Identification of genetic variation in the bovine major histocompatibility complex DRß‐like genes using sequenced bovine genomic probes

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Abstract
Two bovine genomic clones that crosshybridize with HLA-DR.beta. cDNA have been isolated. Nucleotide sequence analysis of the .beta.1, .beta.2 and transmembrane (TM) exon regions of one of these clones revealed 70, 89 and 86% identity with the corresponding HLA-DR.beta. exons. Stop codons are present in the .beta.1 and TM exons and a single base deletion toward the 3'' end of the TM exon negates the consensus sequence for exon/intron splicing. Therefore, we conclude this is a bovine DR.beta.-like pseudogene, BoDR.beta. I. Exon-containing regions have been used as probes in Southern blot analyses of bovine genomic DNA digested with EcoRI. The .beta.2 exon of BoDR.beta. I results in prominent bands of 18.9, 7.8, 7.2, 6.4, 5.6, 3.6, 3.0 and 2.7 kb. Polymorphisms were observed for all but the 18.9 kb band and at least three of these bands were identified in each of the 185 animals sampled. A probe containing the TM exon of BoDR.beta. I hybridizes only to the 5.6- and 3.6-kb bands, suggesitng that these are allelic bands corresponding to this pseudogene. Results from hybridizations of a TM exon-containing probe of the second bovine DR.beta.-like clone (BoDR.beta. II) suggest that the 6.4- and 2.7-kb bands correspond to this second bovine gene. A nonpolymorphic 8.1-kb band results from a probe containing the BoDR.beta. I .beta.1 exon. Major differences in frequency for the 6.4/2.7 alleles were found for the four breeds sampled.