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Short Communication: Identification of Allelic Variation at the Bovine DRA Locus by Polymerase Chain Reaction-Single Strand Conformational Polymorphism

Gene-Marker Laboratory, Cell Biology Group, Agriculture, and Life Sciences Division, PO Box 84, Lincoln University, Lincoln 7647, New Zealand

¹ Corresponding author: Hickford{at}lincoln.ac.nz

The major histocompatibility complex DRA locus is noteworthy among the major histocompatibility complex class II loci for the little or no variation reported in many species. In cattle, DRA has not been investigated in depth, and the extent of variation at the locus is not yet known. In this study, we used PCR-single strand conformational polymorphism (SSCP) analysis to screen for potential sequence variation in the second exon of bovine DRA, which encodes the antigen-presentation groove. Four unique SSCP patterns were detected among 384 cattle from New Zealand. Sequence analysis revealed that these SSCP patterns represent 4 DRA alleles; and 3 single nucleotide polymorphisms were detected in exon 2. However, all of the single nucleotide polymorphisms were synonymous, and no amino acid change was therefore expected in this region. The polymorphism detected may be linked to variation elsewhere in the gene that affects its structure or function.

Key Words: cattle • DRA locus • polymorphism • polymerase chain reaction-single strand conformational polymorphism