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Microsatellites and associated repetitive elements in the sheep genome

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Abstract

To determine the frequency and clustering of a variety of simple di-and trinucleotide repeats, an Artiodactyl short interspersed element (SINE), an ovine satellite repeat, and a human Alu 1 repeat were used to screen a random selection of cosmids containing inserts of ovine genomic DNA. In total, 197 individual cosmids were digested with EcoRI and the fragments separated on 0.7% agarose gels. Southern blots of these gels were then sequentially probed with (AC)7, (CT)9, and (CAC)6 oligonucleotides, and the repeats described above. The frequency at which (AC)1, (CT)n, and (CAC)n repeats were found in the cosmids indicated that they occurred at average intervals of 65 kb, 367 kb, and 213 kb respectively within the ovine genome. The Artiodactyl SINE was the most common, occurring at an average interval of 20 kb. No human Alu 1 sequences were detected. There was a significant positive association between the (AC)n and the Artiodactyl SINE. This association is quite strong as there was significant clustering of the two repeats both within cosmids and also within the EcoRI fragments of the digested genomic fragments. With the exception of the sheep satellite sequence, which occurs in tandem arrays, none of the other repeats showed significant clustering within the 41-kb (average size) cosmid inserts. The first 25 ovine microsatellites we characterized had an average polymorphic information content (PIC) of 0.65. The different microsatellite types, containing either perfect, imperfect, or compound repeats, had similar average PICs of 0.64, 0.65, and 0.66 respectively. There was a weak regression relationship (R2(adj)%=21.9) between the length of the longest uninterrupted dinucleotide repeat in the largest allele and the PIC of the microsatellite.

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References

  • Botstein, 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.

    Google Scholar 

  • Buchanan, F.C. and Crawford, A.M. (1992a). Ovine dinucleotide repeat polymorphism at the MAF33 locus. Anim. Genet. 23, 186.

    Google Scholar 

  • Buchanan, F.C. and Crawford, A.M. (1992b). Ovine dinucleotide repeat polymorphism at the MAF70 locus. Anim. Genet. 23, 185.

    Google Scholar 

  • Buchanan, F.C. and Crawford A.M. (1992c). Ovine dinucleotide repeat at the MAF209 locus. Anim. Genet. 23, 183.

    Google Scholar 

  • Buchanan, F.C. and Crawford, A.M. (1992d). Ovine dinucleotide repeat polymorphism at the MAF214 locus. Anim. Genet. 23, 394.

    Google Scholar 

  • Buchanan, F.C. and Crawford, A.M. (1992e). Ovine dinucleotide repeat polymorphism at the FCB4 locus. Anim. Genet. 23, 393.

    Google Scholar 

  • Buchanan, F.C. and Crawford, A.M. (1993a) Ovine dinucleotide repeat polymorphism at the C4 locus. Anim. Genet., in press.

  • Buchanan, F.C. and Crawford, A.M. (1993b) Ovine microsatellites at the OarFCB11, OarFCB128, OarFCB193, OarFCB266 and OarFCB304 loci. Anim. Genet. in press.

  • Buchanan, F.C., Swarbrick, P.A. and Crawford, A.M. (1991a). Ovine dinucleotide repeat polymorphism at the MAF4 locus. Anim. Genet. 22, 373–374.

    Google Scholar 

  • Buchanan, F.C., Swarbrick, P.A., and Crawford, A.M. (1991b). Ovine dinucleotide repeat polymorphism at the MAF48 locus. Anim. Genet. 22, 379–380.

    Google Scholar 

  • Buchanan, F.C., Swarbrick, P.A., and Crawford, A.M. (1992). Ovine dinucleotide repeat polymorphism at the MAF65 locus. Anim. Genet. 23, 85.

    Google Scholar 

  • Buchanan, F.C., Galloway, S.M., and Crawford, A.M. (1993). Ovine dinucleotide repeat polymorphism at the C48 locus. Anim. Genet., in press.

  • Chapman, H.M. and Bruere, A.N. (1977). Chromosome morphology during meiosis of normal and Robertsonian translocationcarrying rams (Ovis aries). Can. J. Genet. Cytol. 19, 93–102.

    Google Scholar 

  • Crawford, A.M., Buchanan, F.C., and Swarbrick, P.A. (1990). Ovine dinucleotide repeat polymorphism at the MAF18 locus. Anim. Genet. 21, 433–434.

    Google Scholar 

  • Crawford, A.M., Buchanan, F.C., Swarbrick, P.A. (1991). Ovine dinucleotide repeat polymorphism at the MAF92 locus. Anim. Genet. 22, 371–372.

    Google Scholar 

  • Daniels, G.R. and Deininger, P.L. (1985). Repeat sequence families derived from mammalian tRNA genes. Nature 317, 819–822.

    Google Scholar 

  • DiLella, A.G. and Woo, S.L.C. (1987). Cloning large segments of genomic DNA using cosmid vectors. Methods Enzymol. 152, 199–212.

    Google Scholar 

  • Gross, D.S. and Garrard, W.T. (1986). The ubiquitous potential z-forming sequence of eucaryotes (dT-dG)n • (dC-dA)n is not detectable in the genomes of eubacteria, archaebacteria or mitochondria. Mol. Cell. Biol. 6, 3010–3013.

    Google Scholar 

  • Grosveld, F.G., Lund, T., Murray, E.L., Mellor, A.L., Dahl, H.H.M., and Flavell, R.A. (1982). The construction of cosmid libraries which can be used to transform eukaryotic cells. Nucleic Acids Res. 10, 6715–6732.

    Google Scholar 

  • Hamada, H., Petrino, M.G., and Kakunaga, T. (1982). A novel repeated element with z-DNA-forming potential is widely found in evolutionary diverse eukaryotic genomes. Proc. Natl. Acad. Sci. USA 79, 6465–6469.

    Google Scholar 

  • Hamada, H., Seidman, M., Howard, B.H., and Gorman, C.M. (1984). Enhanced gene expression by the poly(dT-dG) · poly(dC-dA) sequence. Mol. Cell. Biol. 4, 2622–2630.

    Google Scholar 

  • Jelinek, W.R., Toomey, T.P., Leinwand, L., Duncan, C.H., Biro, P.A., Choudary, P.V., Weissman, S.M., Rubin, C.M., Houck, C.M., Deininger, P.L., and Schmid, C.W. (1980) Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc. Natl. Acad. Sci. USA 77, 1398–1402.

    Google Scholar 

  • Kaukinen, J. and Varvio, S-L. (1992). Artiodactyl retroposons: association with microsatellites and use in SINEmorph detection by PCR. Nucleic Acids Res. 20, 2955–2958.

    Google Scholar 

  • 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.

    Google Scholar 

  • Luty, J.A., Guo, Z., Willard, H.F., Ledbetter, D.H., Ledbetter, S., and Litt, M. (1990). Five polymorphic microsatellite VNTRs on the human X chromosome. Am. J. Hum. Genet. 46, 776–783.

    Google Scholar 

  • Matsutani, A., Janssen, R., Donis-Keller, H., and Permutt, M.A. (1992). A polymorphic (CA)n repeat element maps the human glucokinase gene (GCK) to chromosome 7p. Genomics 12, 319–325.

    Google Scholar 

  • Montgomery, G.W. and Sise, J.A. (1990). Extraction of DNA from sheep white blood cells. N. Z. J. Agric. Res. 33, 437–441.

    Google Scholar 

  • Moore, S.S., Sargeant, L.L., King, T.J., Mattick, J.S., Georges, M., and Hetzel, D.J.S. (1991). The conservation of dinucleotide microsatellites among mammalian genomes allows the use of heterologous PCR primer pairs in closely related species. Genomics, 10, 654–660

    Google Scholar 

  • Morral, N., Nunes, V., Casals, T., and Estivill, X. (1991). CA/GT microsatellite alleles within the cystic fibrosis transmembrane conductance regulator (CFTR) gene are not generated by unequal crossing over. Genomics 10, 692–698.

    Google Scholar 

  • Murphy, K.E. and Stringer, J.R. (1986). RecA independent recombination of poly[d(GT)-d(CA)] in pBr322. Nucleic Acids Res. 14, 7325–7340.

    Google Scholar 

  • Naylor, L.H. and Clark, E.M. (1990). d(TG)n · d(CA)n sequences upstream of the rat prolactin gene from Z-DNA and inhibit gene transcription. Nucleic Acids Res. 18, 1595–1601.

    Google Scholar 

  • Nordheim, A. and Rich, A. (1983). The sequence (dC-dA)n · (dG-dT)n forms left-handed z-DNA in negatively supercoiled plasmids. Proc. Natl. Acad. Sci. USA 80, 1821–1825.

    Google Scholar 

  • Novak, U. (1984). Structure and properties of a highly repetitive DNA sequence in sheep. Nucleic Acids Res. 12, 2343–2350.

    Google Scholar 

  • O'Brien, S.J. (1990). Genetic Maps: Book 4 Nonhuman Vertebrates. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press).

    Google Scholar 

  • Pardue, M.L., Lowenhaupt, K., Rich, A., and Nordheim, A. (1987). (dC-dA)n · (dG-dT)n sequences have evolutionarily conserved chromosomal locations in Drosophila with implications for roles in chromosome structure and function. EMBO 6, 1781–1789.

    Google Scholar 

  • Reisner, A.H. and Bucholtz, C.A. (1983). Apparent relatedness of the main component of ovine 1.714 satellite DNA to bovine 1.715 satellite DNA. EMBO J. 2, 1145–1149.

    Google Scholar 

  • Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, 2nd ed. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press).

    Google Scholar 

  • Sinnet, D., Deragon, J-M., Simard, L.R., and Labuda, D. (1990). Alumorphs-human DNA polymorphisms detected by polymerase chain reaction using Alu-specific primers. Genomics 7, 331–334.

    Google Scholar 

  • Smeets, H.J.M., Brunner, H.G., Ropers, H-H., and Wieringa, B. (1989). Use of variable simple sequence motifs as genetic markers: application to study of myotonic dystrophys. Hum. Genet. 83, 245–251.

    Google Scholar 

  • Stallings, R.L., Ford, A.F., Nelson, D., Torney, D.C., Hildebrand, C.E., and Moyzis, R.K. (1991). Evolution and distribution of (GT)n repetitive sequences in mammalian genomes. Genomics 10, 807–815.

    Google Scholar 

  • Swarbrick, P.A., and Crawford, A.M. (1992). Ovine dinucleotide repeat polymorphism at the MAF109 locus. Anim. Genet. 23, 84.

    Google Scholar 

  • Swarbrick, P.A., Buchanan, F.C., and Crawford, A.M. (1990). Ovine dinucleotide repeat polymorphism at the MAF23 locus. Anim. Genet. 21, 191.

    Google Scholar 

  • Swarbrick, P.A., Buchanan, F.C., and Crawford, A.M. (1991a). Ovine dinucleotide repeat polymorphism at the MAF35 locus. Anim. Genet. 22, 369–370.

    Google Scholar 

  • Swarbrick, P.A., Buchanan, F.C., and Crawford, A.M. (1991b). Ovine dinucleotide repeat polymorphism at the MAF36 locus. Anim. Genet. 22, 377–378.

    Google Scholar 

  • Swarbrick, P.A., Buchanan, F.C., and Crawford, A.M. (1991c). Ovine dinucleotide repeat polymorphism at the MAF64 locus. Anim. Genet. 22, 375–376.

    Google Scholar 

  • Swarbrick, P.A., Schmack, A.E., and Crawford, A.M. (1992a). MAF45, a highly polymorphic marker for the pseudoautosomal region of the sheep genome, is not linked to the FecX' (Inverdale) gene. Genomics 13, 849–851.

    Google Scholar 

  • Swarbrick, P.A., Dietz, A.B., Womack, J.E., and Crawford, A.M. (1992b). Ovine and bovine dinucleotide repeat polymorphism at the MAF46 locus. Anim. Genet. 23, 182.

    Google Scholar 

  • Swarbrick, P.A., Howes, J., and Crawford, A.M. (1992c). Ovine dinucleotide repeat polymorphism at the MAF50 locus. Anim. Genet. 23, 187.

    Google Scholar 

  • Tautz, D. (1989). Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17, 6463–6471.

    Google Scholar 

  • Watanabe, Y., Tsukada, T., Notake, M., Nakanishi, S., and Numa, S. (1982). Structural analysis of repetitive DNA sequences in the bovine corticotropin-β-lipotrophin precursor region. Nucleic Acids Res. 10, 1459–1469.

    Google Scholar 

  • Weber, J.L. (1990). Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms. Genomics 7, 523–530.

    Google Scholar 

  • 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.

    Google Scholar 

  • Zuliani, G. and Hobbs, H.H. (1990). A high frequency of length polymorphisms in repeated sequences adjacent to Alu sequences. Am. J. Hum. Genet. 46, 963–969.

    Google Scholar 

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Authors and Affiliations

  1. AgResearch Molecular Biology Unit, Department of Biochemistry, University of Otago, Dunedin, New Zealand

    Fiona C. Buchanan, Sue M. Galloway & Allan M. Crawford

  2. Centre for Gene Research, University of Otago, Dunedin, New Zealand

    Fiona C. Buchanan, Sue M. Galloway & Allan M. Crawford

  3. AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, New Zealand

    Roger P. Littlejohn

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  1. Fiona C. Buchanan
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Buchanan, F.C., Littlejohn, R.P., Galloway, S.M. et al. Microsatellites and associated repetitive elements in the sheep genome. Mammalian Genome 4, 258–264 (1993). https://doi.org/10.1007/BF00417432

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