The caprine MHC contains DYA genes

Investigation of such associations requires definition of the caprine MHC class II region. In order to detect new genes in this region, we have used a genomic probe for a recently described bovine class II gene, Bota-DYA to examine the goat genome by pulsed field gel electrophoresis (PFGE). Goat DNA contained in agarose plugs was digested with a variety of rare cutting restriction enzymes and analyzed by PFGE. Southern hybridization analysis and probing sequentially with a Bota-DYA exon 3 fragment (347 base pairs (bp); van der Poel et al. 1990) and DRB (786 bp; Long et al. 1983) revealed that both DY and DR-hybridizing sequences are present on a 250 kilobase (kb) Not I fragment in all animals tested. One sample showed an additional 340 kb Not I fragment with both probes. Although partial digestion cannot be excluded, the detection of an additional fragment hybridizing to both DR and DY supports previous data that indicate the structure of the class II region may vary in different goat MHC haplotypes.