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We are constructing high-resolution, chromosomal ‘test’ maps for the entire pig genome using a 12,000-rad WG-RH panel (IMNpRH212,000-rad)to provide a scaffold for the rapid assembly of the porcine genome sequence. Here we present an initial, comparative map of human chromosome (HSA) 11 with pig chromosomes (SSC) 2p and 9p. Two sets of RH mapping vectors were used to construct the RH framework (FW) maps for SSC2p and SSC9p. One set of 590 markers, including 131 microsatellites (MSs), 364 genes/ESTs, and 95 BAC end sequences (BESs) was typed on the IMNpRH212,000-rad panel. A second set of 271 markers (28 MSs, 138 genes/ESTs, and 105 BESs) was typed on the IMpRH7,000-rad panel. The two data sets were merged into a single data-set of 655 markers of which 206 markers were typed on both panels. Two large linkage groups of 72 and 194 markers were assigned to SSC2p, and two linkage groups of 84 and 168 markers to SSC9p at a two-point LOD score of 10. A total of 126 and 114 FW markers were ordered with a likelihood ratio of 1000:1 to the SSC2p and SSC9p RH12,000-rad FW maps, respectively, with an accumulated map distance of 4046.5 cR12,000 and 1355.2 cR7,000 for SSC2p, and 4244.1 cR12,000 and 1802.5 cR7,000 for SSC9p. The kb/cR ratio in the IMNpRH212,000-rad FW maps was 15.8 for SSC2p, and 15.4 for SSC9p, while the ratio in the IMpRH7,000-rad FW maps was 47.1 and 36.3, respectively, or an ∼3.0-fold increase in map resolution in the IMNpRH12,000-rad panel over the IMpRH7,000-rad panel. The integrated IMNpRH12,000-rad andIMpRH7,000-rad maps as well as the genetic and BAC FPC maps provide an inclusive comparative map between SSC2p, SSC9p and HSA11 to close potential gaps between contigs prior to sequencing, and to identify regions where potential problems may arise in sequence assembly. Copyright © 2008 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Bi- and uni-directional chromosome painting (ZOO-FISH) and gene mapping have revealed correspondences between human chromosome (HSA) 17 and porcine chromosome (SSC) 12 harboring economically important quantitative trait loci. In the present study, we have assigned 204 genes localized on HSA17 to SSC12 to generate a comprehensive comparative map between HSA17 and SSC12. Two hundred fifty-five primer pairs were designed using porcine sequences orthologous with human genes. Of the 255 primer pairs, 208 (81.6%) were used to assign the corresponding genes to porcine chromosomes using the INRA-Minnesota 7000-rad porcine × Chinese hamster whole genome radiation hybrid (IMpRH) panel. Two hundred three genes were integrated into the SSC12 IMpRH linkage maps; and one gene, PPARBP, was found to link to THRA1 located in SSC12 but not incorporated into the linkage maps. Three genes (GIT1, SLC25A11, and HT008) were suggested to link to SSC12 markers, and the remaining gene (RPL26) did not link to any genes/expressed sequence tags/markers registered, including those in the present study. A comparison of the gene orders among SSC12, HSA17, and mouse chromosome 11 indicates that intra-chromosomal rearrangements occurred frequently in this ancestral mammalian chromosome during speciation. Copyright © 2006 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]