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. 2005 Jun;6(4):194–203. doi: 10.1002/cfg.476

A 4 Mb High Resolution BAC Contig on Bovine Chromosome 1q12 and Comparative Analysis With Human Chromosome 21q22

Cord Drögemüller 2,✉, Anne Wöhlke 1, Tosso Leeb 1, Ottmar Distl 1
PMCID: PMC2447486  PMID: 18629192

Abstract

The bovine RPCI-42 BAC library was screened to construct a sequence-ready ~4 Mb single contig of 92 BAC clones on BTA 1q12. The contig covers the region between the genes KRTAP8P1 and CLIC6. This genomic segment in cattle is of special interest as it contains the dominant gene responsible for the hornless or polled phenotype in cattle. The construction of the BAC contig was initiated by screening the bovine BAC library with heterologous cDNA probes derived from 12 human genes of the syntenic region on HSA 21q22. Contig building was facilitated by BAC end sequencing and chromosome walking. During the construction of the contig, 165 BAC end sequences and 109 single-copy STS markers were generated. For comparative mapping of 25 HSA 21q22 genes, genomic PCR primers were designed from bovine EST sequences and the gene-associated STSs mapped on the contig. Furthermore, bovine BAC end sequence comparisons against the human genome sequence revealed significant matches to HSA 21q22 and allowed the in silico mapping of two new genes in cattle. In total, 31 orthologues of human genes located on HSA 21q22 were directly mapped within the bovine BAC contig, of which 16 genes have been cloned and mapped for the first time in cattle. In contrast to the existing comparative bovine–human RH maps of this region, these results provide a better alignment and reveal a completely conserved gene order in this 4 Mb segment between cattle, human and mouse. The mapping of known polled linked BTA 1q12 microsatellite markers allowed the integration of the physical contig map with existing linkage maps of this region and also determined the exact order of these markers for the first time. Our physical map and transcript map may be useful for positional cloning of the putative polled gene in cattle. The nucleotide sequence data reported in this paper have been submitted to EMBL and have been assigned Accession Numbers AJ698510–AJ698674.

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Selected References

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  1. Band M. R., Larson J. H., Rebeiz M., Green C. A., Heyen D. W., Donovan J., Windish R., Steining C., Mahyuddin P., Womack J. E. An ordered comparative map of the cattle and human genomes. Genome Res. 2000 Sep;10(9):1359–1368. doi: 10.1101/gr.145900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chowdhary B. P., Frönicke L., Gustavsson I., Scherthan H. Comparative analysis of the cattle and human genomes: detection of ZOO-FISH and gene mapping-based chromosomal homologies. Mamm Genome. 1996 Apr;7(4):297–302. doi: 10.1007/s003359900086. [DOI] [PubMed] [Google Scholar]
  3. Drögemüller C., Bader A., Wöhlke A., Kuiper H., Leeb T., Distl O. A high-resolution comparative RH map of the proximal part of bovine chromosome 1. Anim Genet. 2002 Aug;33(4):271–279. doi: 10.1046/j.1365-2052.2002.00866.x. [DOI] [PubMed] [Google Scholar]
  4. Georges M., Drinkwater R., King T., Mishra A., Moore S. S., Nielsen D., Sargeant L. S., Sorensen A., Steele M. R., Zhao X. Microsatellite mapping of a gene affecting horn development in Bos taurus. Nat Genet. 1993 Jun;4(2):206–210. doi: 10.1038/ng0693-206. [DOI] [PubMed] [Google Scholar]
  5. Grisart Bernard, Coppieters Wouter, Farnir Frédéric, Karim Latifa, Ford Christine, Berzi Paulette, Cambisano Nadine, Mni Myriam, Reid Suzanne, Simon Patricia. Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res. 2002 Feb;12(2):222–231. doi: 10.1101/gr.224202. [DOI] [PubMed] [Google Scholar]
  6. Grisart Bernard, Farnir Frédéric, Karim Latifa, Cambisano Nadine, Kim Jong-Joo, Kvasz Alex, Mni Myriam, Simon Patricia, Frère Jean-Marie, Coppieters Wouter. Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2398–2403. doi: 10.1073/pnas.0308518100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Harlizius B., Tammen I., Eichler K., Eggen A., Hetzel D. J. New markers on bovine chromosome 1 are closely linked to the polled gene in Simmental and Pinzgauer cattle. Mamm Genome. 1997 Apr;8(4):255–257. doi: 10.1007/s003359900404. [DOI] [PubMed] [Google Scholar]
  8. Hattori M., Fujiyama A., Taylor T. D., Watanabe H., Yada T., Park H. S., Toyoda A., Ishii K., Totoki Y., Choi D. K. The DNA sequence of human chromosome 21. Nature. 2000 May 18;405(6784):311–319. doi: 10.1038/35012518. [DOI] [PubMed] [Google Scholar]
  9. Lander E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860–921. doi: 10.1038/35057062. [DOI] [PubMed] [Google Scholar]
  10. Larkin Denis M., Everts-van der Wind Annelie, Rebeiz Mark, Schweitzer Peter A., Bachman Sharon, Green Cheryl, Wright Chris L., Campos Edhilvia J., Benson Leslie D., Edwards Jennifer. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res. 2003 Aug;13(8):1966–1972. doi: 10.1101/gr.1560203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Laurent P., Elduque C., Hayes H., Saunier K., Eggen A., Levéziel H. Assignment of 60 human ESTs in cattle. Mamm Genome. 2000 Sep;11(9):748–754. doi: 10.1007/s003350010159. [DOI] [PubMed] [Google Scholar]
  12. Martins-Wess Flávia, Leeb Tosso. Increased throughput of BAC/PAC insert size determinations by stacking gels during pulsed-field gel electrophoresis. Biotechniques. 2003 Apr;34(4):718–720. doi: 10.2144/03344bm07. [DOI] [PubMed] [Google Scholar]
  13. Rexroad C. E., 3rd, Owens E. K., Johnson J. S., Womack J. E. A 12,000 rad whole genome radiation hybrid panel for high resolution mapping in cattle: characterization of the centromeric end of chromosome 1. Anim Genet. 2000 Aug;31(4):262–265. doi: 10.1046/j.1365-2052.2000.00641.x. [DOI] [PubMed] [Google Scholar]
  14. Rexroad C. E., Schlapfer J. S., Yang Y., Harlizius B., Womack J. E. A radiation hybrid map of bovine chromosome one. Anim Genet. 1999 Oct;30(5):325–332. doi: 10.1046/j.1365-2052.1999.00504.x. [DOI] [PubMed] [Google Scholar]
  15. Schibler L., Vaiman D., Oustry A., Giraud-Delville C., Cribiu E. P. Comparative gene mapping: a fine-scale survey of chromosome rearrangements between ruminants and humans. Genome Res. 1998 Sep;8(9):901–915. doi: 10.1101/gr.8.9.901. [DOI] [PubMed] [Google Scholar]
  16. Schibler Laurent, Roig Anne, Mahé Marie-Françoise, Save Jean-Claude, Gautier Mathieu, Taourit Sead, Boichard Didier, Eggen André, Cribiu Edmond P. A first generation bovine BAC-based physical map. Genet Sel Evol. 2004 Jan-Feb;36(1):105–122. doi: 10.1186/1297-9686-36-1-105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Schmutz S. M., Marquess F. L., Berryere T. G., Moker J. S. DNA marker-assisted selection of the polled condition in Charolais cattle. Mamm Genome. 1995 Oct;6(10):710–713. doi: 10.1007/BF00354293. [DOI] [PubMed] [Google Scholar]
  18. Smith T. P., Grosse W. M., Freking B. A., Roberts A. J., Stone R. T., Casas E., Wray J. E., White J., Cho J., Fahrenkrug S. C. Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res. 2001 Apr;11(4):626–630. doi: 10.1101/gr.170101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Stone Roger T., Grosse W. Michael, Casas Eduardo, Smith Timothy P. L., Keele John W., Bennett Gary L. Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mamm Genome. 2002 Apr;13(4):211–215. doi: 10.1007/s00335-001-2124-9. [DOI] [PubMed] [Google Scholar]
  20. Takeda Haruko, Sugimoto Yoshikazu. Construction of YAC/BAC contig map for the BTA 6q21 region containing a locus for bovine chondrodysplastic dwarfism. Anim Biotechnol. 2003 May;14(1):51–59. doi: 10.1081/ABIO-120020185. [DOI] [PubMed] [Google Scholar]
  21. Taylor J. F., Eggen A., Aleyasin A., Armitage S. M., Barendse W., Beever J. E., Bishop M. D., Brenneman R. A., Burns B. M., Davis S. K. Report of the first workshop on the genetic map of bovine chromosome 1. Anim Genet. 1998 Jun;29(3):228–235. doi: 10.1111/j.1365-2052.1998.00287.x. [DOI] [PubMed] [Google Scholar]
  22. Threadgill D. S., Kraus J. P., Krawetz S. A., Womack J. E. Evidence for the evolutionary origin of human chromosome 21 from comparative gene mapping in the cow and mouse. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):154–158. doi: 10.1073/pnas.88.1.154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Warren W., Smith T. P., Rexroad C. E., 3rd, Fahrenkrug S. C., Allison T., Shu C. L., Catanese J., de Jong P. J. Construction and characterization of a new bovine bacterial artificial chromosome library with 10 genome-equivalent coverage. Mamm Genome. 2000 Aug;11(8):662–663. doi: 10.1007/s003350010126. [DOI] [PubMed] [Google Scholar]
  24. Winter Andreas, Alzinger Ariane, Fries Ruedi. Assessment of the gene content of the chromosomal regions flanking bovine DGAT1. Genomics. 2004 Jan;83(1):172–180. doi: 10.1016/s0888-7543(03)00238-6. [DOI] [PubMed] [Google Scholar]
  25. Winter Andreas, Krämer Wolfgang, Werner Fabian A. O., Kollers Sonja, Kata Srinivas, Durstewitz Gregor, Buitkamp Johannes, Womack James E., Thaller Georg, Fries Ruedi. Association of a lysine-232/alanine polymorphism in a bovine gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content. Proc Natl Acad Sci U S A. 2002 Jun 20;99(14):9300–9305. doi: 10.1073/pnas.142293799. [DOI] [PMC free article] [PubMed] [Google Scholar]

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