Abstract
Characterization of nearly 1,000 cultivated potato accessions with simple sequence repeats (SSRs; also referred to as microsatellites) has allowed the identification of a reference set of SSR markers for accurate and efficient genotyping. In addition, 31 SSRs are reported here for a potato genetic map, including new map locations for 24 of them. A first criterion for this proposed reference set was ubiquity of the SSRs in the eight landrace cultivar groups of the potato, Solanum tuberosum. All SSRs tested in the present study displayed the same allele phenotypes and allele size range in the diverse germplasm set as in the advanced potato cultivar germplasm in which they were originally discovered. Thirteen of 13 SSR products from all cultivar groups are shown to cross-hybridize with the corresponding SSR product of the source cultivar to ascertain sequence homology. Other important SSR selection criteria are quality of amplification products, locus complexity, polymorphic index content, and well-dispersed location on a potato genetic map. Screening of 156 SSRs allowed the identification of a highly informative and user-friendly set comprising 18 SSR markers for use in characterization of potato genetic resources. In addition, we have identified true- and pseudo-multiplexing SSRs for even greater efficiency.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bamberg JB, Kiru D, Del Rio AH (2001) Comparison of reputed duplicate populations in the Russian and potato gene banks using RAPD markers. Am J Potato Res 78:365–369
Ghislain M, Zhang D, Fajardo D, Huamán Z, and Hijmans R (1999a) Marker-assisted sampling of the cultivated Andean potato Solanum phureja collection using RAPD markers. Genet Res Crop Evol 46:547–555
Ghislain M, Zhang D, Herrera MR (eds) (1999b) Molecular biology laboratory protocols: plant genotyping training manual, 2nd edn. International Potato Center (CIP), Lima, Peru
Ghislain M, Rodríguez F, Núñez J, Naik P, Huamán Z, and Bonierbale M (2001a) Comparison of genetic diversity of potato varieties from India and South America. Proceedings of the Plant and Animal Genome Conference IX, January 2001. Poster 287, p 132
Ghislain M, Trognitz B, Herrera MR, Solis J, Casallo G, Vasquez C, Hurtado O, Castillo R, Portal L, and Orrillo, M (2001b) Genetic loci associated with field resistance to late blight in offspring of Solanum phureja and tuberosum grown under short-day conditions. Theor Appl Genet 103:433–442
Hawkes JG (1990) The potato: evolution, biodiversity and genetic resources. Belhaven, Washington, DC
Huamán Z, Spooner DM (2002) Reclassification of landrace populations of cultivated potatoes (Solanum sect. Petota). Am J Bot 89:947–965
Huamán Z, Golmirzaie A, Amoros W (1997) The Potato. In: Fuccillo D, Sears L, Stapleton P (eds), Biodiversity in trust. Cambridge University Press, Cambridge, pp 21–28
Huamán Z, Ortiz R, Gómez R (2000a) Selecting a Solanum tuberosum subsp. andigena core collection using morphological, geographical, disease and pest descriptors. Am J Potato Res 77:183–190
Huamán Z, Ortiz R, Zhang D, Rodríguez F (2000b) Isozyme analysis of entire and core collections of Solanum tuberosum subsp. andigena potato cultivars. Crop Sci 40:273–276
Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vasquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP, and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390
Kawchuk LM, Lynch DR, Thomas J, Penner B, Sillito D, Kulcsar F (1996) Characterization of Solanum tuberosum simple sequence repeats and application to potato cultivar identification. Am Potato J 73:325–335
Kruglyak S, Durrett RT, Schug MD, and Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci USA 95:10774–10778
Lara-Cabrera S, Spooner DM (2003) Taxonomy of Mexican diploid wild potato (Solanum sect. Petota) species: morphological and microsatellite data. Monogr Syst Bot Moi Bot Gard (in press)
Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterization and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245
Mitchell SE, Kresovich S, Jester CA, Hernandez CJ, Szewc-McFadden AK (1997) Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci 37:617–624
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: Implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275–1287
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222
Provan J, Powell W, Waugh R (1996) Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92:1078–1084
Raker C, Spooner DM (2002) The Chilean tetraploid cultivated potato, Solanum tuberosum, is distinct from the Andean populations; microsatellite data. Crop Sci 42:1451–1458
Schneider K, Douches DS (1997) Assessment of PCR-based simple sequence repeats to fingerprint North American potato cultivars. Am Potato J 74:149–160
Veilleux RE, Shen LY, Paz MM (1995) Analysis of the genetic composition of anther-derived potato by randomly amplified polymorphic DNA and simple sequence repeats. Genome 38:1153–1162
Westman AL, Kresovich S (1998) The potential of cross-taxa simple-sequence repeat (SSR) amplification between Arabidopsis thaliana L. and crop brassicas. Theor Appl Genet 96:272–281
Acknowledgements
The authors are grateful to Drs. Zosimo Huamán, William Roca, Rene Gomez, Ana Panta and Judith Toledo for providing the experimental materials. We also thank Daniel Andrade, Olenka Frías, Mercedes Ames, Giovana Perazzo and María del Rosario Herrera for polymorphism index content on subsets of the germplasm collection and help in mapping SSR markers; our collaborators at the SCRI, Dan Milbourne and Walter De Jong for providing SSR sequences and EST sequences. This work was made possible through grants from the United Nations Development Special Project Program, the Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung (BMZ) and the Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ) (project no 96.7860.8-001.00).
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by F. Salamini
Rights and permissions
About this article
Cite this article
Ghislain, M., Spooner, D.M., Rodríguez, F. et al. Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108, 881–890 (2004). https://doi.org/10.1007/s00122-003-1494-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-003-1494-7