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Comparative mapping in the pig: localization of 214 expressed sequence tags

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Abstract

In total, 214 ESTs (Expressed Sequence Tags) were assigned to the porcine gene map by using somatic cell hybrid mapping, radiation hybrid mapping, and FISH. The ESTs were isolated from a porcine small intestine cDNA library on the basis of significant sequence identity with human annotated genes. In total, 390 primer pairs were designed primarily in the 3′ UTR of the sequences. Overall, 58.6% of the ESTs were successfully mapped by this approach. In total, 191 of the localizations are in agreement with the human comparative map, strongly indicating that these represent true orthologous genes. The remaining 23 ESTs provide new comparative mapping data, which should be considered as preliminary until confirmed by other studies. Our mapping efforts provide a significant contribution to the porcine map as well as to the comparative map for human and pig.

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References

  1. Anderson SI, Lopez-Corrales NL, Gorick B, Archibald AL (2000) A large-fragment porcine genomic library resource in a BAC vector. Mamm Genome 11, 811–814

    Article  PubMed  CAS  Google Scholar 

  2. Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW et al. (2000) An ordered comparative map of the cattle and human genomes. Genome Res 10, 1359–1368

    Article  PubMed  CAS  Google Scholar 

  3. Breen M, Jouquand S, Renier C, Mellersh CS, Hitte C et al. (2001) Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Res 11, 1784–1795

    Article  PubMed  CAS  Google Scholar 

  4. Chevalet C, Gouzy J, SanCristobal-Gaudy M (1997) Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome. Comput Appl Biosci 13, 69–73

    PubMed  CAS  Google Scholar 

  5. Chowdhary BP, Raudsepp T, Honeycutt D, Owens EK, Piumi F et al. (2002) Construction of a 5000(rad) wholegenome radiation hybrid panel in the horse and generation of a comprehensive and comparative map for ECA11. Mamm Genome 13, 89–94

    Article  PubMed  CAS  Google Scholar 

  6. Chowdhary BP, de la Sena C, Harbitz I, Eriksson L, Gustavsson I (1995) FISH on metaphase and interphase chromosomes demonstrates the physical order of the genes for GPI, CRC, and LIPE in pigs. Cytogenet Cell Genet 71, 175–178

    Article  PubMed  CAS  Google Scholar 

  7. Fridolfsson AK, Hori T, Wintern AK, Fredholm M, Yerle M et al. (1997) Expansion of the pig comparative map by expressed sequence tags (EST) mapping. Mamm Genome 8, 907–912

    Article  PubMed  CAS  Google Scholar 

  8. Gustavsson I (1988) Standard karyotype of the domestic pig. Committee for the Standardized Karyotype of the Domestic Pig. Hereditas 109(2), 151–7

    Article  PubMed  CAS  Google Scholar 

  9. Hawken RJ, Murtaugh J, Flickinger GH, Yerle M, Robic A et al. (1999) A first-generation porcine wholegenome radiation hybrid map. Mamm Genome 10, 824–830

    Article  PubMed  CAS  Google Scholar 

  10. Hudson TJ, Church DM, Greenaway S, Nguyen H, Cook A et al. (2001) A radiation hybrid map of the mouse genes. Nat Genet 29, 201–205

    Article  PubMed  CAS  Google Scholar 

  11. Jorgensen CB, Wintero AK, Fredholm M (1997) Mapping of 22 expressed sequence tags isolated from a porcine small intestine cDNA library. Mamm Genome 6, 423–427

    Article  Google Scholar 

  12. Karsenty E, Barillot E, Tosser-Klopp G, Lahbib-Mansais Y, Denis Milan et al. (2003) The Genetpig database: a tool for comparative mapping in pig (Sus scrofa). Nucleic Acids Res 31, 138–141

    Article  PubMed  CAS  Google Scholar 

  13. Kwitek AE, Tonellato PJ, Chen D, Gullings-Handley J, Cheng YS et al. (2001) Automated construction of high-density comparative maps between rat, human, and mouse. Genome Res 11, 1935–1943

    PubMed  CAS  Google Scholar 

  14. Lahbib-Mansais Y, Leroux S, Milan D, Yerle M, Robic A et al. (2000) Comparative mapping between humans and pigs: localization of 58 anchored markers (TOASTs) by use of porcine somatic cell and radiation hybrid panels. Mamm Genome 11, 1098–1106

    Article  PubMed  CAS  Google Scholar 

  15. Lahbib-Mansais Y, Tosser-Klopp G, Leroux S, Cabau C, Karsenty E et al. (2003). Contribution to high-resolution mapping in pigs with 101 Type I markers and progress in comparative map between humans and pigs Mamm Genome 14, 275–288

    Article  PubMed  CAS  Google Scholar 

  16. Meijerink E, Fries R, Vogeli P, Masabanda J, Wigger G et al. (1997) Two alpha (1,2) fucosyltransferase genes on porcine chromosome 6q11 are closely linked to the blood group inhibitor (S) and Escherichia coli F18 receptor (ECF18R) loci. Mamm Genome 8, 736–741

    Article  PubMed  CAS  Google Scholar 

  17. Milan D, Jeon JT, Looft C, Amarger V, Robic A (2000a) A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science 288, 1248–1251

    Article  PubMed  CAS  Google Scholar 

  18. Milan D, Hawken R, Cabau C, Leroux S, Genet C et al. (2000b) IMpRH server: an RH mapping server available on the Web. Bioinformatics 16, 558–559

    Article  PubMed  CAS  Google Scholar 

  19. O’Brien SJ, Womack JE, Lyons LA, Moore KJ, Jenkins NJ et al. (1993) Anchored reference loci for comparative genome mapping in mammals. Nat Genet 3, 103–112

    Article  PubMed  Google Scholar 

  20. Pinton P, Schibler L, Cribiu E, Gellin J, Yerle M (2000) Localization of 113 anchor loci in pigs: improvement of the comparative map for humans, pigs and goats. Mamm Genome 11, 306–315

    Article  PubMed  CAS  Google Scholar 

  21. Ponsuksili S, Wimmers K, Yerle M, Schellander K (2001) Mapping of 93 porcine ESTs preferentially expressed in liver. Mamm Genome 12, 869–872

    Article  PubMed  CAS  Google Scholar 

  22. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132, 365–386

    PubMed  CAS  Google Scholar 

  23. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: A Laboratory Manual. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory)

    Google Scholar 

  24. Sun HS, Cai L, Davis SK, Taylor JF, Doud LK (1997) Comparative linkage mapping of human chromosome 13 and bovine chromosome 12. Genomics 39, 47–54

    Article  PubMed  CAS  Google Scholar 

  25. Walling GA, Archibald AL, Cattermole JA, Downing AC, Finlayson HA et al. (1998) Mapping of quantitative trait loci on porcine chromosome 4. Anim Genet 29, 415–424

    Article  PubMed  CAS  Google Scholar 

  26. Wimmers K, Ponsuksili S, Blaser U, Gellin J, Schellander K (2002) Chromosomal assignments for porcine genes encoding enzymes in hepatic metabolic pathways. Anim Genet 33, 255–263

    Article  PubMed  CAS  Google Scholar 

  27. Winterø AK, Fredholm M, Davies W (1996) Evaluation and characterization of a porcine small intestine cDNA library: analysis of 839 clones. Mamm Genome 7, 509–517

    Article  PubMed  Google Scholar 

  28. Wintere AK, Jorgensen CB, Robic A, Yerle M, Fredholm M (1998) Improvement of the porcine transcription map: localization of 33 genes, of which 24 are orthologous. Mamm Genome 9, 366–372

    Article  Google Scholar 

  29. Yang YP, Rexroad CE 3rd, Schlapfer J, Womack JE (1998) An integrated radiation hybrid map of bovine chromosome 19 and ordered comparative mapping with human chromosome 17. Genomics 48, 93–99

    Article  PubMed  CAS  Google Scholar 

  30. Yerle M, Echard G, Robic A, Mairal A, Dubut-Fontana C et al. (1996) A somatic cell hybrid panel for pig regional gene mapping characterized by molecular cytogenetics. Cytogenet Cell Genet 73, 194–202

    Article  PubMed  CAS  Google Scholar 

  31. Yerle M, Pinton P, Robic A, Alfonso A, Palvadeau Y et al. (1998) Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs. Cytogenet Cell Genet 82, 182–188

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Animal Science and Animal Health, Division of Genetics, The Royal Veterinary and Agricultural University, Groennegaardsvej 3, 1870, Frederiksberg C, Denmark

    Susanna Cirera, Claus B. Jørgensen, Milena Sawera, Terje Raudsepp, Bhanu P. Chowdhary & Merete Fredholm

  2. Department of Veterinary Anatomy and Public Health, Texas A&M University, 77843, College Station, Texas, USA

    Terje Raudsepp & Bhanu P. Chowdhary

Authors
  1. Susanna Cirera
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  2. Claus B. Jørgensen
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  3. Milena Sawera
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  4. Terje Raudsepp
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  5. Bhanu P. Chowdhary
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  6. Merete Fredholm
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Correspondence to Merete Fredholm.

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Cirera, S., Jørgensen, C.B., Sawera, M. et al. Comparative mapping in the pig: localization of 214 expressed sequence tags. Mammalian Genome 14, 405–426 (2003). https://doi.org/10.1007/s00335-002-2242-z

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  • DOI: https://doi.org/10.1007/s00335-002-2242-z

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