Mammalian Genome

, Volume 6, Issue 10, pp 714–724 | Cite as

A small-insert bovine genomic library highly enriched for microsatellite repeat sequences

  • R. T. Stone
  • J. C. Pulido
  • G. M. Duyk
  • S. M. Kappes
  • J. W. Keele
  • C. W. Beattie
Original Contributions

Abstract

A bovine genomic phagemid library was constructed with randomly sheared DNA. Enrichment of this single-stranded DNA library with CA or GT primers resulted in 45% positive clones. The 14% of positive clones with (CA · GT)>12, and not containing flanking repetitive elements, were sequenced, and the efficiency of marker production was compared with random M13 bacteriophage libraries. Primer sequences and genotyping information are presented for 390 informative bovine microsatellite markers. The genomic frequency for 11 tri- and tetranucleotide repeats was estimated by hybridization to a lambda genomic library. Only GCT, GGT, and GGAT were estimated to have a frequency of >100 per genome. Enrichment of the phagemid library for these repeats failed to provide a viable source of microsatellite markers in the bovine. Comparison of map interval lengths between 100 markers from the enriched library prepared from randomly sheared DNA and M13 bacteriophage libraries prepared from Mbo1 restriction digests suggested no bias in skeletal genomic coverage based on source of small insert DNA. In conclusion, enrichment of the bovine phagemid library provides a sufficient source of microsatellites so that small repeat lengths and flanking repetitive sequences common in the bovine can be eliminated, resulting in a high percentage of informative markers.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Akaboshi, E. (1985). Cloning of the human myoglobin gene. Gene 33, 241–249.Google Scholar
  2. Alexander, L.J., Rohrer, G.A., Stone, R.T., Beattie, C.W. (1995). Porcine SINE associated microsatellite markers: evidence for new artiodactyl SINEs. Mamm. Genome, in press.Google Scholar
  3. Andersson, L., Haley, C.S., Ellegren, H., Knott, S.A., Johansson, M., Andersson, K., Andersson-Eklund, L., Edfors-Lilja, I., Fredholm, M., Hansson, I., Håkansson, J., Lundström, K. (1994). Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 263, 1771–1774.Google Scholar
  4. Archibald, A.L., Haley, C.S., Brown, J.F., Couperwhite, S., McQueen, H.A., Nicholson, D., Coppieters, W., Van de Weghe, A., Stratil, A., Winterø, A.K., Fredholm, M., Larsen, N.J., Nielsen, V.H., Milan, D., Woloszyn, N., Robic, A., Dalens, M., Riquet, J., Gellin, J., Caritez, J.-C., Burgaud, G., Ollivier, L., Bidanel, J.-P., Vaiman, M., Renard, C., Geldermann, H., Davoli, R., Ruyter, D., Verstege, E.J.M., Groenen, M.A.M., Davies, W., Høyheim, B., Keiserud, A., Andersson, L., Ellegren, H., Johansson, M., Marklund, L., Miller, J.R., Anderson Dear, D.V., Signer, E., Jeffreys, A.J., Moran, C., Le Tissier, P., Muladno, Rothschild, M.F., Tuggle, C.K., Vaske, D., Helm, J., Liu, H.-C., Rahman, A., Yu, T.-P., Larson, R.G., Schmitz, C.B. (1995). The PiGMaP consortium linkage map of the pig (Sus scrofa). Mamm. Genome 6, 157–175.Google Scholar
  5. Barendse, W., Armitage, S.M., Kossarek, L.M., Shalom, A., Kirkpatrick, B.W., Ryan, A.M., Clayton, D., Li, L., Neibergs, H.L., Zhang, N., Grosse, W.M., Weiss, J., Creighton, P., McCarthy, F., Ron, M., Teale, A.J., Fries, R., McGraw, R.A., Moore, S.S., Georges, M., Soller, M., Womack, J.E., Hetzel, D.J.S. (1994). A genetic linkage map of the bovine genome. Nature Genet. 227–235.Google Scholar
  6. Beckman, J., Weber, J.L., (1992). Survey of human and rat microsatellites. Genomics 12, 627–631.Google Scholar
  7. Benson, D., Lipman, D.J., Ostell, J. (1993). GenBank. Nucleic Acids Res. 21, 2963–2965.Google Scholar
  8. Bishop, M.D., Kappes, S.M., Keele, J.W., Stone, R.T., Sunden, S.L.F., Hawkins, G.A., Toldo, S.S., Fries, R., Grosz, M.D., Yoo, J., Beattie, C.W. (1994). A genetic linkage map for cattle. Genetics 136, 619–639.Google Scholar
  9. Buchanan, F.C., Littlejohn, R.P., Galloway, S.M., Crawford, A.M. (1993). Microsatellites and associated repetitive elements in the sheep genone. Mamm. Genome 4, 258–264.Google Scholar
  10. Cockett, N.E., Jackson, S.P., Shay, T.L., Nielsen, D., Moore, S.S., Steele, M.R., Barendse, W., Green, R.D., Georges, M. (1994). Chromosomal localization of the callipyge gene in sheep (Ovis aries) using bovine DNA markers. Proc. Natl. Acad. Sci. USA 91, 3019–3023.Google Scholar
  11. Crawford, A.M., Montgomery, G.W., Pierson, C.A., Brown, T., Dodds, K.G., Sunden, S.L.F., Henry, H.M., Ede, A.J., Swarbrick, P.A., Berryman, T., Penty, J.M., Hill, D.F. (1994). Sheep linkage mapping: nineteen linkage groups derived from the analysis of paternal half-sib families. Genetics 137, 573–579.Google Scholar
  12. Crawford, A.M., Dodds, K.G., Pierson, C.A., Ede, A.J., Montgomery, G.W., Garmonsway, H.G., Beattie, A.E., Davies, K., Maddox, J.F., Kappes, S.M., Stone, R.T., Nguyen, T.C., Penty, J.M., Lord, E.A., Broom, J.E., Buitkamp, J., Schwaiger, W., Epplen, J.T., Matthew, P., Matthews, M.E., Hulme, D.J., Beh, K.J., McGraw, R.A., Beattie, C.W. (1995). An autosornal genetic linkage map of sheep genome. Genetics, in press.Google Scholar
  13. Dietrich, W., Katz, H., Lincoln, S.E., Shin, H.S., Friedman, J., Dracopoli, N.C., Lander, E.S. (1992). A genetic map of the mouse suitable for typing intraspecific crosses. Genetics 131, 423–447.Google Scholar
  14. Dyer, M.R., Gay, N.J., Powell, S.J., Walker, J.E. (1989). ATP synthase from bovine mitochondria: complementary DNA sequence of the mitochondrial import precursor of the γ-subunit and the genomic sequence of the mature protein. Biochemistry 28, 3670–3680.Google Scholar
  15. Ellegren, H., Chowdhary, B.P., Johansson, M., Marklund, L., Fredholm, M., Gustavsson, I., Andersson, L. (1994). A primary linkage map of the porcine genome reveals a low rate of genetic recombination. Genetics 137, 1089–1100.Google Scholar
  16. GCG (1994). Program Manual for the Wisconsin Genetics Computer Group, page 8, version 8. Genetics Computer Group, 575 Science Drive, Madison, WI.Google Scholar
  17. Georges, M., Dietz, A.B., Mishra, A., Nielsen, D., Sargeant, L.S., Sorensen, A., Steele, M.R., Zhao, X., Leipold, H., Womack, J.E. (1993a). Microsatellite mapping of the gene causing weaver disease in cattle will allow the study of an associated quantitative trait locus. Proc. Natl. Acad. Sci. USA 90, 1058–1062.Google Scholar
  18. Georges, M., Drinkwater, R., King, T., Mishra, A., Moore, S.S., Nielsen, D., Sargeant, L.S., Sorensen, A., Steele, M.R., Zhao, X., Womack, J.E., Hetzel, J. (1993b). Microsatellite mapping of a gene affecting horn development in Bos taurus. Nature Genet. 4, 206–210.Google Scholar
  19. Kaukinen, J., Varvio, S.-L. (1992). Artiodactyl retroposons: association with microsatellites and use in SINEmorph detection by PCR. Nucleic Acids Res. 20, 2955–2958.Google Scholar
  20. Keele, J.W., Wray, J.E., Behrens, D.W., Rohrer, G.A., Sunden, S.L.F., Kappes, S.M., Bishop, M.D., Stone, R.T., Alexander, L.J., Beattie, C.W., (1994). A conceptual database model for genomic research. J. Computat. Biol. 1, 65–76.Google Scholar
  21. Kunkel, T.A. (1985). Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82, 488–492.Google Scholar
  22. Levin, I., Santangelo, L., Cheng, H., Crittenden, L.B., Dodgson, J.B. (1994). An autosomal genetic linkage map of the chicken. J. Hered. 85, 79–85.Google Scholar
  23. Luty, J.A., Guo, Z., Willard, H.F., Ledbetter, D.H., Ledbetter, S., Litt, M. (1990). Five polymorphic microsatellite VNTRs on the human X chromosome. Am. J. Hum. Genet. 46, 776–783.Google Scholar
  24. Montgomery, G.W., Lord, E.A., Penty, J.M., Dodds, K.G., Broad, T.E., Cambridge, L., Sunden, S.L.F., Stone, R.T., Crawford, A.M. (1994). The Booroola fecundity (FecB) gene maps to sheep chromosome 6. Genomics 22, 148–153.Google Scholar
  25. Moore, S.S., Byrne, K., Berger, K.T., Barendse, W., McCarthy, F., Womack, J.E., Hetzel, D.J.S. (1994). Characterization of 65 bovine microsatellites. Mamm. Genome 5, 84–90.Google Scholar
  26. Ostrander, E.A., Jong, P.M., Rine, J., Duyk, G. (1992). Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc. Natl. Acad. Sci. USA 89, 3419–3423.Google Scholar
  27. Pulido, J.C., Duyk, G.M. (1994). Construction of small insert libraries enriched for short tandem repeat sequences by marker selection. In Current Protocols in Human Genetics, N.C. Dracopoli, J.L. Haines, B.R., Korf, D.T. Moir, C.C. Morton, C.E. Seidman, J.G. Seidman, and D.R. Smith, eds. (New York, NY: Current Protocols) Volume 1.Google Scholar
  28. Rogers, J.H. (1985). The origin and evolution of retroposons. Int. Rev. Cytol. 93, 188–279.Google Scholar
  29. Rohrer, G.A., Alexander, L.J., Keele, J.W., Smith, T.P., Beattie, C.W. (1994). A microsatellite linkage map of the porcine genome. Genetics 136, 231–245.Google Scholar
  30. Sambrook, J., Fritsch, E.F., Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, 2nd ed. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press).Google Scholar
  31. Skowronski, J., Plucienniczak, A., Bednarek, A., Jaworski, J. (1984). Bovine 1.709 satellite: recombination hotspots and dispersed repeated sequences. J. Mol. Biol. 177, 399–416.Google Scholar
  32. Vaiman, D., Mercier, D., Moazami-Goudarzi, K., Eggen, A., Ciampolini, R., Lépingle, A., Velmala, R., Kaukinen, J., Varvio, S.L., Martin, P., Levéziel, H., Guérin, G. (1994). A set of 99 cattle microsatellites: characterization, synteny mapping, and polymorphism. Mamm. Genome 5, 288–297.Google Scholar
  33. Watanabe, Y., Tsukada, T., Notake, M., Nakanishi, S., Numa, S. (1982). Structural analysis of repetitive DNA sequences in the bovine corticotropin-β-lipotropin precursor gene region. Nucleic Acids Res. 10, 1459–1469.Google Scholar
  34. Weber, J.L., 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.Google Scholar
  35. Zühlke, C., Riess, O., Schröder, K., Siedlaczck, I., Epplen, J.T., Engel, W., Thies, U. (1993). Expansion of the (CAG), repeat causing Huntington's disease in 352 patients of German origin. Hum. Mol. Genet. 2, 1467–1469.Google Scholar

Copyright information

© Springer-Verlag New York Inc 1995

Authors and Affiliations

  • R. T. Stone
    • 1
  • J. C. Pulido
    • 2
  • G. M. Duyk
    • 2
  • S. M. Kappes
    • 1
  • J. W. Keele
    • 1
  • C. W. Beattie
    • 1
  1. 1.ARS, Roman L. Hruska U.S. Meat Animal Research Center (MARC)U.S. Department of AgricultureClay CenterUSA
  2. 2.Millennium Pharmaceuticals, Inc.CambridgeUSA

Personalised recommendations