High-resolution comprehensive radiation hybrid maps of the porcine chromosomes 2p and 9p compared with the human chromosome 11

We are constructing high-resolution, chromosomal ‘test’ maps for the entire pig genome using a 12,000-rad WG-RH panel (IMNpRH2 12,000-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 IMNpRH2 12,000-rad panel. A second set of 271 markers (28 MSs, 138 genes/ESTs, and 105 BESs) was typed on the IMpRH 7,000-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 RH 12,000-rad FW maps, respectively, with an accumulated map distance of 4046.5 cR 12,000 and 1355.2 cR 7,000 for SSC2p, and 4244.1 cR 12,000 and 1802.5 cR 7,000 for SSC9p. The kb/cR ratio in the IMNpRH2 12,000-rad FW maps was 15.8 for SSC2p, and 15.4 for SSC9p, while the ratio in the IMpRH 7,000-rad FW maps was 47.1 and 36.3, respectively, or an ∼3.0-fold increase in map resolution in the IMNpRH 12,000-rad panel over the IMpRH 7,000-rad panel. The integrated IMNpRH 12,000-rad andIMpRH 7,000-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.