Swine Genome Sequencing Consortium (SGSC): A Strategic Roadmap for Sequencing The Pig Genome (original) (raw)

Abstract

The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human–pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome.

Full Text

The Full Text of this article is available as a PDF (112.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson S. I., Lopez-Corrales N. L., Gorick B., Archibald A. L. A large-fragment porcine genomic library resource in a BAC vector. Mamm Genome. 2000 Sep;11(9):811–814. doi: 10.1007/s003350010155. [DOI] [PubMed] [Google Scholar]
  2. Andersson L., Haley C. S., Ellegren H., Knott S. A., Johansson M., Andersson K., Andersson-Eklund L., Edfors-Lilja I., Fredholm M., Hansson I. Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science. 1994 Mar 25;263(5154):1771–1774. doi: 10.1126/science.8134840. [DOI] [PubMed] [Google Scholar]
  3. 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. The PiGMaP consortium linkage map of the pig (Sus scrofa). Mamm Genome. 1995 Mar;6(3):157–175. doi: 10.1007/BF00293008. [DOI] [PubMed] [Google Scholar]
  4. Chowdhary B. P., Raudsepp T., Frönicke L., Scherthan H. Emerging patterns of comparative genome organization in some mammalian species as revealed by Zoo-FISH. Genome Res. 1998 Jun;8(6):577–589. doi: 10.1101/gr.8.6.577. [DOI] [PubMed] [Google Scholar]
  5. Ellegren H., Chowdhary B. P., Johansson M., Marklund L., Fredholm M., Gustavsson I., Andersson L. A primary linkage map of the porcine genome reveals a low rate of genetic recombination. Genetics. 1994 Aug;137(4):1089–1100. doi: 10.1093/genetics/137.4.1089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Engler Friedrich W., Hatfield James, Nelson William, Soderlund Carol A. Locating sequence on FPC maps and selecting a minimal tiling path. Genome Res. 2003 Aug 12;13(9):2152–2163. doi: 10.1101/gr.1068603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fahrenkrug S. C., Rohrer G. A., Freking B. A., Smith T. P., Osoegawa K., Shu C. L., Catanese J. J., de Jong P. J. A porcine BAC library with tenfold genome coverage: a resource for physical and genetic map integration. Mamm Genome. 2001 Jun;12(6):472–474. doi: 10.1007/s003350020015. [DOI] [PubMed] [Google Scholar]
  8. Goureau A., Yerle M., Schmitz A., Riquet J., Milan D., Pinton P., Frelat G., Gellin J. Human and porcine correspondence of chromosome segments using bidirectional chromosome painting. Genomics. 1996 Sep 1;36(2):252–262. doi: 10.1006/geno.1996.0460. [DOI] [PubMed] [Google Scholar]
  9. Gregory Simon G., Sekhon Mandeep, Schein Jacqueline, Zhao Shaying, Osoegawa Kazutoyo, Scott Carol E., Evans Richard S., Burridge Paul W., Cox Tony V., Fox Christopher A. A physical map of the mouse genome. Nature. 2002 Aug 4;418(6899):743–750. doi: 10.1038/nature00957. [DOI] [PubMed] [Google Scholar]
  10. Hamernik Debora L., Lewin Harris A., Schook Lawrence B. Allerton III. Beyond livestock genomics. Anim Biotechnol. 2003 May;14(1):77–82. doi: 10.1081/ABIO-120022137. [DOI] [PubMed] [Google Scholar]
  11. Hawken R. J., Murtaugh J., Flickinger G. H., Yerle M., Robic A., Milan D., Gellin J., Beattie C. W., Schook L. B., Alexander L. J. A first-generation porcine whole-genome radiation hybrid map. Mamm Genome. 1999 Aug;10(8):824–830. doi: 10.1007/s003359901097. [DOI] [PubMed] [Google Scholar]
  12. Malek M., Dekkers J. C., Lee H. K., Baas T. J., Rothschild M. F. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. I. Growth and body composition. Mamm Genome. 2001 Aug;12(8):630–636. doi: 10.1007/s003350020018. [DOI] [PubMed] [Google Scholar]
  13. Maruyama K., Sugano S. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene. 1994 Jan 28;138(1-2):171–174. doi: 10.1016/0378-1119(94)90802-8. [DOI] [PubMed] [Google Scholar]
  14. Milan D., Jeon J. T., Looft C., Amarger V., Robic A., Thelander M., Rogel-Gaillard C., Paul S., Iannuccelli N., Rask L. A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science. 2000 May 19;288(5469):1248–1251. doi: 10.1126/science.288.5469.1248. [DOI] [PubMed] [Google Scholar]
  15. Nezer Carine, Moreau Laurence, Wagenaar Danny, Georges Michel. Results of a whole genome scan targeting QTL for growth and carcass traits in a Piétrain x Large White intercross. Genet Sel Evol. 2002 May-Jun;34(3):371–387. doi: 10.1186/1297-9686-34-3-371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Paszek A. A., Wilkie P. J., Flickinger G. H., Rohrer G. A., Alexander L. J., Beattie C. W., Schook L. B. Interval mapping of growth in divergent swine cross. Mamm Genome. 1999 Feb;10(2):117–122. doi: 10.1007/s003359900955. [DOI] [PubMed] [Google Scholar]
  17. Rettenberger G., Klett C., Zechner U., Kunz J., Vogel W., Hameister H. Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting. Genomics. 1995 Mar 20;26(2):372–378. doi: 10.1016/0888-7543(95)80222-8. [DOI] [PubMed] [Google Scholar]
  18. Rink Anette, Santschi Elizabeth M., Eyer Katie M., Roelofs Benjamin, Hess Markus, Godfrey Myra, Karajusuf Elif K., Yerle Martine, Milan Denis, Beattie Craig W. A first-generation EST RH comparative map of the porcine and human genome. Mamm Genome. 2002 Oct;13(10):578–587. doi: 10.1007/s00335-002-2192-5. [DOI] [PubMed] [Google Scholar]
  19. Rogel-Gaillard C., Bourgeaux N., Billault A., Vaiman M., Chardon P. Construction of a swine BAC library: application to the characterization and mapping of porcine type C endoviral elements. Cytogenet Cell Genet. 1999;85(3-4):205–211. doi: 10.1159/000015294. [DOI] [PubMed] [Google Scholar]
  20. Rohrer G. A., Alexander L. J., Hu Z., Smith T. P., Keele J. W., Beattie C. W. A comprehensive map of the porcine genome. Genome Res. 1996 May;6(5):371–391. doi: 10.1101/gr.6.5.371. [DOI] [PubMed] [Google Scholar]
  21. Rohrer G. A., Ford J. J., Wise T. H., Vallet J. L., Christenson R. K. Identification of quantitative trait loci affecting female reproductive traits in a multigeneration Meishan-White composite swine population. J Anim Sci. 1999 Jun;77(6):1385–1391. doi: 10.2527/1999.7761385x. [DOI] [PubMed] [Google Scholar]
  22. She Xinwei, Jiang Zhaoshi, Clark Royden A., Liu Ge, Cheng Ze, Tuzun Eray, Church Deanna M., Sutton Granger, Halpern Aaron L., Eichler Evan E. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature. 2004 Oct 21;431(7011):927–930. doi: 10.1038/nature03062. [DOI] [PubMed] [Google Scholar]
  23. Thomas J. W., Touchman J. W., Blakesley R. W., Bouffard G. G., Beckstrom-Sternberg S. M., Margulies E. H., Blanchette M., Siepel A. C., Thomas P. J., McDowell J. C. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 2003 Aug 14;424(6950):788–793. doi: 10.1038/nature01858. [DOI] [PubMed] [Google Scholar]
  24. Wilkie P. J., Paszek A. A., Beattie C. W., Alexander L. J., Wheeler M. B., Schook L. B. A genomic scan of porcine reproductive traits reveals possible quantitative trait loci (QTLs) for number of corpora lutea. Mamm Genome. 1999 Jun;10(6):573–578. doi: 10.1007/s003359901047. [DOI] [PubMed] [Google Scholar]
  25. Yerle M., Echard G., Robic A., Mairal A., Dubut-Fontana C., Riquet J., Pinton P., Milan D., Lahbib-Mansais Y., Gellin J. A somatic cell hybrid panel for pig regional gene mapping characterized by molecular cytogenetics. Cytogenet Cell Genet. 1996;73(3):194–202. doi: 10.1159/000134338. [DOI] [PubMed] [Google Scholar]
  26. Yerle M., Pinton P., Delcros C., Arnal N., Milan D., Robic A. Generation and characterization of a 12,000-rad radiation hybrid panel for fine mapping in pig. Cytogenet Genome Res. 2002;97(3-4):219–228. doi: 10.1159/000066616. [DOI] [PubMed] [Google Scholar]