Differences between the radiation hydrid and genetic linkage maps of bovine Chromosome 5 resolved with a quasi-phylogenetic method of analysis

Two major differences were detected in gene order between the radiation hyb rid map and the genetic linkage map of bovine Chromosome (Chr) 5, and these were resolved by analyzing the raw radiation hybrid data by a quasi-phylog enetic method. Seventeen loci were typed on the new cattle whole genome rad iation hybrid panel. Most of these loci are framework loci and include AGLA 293, BM315, BM6026, BP1, BZRP, CD9, CSSM22, CSSM34, CYP2D@, ETH2, ETH10, ET H152, IGF1, LALBA, SLC2A3, SYT1, and TP11. BP1 was found to be closer to th e centromere than either BM6026 or SYT1 with two standard computer software packages for analyzing radiation hybrid panel data. This is inconsistent w ith any of the genetic linkage maps as well as their consensus. CYP2D@ was placed between ETH2 and BZRP, and this is also inconsistent with the geneti c linkage maps, since CYP2D@ should be the most telomeric of the loci teste d in this study. Resolution was reached by analyzing the raw radiation hy b rid data for clones that bind some but not all of the loci, and the binding pattern was more consistent with the linkage maps and less consistent with the software-generated radiation hybrid map. The comparative mapping data confirm the relative inversion of gene order of SYT1 compared with humans a nd mice. A nonpolymorphic fragment for CD9 indicates the conservation of ge ne order for three loci located on human Chr 12p. The genes of bovine Chr 5 conserved on human Chr 12p are located separately from the genes conserved on human Chr 12q. It is recommended that the raw data for radiation hybrid maps be made publicly available so that conflicts in gene order can be eva luated explicity.