High-resolution comparative mapping of pig Chromosome 4, emphasizing the FAT1 region Maria Moller, 1 * Frida Berg, 1 Juliette Riquet, 2 Daniel Pomp, 3 Alan Archibald, 4 Susan Anderson, 4 Katia Feve, 2 Yuandan Zhang, 5 Max Rothschild, 5 Denis Milan, 2 Leif Andersson, 1,6 Christopher K. Tuggle 5 1 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, 75124 Uppsala, Sweden 2 Laboratoire de Ge ´ne ´tique Cellulaire, Institut National de la Recherche Agronomique (INRA), BP 27, 31326 Castanet-Tolosan, France 3 Department of Animal Science, University of Nebraska, Lincoln, Nebraska 68583, USA 4 Department of Genomics and Bioinformatics, Roslin Institute, Midlothian EH25 9PS, Scotland, UK 5 Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 225 Kildee Hall, Ames, Iowa 50011, USA 6 Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, 75124 Uppsala, Sweden Received: 6 January 2004 / Accepted: 30 April 2004 Abstract The first quantitative trait locus (QTL) in pigs, FAT1, was found on Chromosome 4 (SSC4) using a Wild Boar intercross. Further mapping has refined the FAT1 QTL to a region with conserved synteny to both human Chromosomes 1 and 8. To both improve the comparative map of the entire SSC4 and to de- fine the specific human chromosome region with conserved synteny to FAT1, we have now mapped 103 loci to pig Chromosome 4 using a combination of radiation hybrid and linkage mapping. The phys- ical data and linkage analysis results are in very good agreement. Comparative analysis revealed that gene order is very well conserved across SSC4 compared to both HSA1 and HSA8. The breakpoint in con- served synteny was refined to an area of about 23 cR on the q arm of SSC4 corresponding to a genetic distance of less than 0.5 cM. Localizations of the centromeres do not seem to have been conserved between the two species. No remnants of the HSA1 centromere were detected on the corresponding re- gion on SSC4 and traces from the centromeric region of SSC4 cannot clearly be revealed on the homolo- gous region on HSA8. This refined SSC4 map and the comparative analysis will be a great aid in the search for the genes underlying the FAT1 locus. Comparative genome analysis is a powerful tool in the postgenomic era where a wealth of information has been generated for many eukaryotic genomes. Although significant effort and resources have been dedicated to farm animal research, their genome maps have not reached the high resolution availa- ble for the human and mouse genome maps (International Human Genome Sequencing Con- sortium 2001; Waterston et al. 2002). Analysis of the genomes of farm animals, such as the search for genes underlying quantitative trait loci (QTL), can therefore greatly benefit from extraction of information from homologous regions of other ge- nomes. Comparative genome analysis can also shed light on genome evolution and genome structure. Porcine Chromosome 4 (SSC4) harbors QTL af- fecting growth, carcass traits, and fat deposition. The first QTL discovered on SSC4, denoted FAT1, was identified in a European Wild Boar · Large White intercross (Andersson et al. 1994) and has subse- quently been confirmed in further backcross genera- tions (Marklund et al. 1999; F. Berg et al. unpublished). Other intercrosses where QTL on SSC4q have been identified include Meishan · Large White (Walling et al. 2000; Bidanel et al. 2001) and Iberian Landrace · Large White (Perez–Encisco et al. 2000). Evidence for *Present address: Experimental Medicine Unit, Swansea Clinical School, University of Wales, Swansea, Singleton Park, Swansea, SA2 8PP, Wales Correspondence to: C.K. Tuggle; E-mail: cktuggle@iastate.edu DOI: 10.1007/s00335-004-2366-4  Volume 15, 717–731 (2004)  Ó Springer Science+Business Media, Inc. 2004 717