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Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato

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Abstract

The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed.

Abbreviations: PCR, polymerase chain reaction; AFLP, amplified fragment length polymorphism; RAPD, randomly amplified polymorphic DNA; DNA, deoxyribonucleic acid; EMR, effective multiplex ratio; DI, diversity index; MI, marker index; RFLP, restriction fragment length polymorphism.

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References

  1. Akkaya MS, Bhagwat AA, Cregan PB: Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132: 1131–1139 (1992).

    Google Scholar 

  2. Al-Janabi SM, Honeycutt RJ, McClelland M, Sobral BWS: A genetic linkage map of Saccharum spontaneum L. 'sES 208'. Genetics 134: 1249–1260 (1993).

    Google Scholar 

  3. Baird E, Cooper-Bland S, Waugh R, De Maine M, Powell W: Molecular characterisation of inter-specific and intra-specific somatic hybrids of potato using randomly amplified polymorphic DNA (RAPD) markers. Mol Gen Genet 233: 469–475 (1992).

    Google Scholar 

  4. Bonierbale MW, Plaisted RL, Tanksley SD: RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120: 1095–1103 (1988).

    Google Scholar 

  5. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL: High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455–457 (1994).

    Google Scholar 

  6. Condit R, Hubell SP: Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34: 66–71 (1991).

    Google Scholar 

  7. Debener T, Salamini F, Gebhardt C: Phylogeny of wild and cultivated Solanum species based on nuclear restriction fragment length polymorphisms (RFLPs). Theor Appl Genet 79: 360–368 (1990)

    Google Scholar 

  8. Edwards K, Johnstone C, Thomson C: A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucl Acids Res 19: 1349 (1991).

    Google Scholar 

  9. Gebhardt C, Blomendahl C, Schachtschabel U, Debener T, Salamini F, Ritter E: Identification of 2n breeding lines and 4n varieties of potato (Solanum tuberosum ssp. tuberosum) with RFLP fingerprints. Theor Appl Genet 78: 16–22 (1989).

    Google Scholar 

  10. Gebhardt C, Ritter E, Debener T, Schachtschabel U, Walkemeier B, Uhrig H, Salamini F: RFLP analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78: 65–75 (1989).

    Google Scholar 

  11. Gorg R, Schachtschabel U, Ritter G, Salamini F, Gebhardt C: Discrimination among 136 tetraploid potato varieties by fingerprints using highly polymorphic DNA markers. Crop Sci 32: 815–819 (1992).

    Google Scholar 

  12. Landry BS, Kesseli R, Leung H, Michelmore RW: Comparison of restriction endonucleases as sources of probes for their efficiency in detecting restriction fragment length polymorphisms in lettuce (Lactuca sativa L.). Theor Appl Genet 74: 646–653 (1987).

    Google Scholar 

  13. Lee M, Godshalk GB, Lankey KR, Woodman WW: Association of restriction fragment length polymorphisms among maize inbreds with agronomic performance of their crosses. Crop Sci 29: 1067–1071 (1989).

    Google Scholar 

  14. Lin J-J, Kuo J, Ma J, Saunders JA, Beard HS, MacDonald MH, Kenworthy W, Ude GN, Matthews BF: Identification of molecular markers in soybean comparing RFLP, RAPD and AFLP DNA mapping techniques. Plant Mol Biol 14: 156–169 (1996).

    Google Scholar 

  15. Liu Z, Furnier GR: Comparison of allozyme, RFLP and RAPD markers for revealing genetic variation within and between trembling aspen and big tooth aspen. Theor Appl Genet 87: 97–105 (1993).

    Google Scholar 

  16. Loarce Y, Gallego R, Ferrer G: A comparative analysis of the genetic relationships between rye cultivars using RFLP and RAPD markers. Euphytica 88: 107–115 (1996).

    Google Scholar 

  17. Morgante M, Olivieri AM: PCR amplified microsatellites in plant genetics. Plant J 3: 175–182 (1993).

    Google Scholar 

  18. Nei M, Li WH: Mathematical modelling for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 74: 5267–5273 (1979).

    Google Scholar 

  19. Nienhuis J, Slocum NK, Devos DA, Muren R: Genetic similarity among Brassica oleracea L. genotypes as measured by restriction fragment length polymorphism. J Amer Hort Sci 18: 298–303 (1993).

    Google Scholar 

  20. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A: The utility of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2: 225–238 (1996).

    Google Scholar 

  21. Powell W, Morgante M, Vogel J, Tingey S, Rafalski AJ: Technology for plant genome analysis and breeding, 177–180. Proceedings of IPBA, Rogla, Slovenia (1994).

  22. Prince JP, Louiza-Figueron F, Tanksley SD: Restriction fragment length polymorphism and genetic distance among Mexican accessions of Capsicum. Genome 35: 726–732 (1992).

    Google Scholar 

  23. Provan J, Powell W, Waugh R: Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92: 1078–1084 (1996).

    Google Scholar 

  24. Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV: Generating and using DNA markers in plants. In: Birren B, Lai E (eds) Nonmammalian Genomic Analysis: A Practical Guide, Academic Press.

  25. Ragot M, Hoisington DA: Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs. Theor Appl Genet 86: 975–984 (1993).

    Google Scholar 

  26. Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R: Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet (in press).

  27. Saghai-Maroof MA, Biyasher RM, Yang GP, Zhang Q, Allard RW: Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations and population dynamics. Proc Natl Acad Sci USA 91: 5466–5470 (1994).

    Google Scholar 

  28. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW: Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81: 8014–8018 (1984).

    Google Scholar 

  29. Spooner DM, Tivang J, Nienhuis J, Miller JT, Douchas DS, Contreras MA: Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe). Theor Appl Genet 92: 532–540 (1996).

    Google Scholar 

  30. Tautz D: Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucl Acids Res 17: 3286–3292 (1989).

    Google Scholar 

  31. Tautz D, Rentz M: Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucl Acids Res 12: 4127–4138 (1984).

    Google Scholar 

  32. Tautz D, Trick M, Dover GA: Cryptic simplicity in DNA is a major source of genetic variation. Nature 322: 652–656 (1986).

    Google Scholar 

  33. Thomas MR, Scott NS: Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence tagged sites (STS). Theor Appl Genet 86: 985–990 (1993).

    Google Scholar 

  34. Thormann CE, Ferreira ME, Camargo LEA, Tirang JG, Osborn TC: Comparison of RFLP and RAPD markers for estimating genetic relationship within and among cruciferous species. Theor Appl Genet 88: 973–980 (1994).

    Google Scholar 

  35. Vos P, Hogers R, Bleeker M, Rerjans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M: AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23: 4407–4414 (1995).

    Google Scholar 

  36. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV: DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 18: 7213–7218 (1990).

    Google Scholar 

  37. Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD: The detection and estimation of linkage in polyploids using single dose restriction fragments. Theor Appl Genet 83: 294–300 (1992).

    Google Scholar 

  38. Wu KS, Tanksley SD: Abundance, polymorphism and genetic mapping of microsatellite in rice. Mol Gen Genet 241: 225–235 (1993).

    Google Scholar 

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Authors and Affiliations

  1. Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    Dan Milbourne, Rhonda Meyer, John E. Bradshaw, Eileen Baird, Nicky Bonar, Jim Provan, Wayne Powell & Robbie Waugh

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  1. Dan Milbourne
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  2. Rhonda Meyer
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  3. John E. Bradshaw
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  4. Eileen Baird
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  5. Nicky Bonar
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  6. Jim Provan
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  7. Wayne Powell
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  8. Robbie Waugh
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Milbourne, D., Meyer, R., Bradshaw, J.E. et al. Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato. Molecular Breeding 3, 127–136 (1997). https://doi.org/10.1023/A:1009633005390

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