Characterisation of major histocompatibility complex class IIa haplotypes in an island sheep population

The ovine MHC class IIa is known to consist of six to eight loci located in close proximity on chromosome 20, forming haplotypes that are typically inherited without recombination. Here, we characterise the class IIa haplotypes within the Soay sheep (Ovis aries) on St. Kilda to assess the diversity present within this unmanaged island population. We used a stepwise sequence-based genotyping strategy to identify alleles at seven polymorphic MHC class IIa loci in a sample of 118 Soay sheep from four cohorts spanning 15years of the long-term study on St. Kilda.DRB1, the most polymorphic MHC class II locus, was characterised first in all 118 sheep and identified six alleles. UsingDRB1homozygous animals, theDQA(DQA1,DQA2andDQA2-like) andDQB(DQB1,DQB2andDQB2-like) loci were sequenced, revealing eight haplotypes. BothDQ1/DQ2andDQ2/DQ2-likehaplotype configurations were identified and a single haplotype carrying threeDQBalleles. A test sample of 94 further individuals typed at theDRB1andDQAloci found no exceptions to the eight identified haplotypes and a haplotype homozygosity of 21.3%. We found evidence of historic positive selection atDRB1,DQAandDQB. The limited variation at MHC class IIa loci in Soay sheep enabled haplotype characterisation but showed that no single locus could capture the full extent of the expressed variation in the region.