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.
Similar content being viewed by others
References
Akaboshi, E. (1985). Cloning of the human myoglobin gene. Gene 33, 241–249.
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.
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.
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.
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.
Beckman, J., Weber, J.L., (1992). Survey of human and rat microsatellites. Genomics 12, 627–631.
Benson, D., Lipman, D.J., Ostell, J. (1993). GenBank. Nucleic Acids Res. 21, 2963–2965.
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.
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.
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.
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.
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.
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.
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.
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.
GCG (1994). Program Manual for the Wisconsin Genetics Computer Group, page 8, version 8. Genetics Computer Group, 575 Science Drive, Madison, WI.
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.
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.
Kaukinen, J., Varvio, S.-L. (1992). Artiodactyl retroposons: association with microsatellites and use in SINEmorph detection by PCR. Nucleic Acids Res. 20, 2955–2958.
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.
Kunkel, T.A. (1985). Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82, 488–492.
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.
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.
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.
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.
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.
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.
Rogers, J.H. (1985). The origin and evolution of retroposons. Int. Rev. Cytol. 93, 188–279.
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.
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).
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.
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.
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.
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.
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.
Author information
Authors and Affiliations
Additional information
The nucleotide sequence data reported in this paper have been submitted to GenBank and have been assigned the accession numbers U25689 and U25690.
Rights and permissions
About this article
Cite this article
Stone, R.T., Pulido, J.C., Duyk, G.M. et al. A small-insert bovine genomic library highly enriched for microsatellite repeat sequences. Mammalian Genome 6, 714–724 (1995). https://doi.org/10.1007/BF00354294
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00354294