A high resolution RH map of the bovine major histocompatibility complex

Abstract

Background: The cattle MHC is termed the bovine leukocyte antigen (BoLA) 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 (Btau_3.1 and 4.0) 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 12,000rad radiation hybrid panel. Seventy-seven unique sequence tagged site (STS) markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000rad bovine radiation hybrid (RH) panel to evaluate the different assemblies of the bovine genome sequence.

Results: Analysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, 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_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36) when reordered to account for the ancestral inversion in the ruminant MHC.

Conclusion: These results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.

Figure 1

High-resolution radiation hybrid and comparative maps of BoLA. To the far left and far right are representations of BTA23 generated using the current genome sequence assemblies (Btau_3.1 and Btau_4.0, respectively). The centromere is represented as a black oval and distances are given in kilobases (Kb). The radiation hybrid map of BoLA is in the center, with map units given as centirays (cR). Just to the left and right of the RH map are marker names given in the order ascertained via radiation hybrid analysis, with connecting lines illustrating their comparative locations on the BTA23 maps.

Figure 2

Comparison of BoLA RH map with homologous human region. Comparison of the high-resolution radiation hybrid map developed in this study with the corresponding region of human chromosome 6 (HSA6). The radiation hybrid map of BoLA is on the left, with units given as cR. Marker names to the right of this are in the order determined through RH mapping. A representative map of HSA6 (with inverted orientation) is located at the far right; connecting lines provide a comparative view of the marker order between the RH map and HSA6. The centromere is represented as a black region in between the two arms, which are labeled "q arm" and "p arm", and distances are given in Kb.

Figure 3

Homologous synteny blocks in cattle and human. Details about human homologs identified for RH-mapped markers used in this study. To the left, the BoLA RH-mapped markers are presented in their homologous HLA positions, with the corresponding megabase position of the human homolog listed to the right. Brackets indicate markers clustered by the RH analysis. These clustered markers have been assigned to the same cR position and therefore can be flipped with equal likelihood; as a result, caution should be exercised when considering these markers as part of an inversion. To the right, arrows indicate locations and orientations of homologous synteny blocks in relation to human, determined by this study, [14], and [29]. Proposed extensions of HSBs are represented as lighter-colored blocks with dotted edges; orientation is indicated by arrows within the blocks.