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Identification of genetic variation in the bovine major histocompatibility complex DRß‐like genes using sequenced bovine genomic probes
Author(s) -
MUGGLICOCKETT N. E.,
STONE R. T.
Publication year - 1988
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/j.1365-2052.1988.tb00810.x
Subject(s) - exon , biology , pseudogene , genomic dna , bovine genome , genetics , exon trapping , microbiology and biotechnology , tandem exon duplication , intron , gene , stop codon , alternative splicing , genome
Summary. Two bovine genomic clones that crosshybridize with HLA‐DRß cDNA have been isolated. Nucleotide sequence analysis of the ß 1 ‐ß 2 and transmembrane (TM) exon regions for one of these clones revealed 70, 89 and 86% identity with the corresponding HLA‐DRß exons. Stop codons are present in the ß 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 DRß‐like pseudogene, BoDRß I. Exon‐containing regions have been used as probes in Southern blot analyses of bovine genomic DNA digested with Eco RI. The ß 2 exon of BoDRß 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 BoDRß I hybridizes only to the 5–6‐ and 3.6‐kb bands, suggesting that these are allelic bands corresponding to this pseudogene. Results from hybridizations of a TM exon‐containing probe of the second bovine DRß‐like clone (BoDRß 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 BoDRß I ß 1 exon. Major differences in frequency for the 6.4/2.7 alleles were found for the four breeds sampled.