We typed over 10,000 markers on the IMNpRH212,000rad panel to obtain 10,030 mapping vectors, including 2635 MSs, 2530 ESTs, 2759 genes, 2043 BESs and 63 SNPs We merged these with the ~ 50% of these markers typed on the IMpRH7000rad panel to construct parallel framework maps at LOD >= 10 and integrate the porcine genetic-RH-FPC-sequence maps and improve the pig-human comparative map. Maps for SSC2, 4, 9, 10, 11, 12, and 18, have been constructed at an average map resolution of ~15 Kb/cR12,000rad or ~250 Kb/marker. The remaining chromosomes will be completed by year-end. Although the order of the majority of MSs on the genetic and RH maps was identical, map discrepancies were observed in several chromosomal regions. This was also true when we compared the RH and FPC maps, particularly for BESs located at/near the end of FPC contigs. We also identified potentially misordered BACs in the FPC maps that may result from segmental duplications in the pig genome. Alignment of the RH map with the draft genome sequence (Sscrofa9) also identified additional regions where the two maps differ from each other, that were further analyzed using the pig-human comparative map. In addition, we are incorporating additional transcriptomic data generated by RNA deep sequencing (Illumina GA2) with the RH and sequence maps. The resulting high-resolution physical maps should be useful in improving the assembly of the pig genome sequence and comparative maps.