Towards a high resolution porcine RH map for sequence assembly

W.S. Liu, A. Rink, K. Eyer, H. Yasue, B. Roelofs, H. Hiraiwa, T. Shimogiri, S.N. Meyers, E. Landrito, J. Ekstrand, M. Treat, M. Yerle, D. Milan, J.E. Beever, L.B. Schook, C.W. Beattie
Plant and Animal Genome XIV Conference, January 9-13, 2006, San Diego, CA


We are integrating the framework markers of the IMpRH.7000-rad map with a new IMNpRH2.12,000-rad WG-RH panel to order over 12,000 markers [ESTs/genes, microsatellites and sufficient BAC-end sequences (BESs)] to provide a high resolution comprehensive map of the porcine genome. The map is intended to m:I as a "scaffold"  for the rapid assembly of the porcine genome sequence. To date, we have assigned a total of -4630  markers,  including -1800 MSs and 2830 genes/ESTs, on the IMNpRH2 panel using the CarthaGene  software to construe our IMNpRH212.000 "scaffold" and high resolution porcine:human comparative map. We are currently genotyping -1600 BES mapped on the IMpRH.7000-rad map (Meym et al. 2005) on the IMNpRH2.12,000-rad panel to integrate the IMpRH2.12,000-rad map with tho BAC fingerprint contig (FPC) maps (, that  potential gaps  between contigs can be closed prior to sequencing and assembly. An initial, comparative map for pig chromosome (SSC) 2p and 9p and human chromosome (HSA)11 has been developed with  250 genes, 115 ESTs, 25 MSs and 60 BESs (450 total markers). We continue designing primer pairs from pig EST database (  as well as MS and gene/ES I primers from literature to improve the resolution of the IMNpRH2.12,000-rad map. We expect -1600 BESs to be typed on the IMNpRH2.12,000-rad panel by early 2006, to close current gaps in the BAC FPC maps, and an integrated, comparative map available by 2007 to aid in sequence assembly.

This work was supported by USDA CSREES (No. 2004-35205-14244).