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Characterization of 24 porcine (dA-dC)n-(dT-dG)n microsatellites: genotyping of unrelated animals from four breeds and linkage studies

Abstract

Twenty-four PCR primer pairs were designed for the detection of porcine microsatellites. Polymorphism was investigated in 76 unrelated animals from four different breeds: Duroc, Landrace, Hampshire, and Yorkshire. Compared with human microsatellites, a general lower heterozygosity was detected; however, for each microsatellite a significant variation between breeds in number of alleles and heterozygosity was seen. Mean heterozygosity was found to be significantly higher (P<0.01%) in the Yorkshire breed than in the other three breeds. Linkage analyses with the CEPH linkage packet were performed in a backcross family comprising 45 animals, of which 43 had informative meioses. Ten of the microsatellites could be assigned to six different linkage groups, demonstrating that linkage mapping with microsatellites can be carried out with great efficiency in a relatively small number of animals. Four of the linkage groups represent Chromosomes (Chrs) 4, 6, 7, and 8 respectively, while two linkage groups are unassigned.

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References

  1. Alexander, L.J. and Beattie, C.W. (1992). The sequence of porcine β-casein cDNA. Anim. Genet, 23, 365–368.

  2. Balazs, I., Neuweiler, J., Gunn, P., Kidd, J., Kidd, K.K., Kuhl, J., and Mingjun, L. (1992). Human population genetic studies using hypervariable loci. I. Analysis of Assamese, Australian, Cambodian, Caucasian, Chinese and Melanesian populations. Genetics 131, 191–198.

  3. Bostein, D., White, R.L., Skolnick, M., and Davis, R.W. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314–331.

  4. Browne, D.L. and Litt, M. (1991). Characterization of (CA)n microsatellites with degenerate sequencing primers. Nucleic Acids Res. 20, 141.

  5. Cornelis, F., Hashimoto, L., Loveridge, J., MacCarthy, A., Buckle, V., Julier, C., and Bell, J. (1992). Identification of a CA repeat at the TCRA locus using yeast artificial chromosomes: a general method for generating highly polymorphic markers at chosen loci. Genomics 13, 820–825.

  6. Davies, W., Harbitz, I., Fries, R., Stranzinger, G., and Hauge, J.G. (1988). Porcine malignant hyperthermia carrier detection and chromosomal assignment using a linked probe. Anim. Genet. 19, 203–212.

  7. Davies, W., Kran, S., Kristensen, T., and Harbitz, I. (1992). Characterization of a porcine variable tandem repeat sequence specific for the glucosephosphat isomerase locus. Anim. Genet. 23, 437–442.

  8. Donis-Keller, H., Green, P., Helms, C., Cartinhour, S., Weiffenbach, B., Stephens, K., Keith, T.P., Bowden, D.W., Smith, D.R., Lander, E.S., Botstein, D., Akots, G., Rediker, K.S., Gravius, T., Brown, V.A., Rising, M.B., Parker, C., Powers, J.A., Watt, D.E., and Kauffman, E.R. (1987). A genetic linkage map of the human genome. Cell 51, 319–337

  9. Ellegren, H., Fredholm, M., Edfors-Lilja, I., Winterø, A.K., and Andersson, L. (1993). Conserved synteny between pig chromosome 8 and human chromosome 4 but Rearranged and Distorted Linkage Maps. Submitted.

  10. Geffrotin, C., Popescu, C.P., Cribiu, E.P., Boscher, J., Renard, C., Chardon, P. and Vaiman, M. (1984). Assignment of MHC in swine to chromosome 7 by in situ hybridization and serological typing. Ann. Genet. 27, 213–219

  11. Hudson, T.J., Engelstein, M., Lee, M.K., Ho, E.C., Rubenfield, M.J., Adams, C.P., Housman, D.E., and Dracopoli, N.C. (1992). Isolation and chromosomal assignment of 100 highly informative human simple sequence repeat polymorphisms. Genomics 13, 622–629.

  12. Jeffreys, A.J., Wilson, V., and Thein, S.L. (1985). Hypervariable “minisatellite” regions in human DNA. Nature 314, 67–73.

  13. Kristensen, B., Phillipsen, M., Lazary, S., Renard, C., and de Weck, A.L. (1985). The swine histocompatibility system SLA: serological studies in the common Swiss and Danish swine breeds. Anim. Blood Groups Biochem. Genet. 16, 109–124.

  14. Lathrop, G.M., Lalouel, J.M., Julier, C., and Ott, J. (1985). Multilocus linkage analysis in humans: detection of linkage and estimation of recombination. Am. J. Hum. Genet. 37, 482–498.

  15. Litt, M. and Luty, J.A. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44, 397–401.

  16. Love, J.M., Knight, A.M., McAleer, M.A., and Todd, J.A. (1990). Towards construction of a high resolution map of the mouse genome using PCR-analysed microsatellites. Nucleic Acids Res. 18, 4123–4130.

  17. Maniatis, T., Fritsch, E.F., and Sambrook, J. (1982). Molecular Cloning: A Laboratory Manual. (Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y.)

  18. Marklund, L., Winterø, A.K., Thomsen, P.D., Johansson, M., Fredholm, M., Gustavsson, U., and Andersson, L. (1993). A linkage group on pig chromosome 4 comprising the loci for blood group L, GBA, ATP1B1 and three microsatellites. Submitted.

  19. Miller, S.A., Dykes, D.D., and Polesky, H.F. (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16, 1215–1215.

  20. Nakamura, Y., Leppert, M., O'Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E., and White, R. (1987). Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235, 1616–1622.

  21. Nielsen, P.B. (1961). The M blood group system of the pig. Acta Vet. Scand. 2, 246–253.

  22. Ostrander, E.A., Jong, P.M., Rine, J., and Duyk, G. (1992). Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc. Natl. Acad. Sci. USA 89, 3419–3423.

  23. Weber, J.L. (1990). Informativeness of human (dC-dA)n-(dG-dT)n polymorphisms. Genomics 7, 524–530.

  24. Weber, J.L. and May, P.E. (1989). Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44, 388–396.

  25. Winterø, A.K., Fredholm, M., and Thomsen P.D.T. (1992). Variable (dG-dT)n-(dC-dA)n sequences in the porcine genome. Genomics 12, 281–288.

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Author information

Correspondence to Merete Fredholm.

Additional information

The nucleotide sequence data reported in this paper have been submitted to GenBank and have been assigned the accession numbers listed in Table 1.

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Fredholm, M., Winterø, A.K., Christensen, K. et al. Characterization of 24 porcine (dA-dC)n-(dT-dG)n microsatellites: genotyping of unrelated animals from four breeds and linkage studies. Mammalian Genome 4, 187–192 (1993). https://doi.org/10.1007/BF00417561

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Keywords

  • Prime Pair
  • Significant Variation
  • Linkage Group
  • Linkage Mapping
  • Linkage Analysis