Abstract:
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. A total of 590 markers, including 131 microsatellites (MS), 364 genes/ESTs, and 95 BESs were typed on the IMNpRH212,000-rad RH panel, 273 of which were previously typed on the IMpRH7000rad panel. By taking advantage of the data set merging function of the CarthaGene software, we were able to rapidly and accurately construct a highresolution framework map using the order of the common markers on both maps. This provided a platform to integrate the IMNpRH12,000-rad map with the IMpRH7000-rad map as well as the BAC fingerprint contig (FPC) maps (http://www.sanger.ac.uk/Projects/S_scrofa/), and rapidly close potential gaps between contigs prior to sequencing and assembly. At a LOD score of 10, two large linkage groups of 72 and 194 markers map to SSC2p, and two linkage groups of 84 and 168 markers map to SSC9p. Except for MS loci, approximately 91% of the typed markers have a homologous sequence (at a cutoff E-value of 1.0e-25) on HSA11 (Build 35). The comparative map indicated that although HSA11 is entirely conserved with SSC2p and 9p, significant macro-rearrangements and micro-rearrangements are present within individual synteny blocks.
This work was supported by USDA CSREES (No. 2004-35205-14244).