BACKGROUND
the typical mammalian major histocompatiblity complex  contains a cohort of closely linked and highly polymorphic genes and gene families, many of which participate in immunity  <cit> .
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 , is similar to the mhcs of other species in that genes within bola encode proteins that participate in the adaptive and innate immune responses  <cit>  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 .
the two segments are located about  <dig> cm apart and are designated class iia and class iib  <cit> .
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  and physical gene maps  <cit>  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  <dig>  and two subsequent assemblies  that differ considerably from each other and from conventional gene maps  <cit> .
the most recent sequence assembly, btau_ <dig> , incorporated additional mapping information  <cit> , fingerprint contig  maps, and bovine and sheep bac end sequences  <cit>  to resolve many of the inconsistencies of the two prior genome assemblies but has not been independently verified.
to compare the accuracies of the  <dig>  and  <dig>  sequence assemblies of the bovine mhc, we generated a high resolution map of bola using a  <dig> rad radiation hybrid panel  <cit> .
the resolution achievable using this panel exceeds that of the  <dig> rad panel  <cit>  previously used to generate medium-density maps for cattle chromosomes  due to the increased frequency of radiation-induced chromosomal breaks.
this makes the  <dig> rad panel suitable for fine mapping genomic regions of interest .
the map described here documents assembly errors in the btau_ <dig>  assembly and largely validates the revisions contained in the  <dig>  assembly.
we also compared the rh map of bola with the version  <dig> 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.
RESULTS
marker development
seventy-seven of the original  <dig> primer pairs were used for mapping.
fourteen of the  <dig> markers were located in the class i and class i extended regions of bola,  <dig> were located within class iia or iia extended regions,  <dig> were located within class iib, and  <dig> were located within class iii .
of the three markers not retained for mapping, one marker  was dropped from analysis due to typing ambiguities and two markers  could not be assigned to specific locations and instead were binned within the iia/iii/i group.
thirty-one of the  <dig> clones in the rh panel consistently gave ambiguous genotyping results  and were excluded from computation of the rh maps.
rh mapping
analysis of the distribution of sts markers across the rh panel resulted in the localization of markers into two groups, corresponding to the bola iib region and the bola iia, iii, and i region.
the iib group of  <dig> markers was distributed along  <dig>  cr, for a resolution of  <dig> marker/ <dig>  cr.
the iia/iii/i group of  <dig> markers was distributed over  <dig>  cr at a resolution of  <dig> marker/ <dig>  cr.
resolution in kb was also determined by dividing by the size in base pairs of each region in btau_ <dig>  by the number of markers with unique vectors .
using this method, resolution of the rh group for the iib region of bola is approximately one marker every ~ <dig> kb and resolution for the iia/iii/i region of bola is one marker every ~ <dig> kb.
twelve  of the markers in the iib group and  <dig>  of the markers in the iia/iii/i group gave unique rh vectors and were designated as mle-consensus  and ordered with highest confidence.
positions, lod scores, and frame/placed status of individual markers are presented in additional file  <dig>  retention frequencies of markers in the iib group ranged from  <dig> % to  <dig> %, with an average value of  <dig> %.
for the iia/iii/i group, retention frequencies ranged from  <dig> % to  <dig> %, with an average value of  <dig> %.
rh maps developed for the two bola regions are presented in figure  <dig>
comparative maps
the physical order of all markers on the rh map was compared with both the btau_ <dig>  and  <dig>  assemblies and the ncbi <dig> assembly of the human genome sequence.
results of these comparisons are shown in figures  <dig> and  <dig> respectively.
comparison of rh map and btau_ <dig>  assembly
the organization of the four scaffolds and the  <dig> markers of the iib region are essentially the same between the rh map and btau_ <dig>  assembly.
exceptions are the inverted order of markers  <dig>  and  <dig>  and markers  <dig> ,  <dig> , and  <dig>  in the btau_ <dig>  assembly relative to the rh map.
all markers from the extended class iia region, with the exceptions of  <dig> ,  <dig> , and  <dig> , are placed more distally in the  <dig>  assembly than in the rh map but with similar marker order.
marker order within the class iia region is also in overall agreement between the rh map and  <dig>  assembly with the single exception that class iia markers  <dig>  and  <dig> , which map together on the rh map, are separated in the  <dig>  assembly: marker  <dig>  is placed within a group that includes class iii markers and has likely been misplaced in the  <dig>  assembly.
both scaffold and marker orders in this group are inconsistent with those identified by the rh map.
the order of  <dig> ,  <dig> , and all scaffold  <dig> class iii markers are in agreement in both the btau_ <dig>  assembly and the rh map, although the placements differ, with the rh map assigning these markers to a more distal location on chromosome  <dig>  finally, overall consistency was observed in marker orders within class i scaffolds  <dig>   <dig>  and 64; nevertheless, scaffold  <dig> appears to be erroneously placed more proximal to scaffold  <dig> in the btau_ <dig>  assembly.
two markers,  <dig>  and  <dig> , were not assigned to bta <dig> in the btau_ <dig>  assembly although they are clearly present within bola based on analysis of the rh mapping data.
marker  <dig>  is chromosomally unassigned within the  <dig>  assembly, although analysis using ensembl blast  <cit>  returned an alignment with bta <dig> at position  <dig> kb – clearly distal to the other markers of bola iia.
in contrast, the rh map shows  <dig>  localized to the expected location near other markers from scaffold  <dig>  the rh map has placed marker  <dig>  at a predictable location near other markers from scaffold  <dig>  while blast comparison against the btau_ <dig>  assembly produced no significant alignment to  <dig> .
comparison of rh map and btau_ <dig>  assembly
the iib region of bola shows good agreement between the btau_ <dig>  assembly and rh map, with the exception of an inverted segment encompassing three markers:  <dig> ,  <dig> , and  <dig> .
this same inverted order was also observed in the comparison between btau_ <dig>  and the rh map.
analysis of the positions of these three markers in an independent, finished assembly of bola iib  <cit>  supported the btau_ <dig>  gene order and indicates that the discordancy is due to the imprecision of the  <dig> rad rh panel to resolve the order of these closely linked markers.
marker order in bola iib did not change from btau_ <dig>  to btau_ <dig> , but marker locations shifted ~ <dig> kb telomeric on the chromosome in version  <dig>  for all iib markers except  <dig>  and  <dig> .
class iia, iii and i marker order is very similar across the btau_ <dig>  assembly of bola and rh map as is the order of markers in the extended iia and i regions .
eleven markers located in two regions show some minor discordancy in gene order between the two maps.
these include markers  <dig> ,  <dig> ,  <dig> ,  <dig> , and  <dig>  from bola iia, and markers  <dig> ,  <dig> ,  <dig> ,  <dig> ,  <dig> , and  <dig>  from bola i. in most cases the difference in marker position is negligible but we were able to independently assess gene order for markers  <dig> ,  <dig> ,  <dig> ,  <dig> ,  <dig> , and  <dig>  in skimmed  sequences of overlapping bac clones .
this analysis determined that the distribution of markers in the bac skims is consistent with the gene order predicted by btau_ <dig> .
again, the few discordancies in gene order appear to be due to imprecise resolution of very closely linked markers in the rh panel limitations.
the only likely misassembly in btau_ <dig>  detected in this study is the class iia marker  <dig> , which is positioned at the boundary of the iia – iii region in the assembly compared with a position in the centromeric region of iia in the rh map.
as a whole, the iia/iii/i region of bola is shifted ~ <dig> kb telomeric in the btau_ <dig>  assembly compared with the btau_ <dig>  assembly.
three markers,  <dig> ,  <dig>  and  <dig> , are all present on the rh map but missing in the bta <dig> sequence and in the chromosomally unassigned contigs of the btau_ <dig>  assembly.
blast analysis of the marker sequences against the ncbi trace archives identified all three marker sequences, revealing that the btau_ <dig>  assembly is missing at least three segments of bola dna.
comparison of rh map and human genome
comparative analysis of the rh map of bola and the corresponding sequence information for hsa6p identified four homologous synteny blocks  .
two hsbs are located in the iib region of bola and correspond to sequences at  <dig> – <dig>  mb and  <dig> – <dig>  mb on hsa <dig>  these hsbs represent the regions of hsa6p <dig> and 6p <dig> that are contiguous in the bovine genome.
the other two hsbs correspond to the iia/iii/i region of bola and to sequences  <dig> – <dig>  mb and  <dig> – <dig>  mb on hsa <dig> as previously described  <cit> .
the positions and boundaries of these blocks were compared with those described in previous studies .
these studies also described a hsb corresponding to the  <dig> – <dig>  mb  <cit>  or  <dig> – <dig>  mb  <cit>  sequence segment of hsa <dig> proximal to the centromere.
based on our results, this region of conserved synteny may be extended to include sequences at  <dig> – <dig>  mb on hsa6p as an extension of this same hsb.
the previous studies also identified a hsb corresponding to sequence at  <dig> – <dig>  mb  <cit>  or  <dig> – <dig>  mb on hsa6p  <cit> ; the lower boundary of this block can be extended to position  <dig>  mb on hsa6p based on our results.
the remaining two hsb found in this study, corresponding to sequences  <dig> – <dig>  mb and  <dig> – <dig>  mb on hsa6p, confirm the results of schibler et al  <cit>  and everts-van der wind et al  <cit> .
although coding sequences were not used as sources of sts markers in this study, the stringent requirements used to select sts for rh mapping enabled us to reliably identify homologous loci within hsa <dig> for all but two of the bovine sts markers mapped in this study.
these conserved sts markers are incorporated into figure  <dig> to integrate the rh map with the sequence-based map of hla.
the two markers that could not be located to hla were marker  <dig> , which returned no significant alignments to the human sequence, and marker  <dig> , which returned multiple alignments to sequences in the hla class i region.
marker  <dig>  may be located in a region of hla that has undergone an expansion not observed in the bovine mhc, thereby making it difficult to identify the location of the orthologous marker on hsa <dig>
discussion
radiation hybrid mapping of bola
the generation of a high-resolution, physically-ordered radiation hybrid map of bola provides an independent test of the order and arrangement of markers and scaffolds within the genome sequence assembly.
this validation is critical for future studies involving the bola region, such as those that seek to identify sequence features  or clarify the evolution of this region.
importantly, the rh map can be used to facilitate comparisons of the region with other species – particularly helpful when the accuracy of an assembly is unknown or uncertain.
the relatively high radiation dose used to construct the  <dig> rad rh panel used in this study generally provided a high resolution of marker order for evaluation of sequence assemblies but caution should be exercised when relying strictly upon rh mapping to order very closely spaced markers.
comparative mapping
comparison of rh map and btau_ <dig>  assembly
discrepancies identified between the rh map described here and the version  <dig>  assembly of the bovine genome sequence highlight major potential errors in the assembly.
although both maps are in general agreement in the order of markers for the bola iib region, the rh mapping data do not support the assembly of much of the iia/iii/i region, as indicated by the many inconsistencies observed between the rh map and sequence assembly .
the rh map compared to the btau_ <dig>  map is in general agreement in the bola iib region  but is far less concordant for the iia/iii/i region.
the arrangements of at least six blocks of sequence , demonstrates a remarkable conservation of gene content and order between cattle and humans.
several rearrangements in marker order are observed between the maps of the two species and these regions are prime candidates for further study to improve our understanding the evolution of the mammalian mhc.
CONCLUSIONS
the findings of this study provide a high resolution physically ordered radiation hybrid map of the bola region encompassing  <dig> markers.
comparisons with the btau_ <dig>  assembly of the bovine genome sequence shed light on a number of discrepancies, indicating that caution should be used when interpreting results and drawing conclusions based on this assembly.
the btau_ <dig>  assembly of the bovine genome shows far better agreement with the rh map; the fact that this assembly can be verified in such a way is indicative of its reliability.
as such, this assembly will be valuable for future studies in which assembly accuracy is paramount, such as searches for conserved elements or interpretation of evolutionary histories.
additionally, the resolution and reliability of the rh map enabled comparisons with the human genome that help to refine boundaries of hsbs.
this map will prove useful for future studies of this region of the cattle genome as it gives clarification regarding the structure and organization of bola and highlights potential inaccuracies in the btau_ <dig>  assembly.

 the typical mammalian major histocompatiblity complex 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, 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. the two segments are located about cm apart and are designated class iia and class iib. 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 and physical gene maps 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 and two subsequent assemblies that differ considerably from each other and from conventional gene maps. the most recent sequence assembly, btau_, incorporated additional mapping information, fingerprint contig 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 and sequence assemblies of the bovine mhc, we generated a high resolution map of bola using a rad radiation hybrid panel. the resolution achievable using this panel exceeds that of the rad panel previously used to generate medium-density maps for cattle chromosomes due to the increased frequency of radiation-induced chromosomal breaks. this makes the rad panel suitable for fine mapping genomic regions of interest. the map described here documents assembly errors in the btau_ assembly and largely validates the revisions contained in the assembly. we also compared the rh map of bola with the version 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.  marker development seventy-seven of the original primer pairs were used for mapping. fourteen of the markers were located in the class i and class i extended regions of bola, were located within class iia or iia extended regions, were located within class iib, and were located within class iii. of the three markers not retained for mapping, one marker was dropped from analysis due to typing ambiguities and two markers could not be assigned to specific locations and instead were binned within the iia/iii/i group. thirty-one of the clones in the rh panel consistently gave ambiguous genotyping results and were excluded from computation of the rh maps. rh mapping analysis of the distribution of sts markers across the rh panel resulted in the localization of markers into two groups, corresponding to the bola iib region and the bola iia, iii, and i region. the iib group of markers was distributed along cr, for a resolution of marker/ cr. the iia/iii/i group of markers was distributed over cr at a resolution of marker/ cr. resolution in kb was also determined by dividing by the size in base pairs of each region in btau_ by the number of markers with unique vectors. using this method, resolution of the rh group for the iib region of bola is approximately one marker every ~ kb and resolution for the iia/iii/i region of bola is one marker every ~ kb. twelve of the markers in the iib group and of the markers in the iia/iii/i group gave unique rh vectors and were designated as mle-consensus and ordered with highest confidence. positions, lod scores, and frame/placed status of individual markers are presented in additional file retention frequencies of markers in the iib group ranged from % to %, with an average value of %. for the iia/iii/i group, retention frequencies ranged from % to %, with an average value of %. rh maps developed for the two bola regions are presented in figure comparative maps the physical order of all markers on the rh map was compared with both the btau_ and assemblies and the ncbi assembly of the human genome sequence. results of these comparisons are shown in figures and respectively. comparison of rh map and btau_ assembly the organization of the four scaffolds and the markers of the iib region are essentially the same between the rh map and btau_ assembly. exceptions are the inverted order of markers and and markers,, and in the btau_ assembly relative to the rh map. all markers from the extended class iia region, with the exceptions of,, and, are placed more distally in the assembly than in the rh map but with similar marker order. marker order within the class iia region is also in overall agreement between the rh map and assembly with the single exception that class iia markers and, which map together on the rh map, are separated in the assembly: marker is placed within a group that includes class iii markers and has likely been misplaced in the assembly. both scaffold and marker orders in this group are inconsistent with those identified by the rh map. the order of,, and all scaffold class iii markers are in agreement in both the btau_ assembly and the rh map, although the placements differ, with the rh map assigning these markers to a more distal location on chromosome finally, overall consistency was observed in marker orders within class i scaffolds and 64; nevertheless, scaffold appears to be erroneously placed more proximal to scaffold in the btau_ assembly. two markers, and, were not assigned to bta in the btau_ assembly although they are clearly present within bola based on analysis of the rh mapping data. marker is chromosomally unassigned within the assembly, although analysis using ensembl blast returned an alignment with bta at position kb – clearly distal to the other markers of bola iia. in contrast, the rh map shows localized to the expected location near other markers from scaffold the rh map has placed marker at a predictable location near other markers from scaffold while blast comparison against the btau_ assembly produced no significant alignment to. comparison of rh map and btau_ assembly the iib region of bola shows good agreement between the btau_ assembly and rh map, with the exception of an inverted segment encompassing three markers:,, and. this same inverted order was also observed in the comparison between btau_ and the rh map. analysis of the positions of these three markers in an independent, finished assembly of bola iib supported the btau_ gene order and indicates that the discordancy is due to the imprecision of the rad rh panel to resolve the order of these closely linked markers. marker order in bola iib did not change from btau_ to btau_, but marker locations shifted ~ kb telomeric on the chromosome in version for all iib markers except and. class iia, iii and i marker order is very similar across the btau_ assembly of bola and rh map as is the order of markers in the extended iia and i regions. eleven markers located in two regions show some minor discordancy in gene order between the two maps. these include markers,,,, and from bola iia, and markers,,,,, and from bola i. in most cases the difference in marker position is negligible but we were able to independently assess gene order for markers,,,,, and in skimmed sequences of overlapping bac clones. this analysis determined that the distribution of markers in the bac skims is consistent with the gene order predicted by btau_. again, the few discordancies in gene order appear to be due to imprecise resolution of very closely linked markers in the rh panel limitations. the only likely misassembly in btau_ detected in this study is the class iia marker, which is positioned at the boundary of the iia – iii region in the assembly compared with a position in the centromeric region of iia in the rh map. as a whole, the iia/iii/i region of bola is shifted ~ kb telomeric in the btau_ assembly compared with the btau_ assembly. three markers,, and, are all present on the rh map but missing in the bta sequence and in the chromosomally unassigned contigs of the btau_ assembly. blast analysis of the marker sequences against the ncbi trace archives identified all three marker sequences, revealing that the btau_ assembly is missing at least three segments of bola dna. comparison of rh map and human genome comparative analysis of the rh map of bola and the corresponding sequence information for hsa6p identified four homologous synteny blocks. two hsbs are located in the iib region of bola and correspond to sequences at – mb and – mb on hsa these hsbs represent the regions of hsa6p and 6p that are contiguous in the bovine genome. the other two hsbs correspond to the iia/iii/i region of bola and to sequences – mb and – mb on hsa as previously described. the positions and boundaries of these blocks were compared with those described in previous studies. these studies also described a hsb corresponding to the – mb or – mb sequence segment of hsa proximal to the centromere. based on our results, this region of conserved synteny may be extended to include sequences at – mb on hsa6p as an extension of this same hsb. the previous studies also identified a hsb corresponding to sequence at – mb or – mb on hsa6p; the lower boundary of this block can be extended to position mb on hsa6p based on our results. the remaining two hsb found in this study, corresponding to sequences – mb and – mb on hsa6p, confirm the results of schibler et al and everts-van der wind et al. although coding sequences were not used as sources of sts markers in this study, the stringent requirements used to select sts for rh mapping enabled us to reliably identify homologous loci within hsa for all but two of the bovine sts markers mapped in this study. these conserved sts markers are incorporated into figure to integrate the rh map with the sequence-based map of hla. the two markers that could not be located to hla were marker, which returned no significant alignments to the human sequence, and marker, which returned multiple alignments to sequences in the hla class i region. marker may be located in a region of hla that has undergone an expansion not observed in the bovine mhc, thereby making it difficult to identify the location of the orthologous marker on hsa discussion radiation hybrid mapping of bola the generation of a high-resolution, physically-ordered radiation hybrid map of bola provides an independent test of the order and arrangement of markers and scaffolds within the genome sequence assembly. this validation is critical for future studies involving the bola region, such as those that seek to identify sequence features or clarify the evolution of this region. importantly, the rh map can be used to facilitate comparisons of the region with other species – particularly helpful when the accuracy of an assembly is unknown or uncertain. the relatively high radiation dose used to construct the rad rh panel used in this study generally provided a high resolution of marker order for evaluation of sequence assemblies but caution should be exercised when relying strictly upon rh mapping to order very closely spaced markers. comparative mapping comparison of rh map and btau_ assembly discrepancies identified between the rh map described here and the version assembly of the bovine genome sequence highlight major potential errors in the assembly. although both maps are in general agreement in the order of markers for the bola iib region, the rh mapping data do not support the assembly of much of the iia/iii/i region, as indicated by the many inconsistencies observed between the rh map and sequence assembly. the rh map compared to the btau_ map is in general agreement in the bola iib region but is far less concordant for the iia/iii/i region. the arrangements of at least six blocks of sequence, demonstrates a remarkable conservation of gene content and order between cattle and humans. several rearrangements in marker order are observed between the maps of the two species and these regions are prime candidates for further study to improve our understanding the evolution of the mammalian mhc.  the findings of this study provide a high resolution physically ordered radiation hybrid map of the bola region encompassing markers. comparisons with the btau_ assembly of the bovine genome sequence shed light on a number of discrepancies, indicating that caution should be used when interpreting results and drawing conclusions based on this assembly. the btau_ assembly of the bovine genome shows far better agreement with the rh map; the fact that this assembly can be verified in such a way is indicative of its reliability. as such, this assembly will be valuable for future studies in which assembly accuracy is paramount, such as searches for conserved elements or interpretation of evolutionary histories. additionally, the resolution and reliability of the rh map enabled comparisons with the human genome that help to refine boundaries of hsbs. this map will prove useful for future studies of this region of the cattle genome as it gives clarification regarding the structure and organization of bola and highlights potential inaccuracies in the btau_ assembly. 
the cattle mhc is termed the bovine leukocyte antigen and, along with the mhcs of other ruminants, is unique in its genomic organization. of the few discordancies between the rh map and btau_, most could be attributed to closely spaced markers that could not be precisely ordered in the rh panel. these results strongly suggest that studies using btau_ for analyses of the bola region should be reevaluated in light of the btau_ assembly and indicate that additional research is needed to produce a complete assembly of the bola genomic sequences. analysis of the data generated a high resolution rh map of bola that was significantly different from the btau_ assembly of the bovine genome but in good agreement with the btau_ assembly. the rh map of bola is also highly concordant with the sequence-based map of hla when reordered to account for the ancestral inversion in the ruminant mhc. the bovine genome sequencing project has produced two assemblies that differ substantially from each other and from conventional gene maps in the bola region. seventy-seven unique sequence tagged site markers chosen at approximately kb intervals from the btau assembly and spanning the iia-iii-i and iib regions of the bovine mhc were mapped on a rad bovine radiation hybrid panel to evaluate the different assemblies of the bovine genome sequence. consequently, correct and reliable gene maps and sequence information are critical to the study of the bola region. to independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of bola using a rad radiation hybrid panel.
 the cattle mhc is termed the bovine leukocyte antigen and, along with the mhcs of other ruminants, is unique in its genomic organization. consequently, correct and reliable gene maps and sequence information are critical to the study of the bola region. the bovine genome sequencing project has produced two assemblies that differ substantially from each other and from conventional gene maps in the bola region. to independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of bola using a rad radiation hybrid panel. seventy-seven unique sequence tagged site markers chosen at approximately kb intervals from the btau assembly and spanning the iia-iii-i and iib regions of the bovine mhc were mapped on a rad bovine radiation hybrid panel to evaluate the different assemblies of the bovine genome sequence.  analysis of the data generated a high resolution rh map of bola that was significantly different from the btau_ assembly of the bovine genome but in good agreement with the btau_ assembly. of the few discordancies between the rh map and btau_, most could be attributed to closely spaced markers that could not be precisely ordered in the rh panel. one probable incorrectly-assembled sequence and three missing sequences were noted in the btau_ assembly. the rh map of bola is also highly concordant with the sequence-based map of hla when reordered to account for the ancestral inversion in the ruminant mhc.  these results strongly suggest that studies using btau_ for analyses of the bola region should be reevaluated in light of the btau_ assembly and indicate that additional research is needed to produce a complete assembly of the bola genomic sequences. 