The typical mammalian major histocompatiblity complex (MHC) contains a cohort of closely linked and highly polymorphic genes and gene families, many of which participate in immunity . These genes are usually organized into a tightly linked complex defined by three regions or classes. Class I molecules are ubiquitously expressed on nucleated cells and function to present endogenous peptides to CD8+ T cells. Class II molecules are expressed exclusively on antigen-presenting cells including macrophages, dendritic cells and B lymphocytes, and present peptides of exogenous origins to CD4+ helper T cells. Loci in the class III region encode a diverse set of proteins, including many cytokines, but not all genes in the class III region are involved in immunity.
The cattle MHC, termed the bovine leukocyte antigen (BoLA), is similar to the MHCs of other species in that genes within BoLA encode proteins that participate in the adaptive and innate immune responses  and play crucial roles in determining host response to pathogens. However, the organizational features of the MHCs of cattle and other ruminants are unique in that class II genes occur in two segments rather than a single segment as observed in other mammalian species (e.g. human , mouse , dog , and horse ). The two segments are located about 20 cM apart and are designated class IIa and class IIb [7–9]. Class IIa is closely associated with the class I and class III regions, while class IIb is positioned closer to the centromere. The unique separation of class II loci, of related function and tightly linked in other species, makes the study of this part of the bovine genome a high priority for understanding the processes involved in coordinated gene regulation, structure and evolution of the MHC.
Linkage analyses (e.g., [10–12]) and physical gene maps [8, 13–16] have defined the general organization of BoLA, but do not provide the detail provided by a sequence-based map. Results from the bovine genome sequencing project have produced a preliminary assembly 2.0 and two subsequent assemblies (Btau_3.1 and 4.0) that differ considerably from each other and from conventional gene maps [16, 17]. The most recent sequence assembly, Btau_4.0, incorporated additional mapping information , fingerprint contig (FPC) maps, and bovine and sheep BAC end sequences  to resolve many of the inconsistencies of the two prior genome assemblies but has not been independently verified.
To compare the accuracies of the 3.1 and 4.0 sequence assemblies of the bovine MHC, we generated a high resolution map of BoLA using a 12,000radradiation hybrid panel . The resolution achievable using this panel exceeds that of the 5,000radpanel  previously used to generate medium-density maps for cattle chromosomes (e.g., [8, 21–25]) due to the increased frequency of radiation-induced chromosomal breaks. This makes the 12,000radpanel suitable for fine mapping genomic regions of interest (e.g., ). The map described here documents assembly errors in the Btau_3.1 assembly and largely validates the revisions contained in the 4.0 assembly. We also compared the RH map of BoLA with the version 36 assembly of HLA to demonstrate overall conservation of gene order between BoLA and HLA and to further validate the hypothesis that a single ancestral inversion accounts for the organizational differences between the bovine and human MHCs. This information is critical for identifying linkage disequilibrium and haplotype structure of the BoLA region and to facilitate accurate comparative genomic studies of BoLA and the MHCs of other species.