This article is part of a series on Bovine: the companion papers for the publication of the bovine genome sequence.

Research article

A high resolution RH map of the bovine major histocompatibility complex

Candice L Brinkmeyer-Langford¹ , Christopher P Childers² , Krista L Fritz¹ , Ashley L Gustafson-Seabury¹ , Marian Cothran¹ , Terje Raudsepp¹ , James E Womack³ and Loren C Skow¹

¹  Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843-4458, USA

²  Department of Biology, Georgetown University, Washington, DC 20057, USA

³  Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA

author email corresponding author email

BMC Genomics 2009, 10:182doi:10.1186/1471-2164-10-182

Published:	24 April 2009

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 12,000_rad 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 12,000_rad 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.