Identification and mapping of a Bovine MHC classical class I locus missing from the reference assembly

The classical class I genes of the major histocompatibility complex are responsible for presenting cytosolic antigens to CD8+ T-cells. Previous expression assays revealed that a major antigen presenting locus, BoLA-BSA (AF396750.1), is missing from the bovine reference assembly and the CHORI 240 BAC library, although the BSA sequence is present in the DNA of Domino, the donor for the CHORI 240 BAC library. Genomic BoLA-BSA is a classical class I MHC locus of eight exons and approximately three kilobases in length. We localized the BSA sequence by high-resolution radiation hybrid mapping and used sequencing to characterize the distribution and diversity of BSA alleles in 92 different BoLA haplotypes. BSA was localized to BoLA on chromosome 23 in the distal end of the class I region. We identified 62 unique alleles of the BSA locus. Approximately 61% of tested BoLA haplotypes contain the BSA sequence, while BSA amplicons were not detected in 39% of the haplotypes.