Theoretical and Applied Genetics

, Volume 111, Issue 3, pp 456–466 | Cite as

Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.)

  • S. Feingold
  • J. Lloyd
  • N. Norero
  • M. Bonierbale
  • J. Lorenzen
Original Paper


Microsatellites, or simple sequence repeats (SSRs) are very useful molecular markers for a number of plant species. They are commonly used in cultivar identification, plant variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Early development of SSRs was hampered by the high cost of library screening and clone sequencing. Currently, large public SSR datasets exist for many crop species, but the number of publicly available, mapped SSRs for potato is relatively low (~100). We have utilized a database mining approach to identify SSR-containing sequences in The Institute For Genomic Research Potato Gene Index database (, focusing on sequences with size polymorphisms present in this dataset. Ninety-four primer pairs flanking SSR sequences were synthesized and used to amplify potato DNA. This study rendered 61 useful SSRs that were located in pre-existing genetic maps, fingerprinted in a set of 30 cultivars from South America, North America, and Europe or a combination thereof. The high proportion of success (65%) of expressed sequence tag-derived SSRs obtained in this work validates the use of transcribed sequences as a source of markers. These markers will be useful for genetic mapping, taxonomic studies, marker-assisted selection, and cultivar identification.


Amplify Fragment Length Polymorphism European Molecular Biology Laboratory Tentative Consensus Sequence Tetraploid Genotype Expected Size Range 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We sincerely acknowledge competitive grants from McKnight Foundation Collaborative Crop Research Program and SECyT BID 1201 pict 8-5212 from Argentina, for partial support of this work. We also thank the Propapa Germplasm Bank at INTA Balcarce, for providing the DNA for the fingerprinting studies.


  1. Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132:1131–1139PubMedGoogle Scholar
  2. Ashkenazi V, Chani E, Lavi U, Levy D, Hillel J, Veilleux E (2001) Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses. Genome 44:50–62CrossRefPubMedGoogle Scholar
  3. Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83CrossRefPubMedGoogle Scholar
  4. Bonierbale MW, Plaisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120:1095–1103Google Scholar
  5. Bonierbale MW, Plaisted RL, Pineda O, Tanksley SD (1994) QTL analysis of trichome-mediated insect resistance in potato. Theor Appl Genet 87:973–987CrossRefGoogle Scholar
  6. Botstein B, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedGoogle Scholar
  7. Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzalez-Candelas F, Kresovich S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum (Sorghum bicolor L. Moench). Theor Appl Genet 93:190–198CrossRefGoogle Scholar
  8. Bryan GJ, Collins AJ, Stephenson P, Orry A, Smith JB, Gale MD (1997) Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet 94:557–563Google Scholar
  9. Bryan GJ, McLean K, Bradshaw JE, De Jong WS, Phillips M, Castelli L, Waugh R (2002) Mapping QTLs for resistance to the cyst nematode Globodera pallida derived from the wild potato species Solanum verneii . Theor Appl Genet 105:68–77CrossRefPubMedGoogle Scholar
  10. Debener T, Salamini F, Gebhardt C (1990) Phylogeny of wild and cultivated Solanum species based on nuclear restriction fragment length polymorphisms (RFLPs). Theor Appl Genet 79:360–368CrossRefGoogle Scholar
  11. Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS (1991) “Touchdown” PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008PubMedGoogle Scholar
  12. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758–760PubMedGoogle Scholar
  13. Feingold S, Lloyd J, Norero N, Lorenzen J (2004) Development, mapping and PIC values for new potato SSRs. In: Plant and Animal Genomes XII Conference Proceedings. San Diego, CAGoogle Scholar
  14. Gebhardt C, Ritter E, Debener T, Schachtschabel U, Walkemeier B, Uhrig H, Salamini F (1989) RFLP analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78:65–75CrossRefGoogle Scholar
  15. Gebhardt C, Ritter E, Barone A, Debener T, Walkemeier B, Schachtschabel U, Kaufmann H, Thompson RD, Bonierbale MW, Ganal MW, Tanksley SD, Salamini F (1991) RFLP maps of potato and their alignment with the homologous tomato genome. Theor Appl Genet 83:49–57CrossRefGoogle Scholar
  16. Gebhardt C, Mugnieri D, Ritter E, Salamini F, Bonnel E (1993) Identification of RFLP markers closely linked to the H1 gene conferring resistance to Globodera rostochiensis in potato. Theor Appl Genet 85:541–544Google Scholar
  17. Gebhardt C, Ballvora A, Walkenmeier B, Oberhagemann P, Schuller K (2004) Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breed 13:93–102CrossRefGoogle Scholar
  18. Ghislain M, Spooner DM, Rodríguez F, Villamón F, Nuñez J, Vásquez C, Waugh R, Bonierbale M (2004) Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108:881–890CrossRefPubMedGoogle Scholar
  19. Görg R, Schachtschabel U, Ritter E, Salamini F, Gebhardt C (1992) Discrimination among 136 tetraploid potato varieties by fingerprints using highly polymorphic DNA markers. Crop Sci 32:815–819Google Scholar
  20. Haymes KM (1996) Mini-prep method suitable for plant breeding programs. Plant Mol Biol Rep 14:280–284Google Scholar
  21. He C, Poysa V, Yu K (2003) Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theor Appl Genet 106:363–373PubMedGoogle Scholar
  22. Izpizua V (2004) Estudio de la diversidad genetica en variedades de Solanum tuberosum ssp. andigenum Juz.& Bukasov de la provincia de Jujuy. Tesis de Magister Scientiae. Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata. ArgentinaGoogle Scholar
  23. Kalendar R (2004) FastPCR, PCR primer design, DNA and protein tools, repeats and own database searches program.
  24. 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 73:325–335Google Scholar
  25. Kijas JMH, Fowler JCS, Garbett CA, Thomas MR (1994) Enrichment of microsatellites from the Citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. Biotechniques 16:657–662Google Scholar
  26. Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115PubMedGoogle Scholar
  27. Liu ZW, Biyashev RM, Saghai Maroof MA (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theor Appl Genet 93:869–876Google Scholar
  28. Manly KF, Cudmore Jr RH, Meer JM (2001) Mapmanager QTX, cross-platformsoftware for genetic mapping. Mamm Genome 12:930–932CrossRefPubMedGoogle Scholar
  29. Marcucci Poltri S (1998) Caracterizacion molecular y cariotipica de la variabilidad genetica de germoplasma argentine en Solanum sp. Tesis de doctorado. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. ArgentinaGoogle Scholar
  30. Mc Gregor CE, Greyling M, Warnich L (2000a) The use of simple sequence repeats (SSRs) to identify commercially important potato (Solanum tuberosum L.) cultivars in South Africa. S Afr J Plant Soil 17(4):177–180Google Scholar
  31. Mc Gregor CE, Lambert CA, Greyling M, Louw JH, Warnich L (2000b) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113:135–144CrossRefGoogle Scholar
  32. Meyer RCD, Milbourne D, Hackett CA, Bradshaw JE, McNicol JW (1998) Linkage analysis in tetraploid potato and association of markers with quantitative resistance to late blight (Phytophthora infestans). Mol Gen Genet 259:233–245CrossRefPubMedGoogle Scholar
  33. Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Provan J, Powell W, Waugh R (1997) Comparison of PCR based marker systems for the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136Google Scholar
  34. Milbourne D, Meyer R, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245CrossRefPubMedGoogle Scholar
  35. Miyao A, Zhong HS, Mona L, Yano M, Yamamoto K, Havukkala I, Minobe Y, Sasaki T (1996) Characterization and genetic mapping of simple sequence repeats in the rice genome. DNA Res 3:233–238PubMedGoogle Scholar
  36. Norero N, Malleville J, Huarte M, Feingold S (2004) Cost efficient potato (Solanum tuberosum L.) cultivar identification by microsatellite amplification. Potato Res 45:131–138Google Scholar
  37. Ooijen JW van, Voorrips RE (2001) Joinmap 3.0, Software for the calculation of genetic linkage maps. Kyazma, Wageningen, The NetherlandsGoogle Scholar
  38. Provan J, Powell W, Waugh R (1996) Microsatellite analysis of relationships between cultivated potato (Solanum tuberosum). Theor Appl Genet 92:1078–1084CrossRefGoogle Scholar
  39. Rafalski JA, Tingey SV (1993) Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends Genet 8(9):275–280CrossRefGoogle Scholar
  40. Raimondi JP, Peralta IE, Massuelli RW, Feingold S, Camadro EL (2005) Examination of the hybrid origin of the wild potato Solanum ruiz-lealii Brucher. Plant Syst Evol: Scholar
  41. Raker C, Spooner DM (2002) The Chilean tetraploid cultivated potato, Solanum tuberosum, is distinct from the Andean populations; microsatellite data. Crop Sci 42:1451–1458Google Scholar
  42. Roder MS, Plaschke J, Konin SU, Borner A, Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333PubMedGoogle Scholar
  43. Rossetto M (2001) Sourcing of SSR markers from related plant species. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CAB International, WallingfordGoogle Scholar
  44. Rouppe van der Voort JNAM, Van Eck HJ, Draaistra J, Zandvoort PV, Jacobsen E, Bakker J (1998) An online catalog of AFLP markers covering the potato genome. Mol Breed 4:73–77CrossRefGoogle Scholar
  45. Saha M (2003) Mapping of genes associated with late blight, cold sweetening, and verticillium resistance in potato. PhD Dissertation. North Dakota State University, FargoGoogle Scholar
  46. Scott KD (2001) Microsatellites derived from ESTs, and their comparison with those derived by other methods. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CAB International, WallingfordGoogle Scholar
  47. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee SL, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726Google Scholar
  48. Smulders MJM, Bredemeijer G, Rus-Kortekaas W, Arens P, Vosman B (1997) Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 97:264–272CrossRefGoogle Scholar
  49. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 12:4127–4138Google Scholar
  50. 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 38:1153–1162PubMedGoogle Scholar
  51. Vekemans X, Jacquemart AJ (1997) Perspectives on the use of molecular markers in plant population biology. Belg J Bot 129:91–100Google Scholar
  52. Vision TJ, Brown DG, Shmoys DB, Durret RT, Tanksley SD (2000) Selective mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics 155:407–420PubMedGoogle Scholar
  53. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP—a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4417PubMedGoogle Scholar
  54. Wang Z, Weber JL, Zhang G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6Google Scholar
  55. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • S. Feingold
    • 1
  • J. Lloyd
    • 2
  • N. Norero
    • 1
  • M. Bonierbale
    • 3
  • J. Lorenzen
    • 2
  1. 1.Laboratorio de Biotecnologìa AgrícolaPropapa EEA Balcarce INTABalcarceArgentina
  2. 2.Potato Molecular Biology Lab, Plant, Soil and Entomological Science (PSES) DepartmentUniversity of IdahoMoscowUSA
  3. 3.Germplasm Enhancement and Crop Improvement DivisionInternational Potato Center (CIP)Lima 12Peru

Personalised recommendations