Chen, Y.M. Zhang, Z.H. Yuan, Z.C. Liu, Y.L. Wang, and Q. Lin. 2009. A method for constructing core collection of Malus sieversii using molecular markers. Scientia Agricultura Sinica Journal 42: 597–602.

    CAS  Google Scholar 

Download references


The authors wish to express their thanks to the staff of the US Potato Genebank for their support and technical assistance.

Author information



Corresponding author

Correspondence to Alfonso del Rio.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

del Rio, A., Bamberg, J. A Core Subset of the ex situ  Collection of S. demissum at the US Potato Genebank. Am. J. Potato Res. 97, 505–512 (2020). https://doi.org/10.1007/s12230-020-09799-9

Download citation


  • AFLP markers
  • Core Subsets
  • Solanum demissum
  • Germplasm organization