The DQA₂ locus of the ovine major histocompatibility complex : characterisation, polymorphism and associations with footrot

Footrot is one of the most economically important diseases affecting the sheep industry in New Zealand. Losses in production from the disease and expenditure on treatment have been estimated to cost the New Zealand agricultural industry up to 100 million dollars per annum. None of the treatment options currently available are completely effective in reducing the economic impact of the disease, and are undesirable because of the possible impact on consumer health and the environment. One option that has not been fully investigated is the possibility of controlling footrot by exploiting natural variation in resistance. Variation in natural resistance to footrot is genetically derived. A number of heritable factors may be involved, and many of these interact with the environment to affect disease status. This implies that genetic markers for footrot resistance may exist, allowing the selection of superior animals. The major histocompatibility complex (MHC) is central to the immune response. Research has shown that genetic variation within this region is associated with natural resistance to footrot. Genes within the MHC may be able to act as a genetic marker to enable the selection of animals that are naturally more resistant to footrot. In this study association between variation within the ovine class II DQA₂ gene and resistance to footrot was investigated in four different flocks from three different sheep breeds; Awassi, Corriedale and Merino. Half-sib progeny were typed at the DQA₂ locus using TaqI RFLP and Southern hybridisation typing. The animals were subjected to a footrot challenge, and their condition subsequently recorded to investigate associations between the inherited DQA₂ haplotype and footrot status. Within the Awassi flock, the D and C alleles associated with resistance (P ≤ 0.05), while the L allele associated with susceptibility (P ≤ 0.05). No significant associations were observed within the Corriedale flock, a result attributed to the challenge, where drought conditions led to poor disease transmission, and unreliable disease classification. Two new banding patterns were observed in the Merinos, and were tentatively defined as alleles Q and R. In the two Merino flocks, the G and C alleles were observed to significantly associate with resistance (P ≤ 0.05), while the E allele associated with susceptibility (P ≤ 0.05). The data from the four flocks were pooled, which enabled twelve DQA₂ alleles (B, C, D, E, F, G, H, I, J, K, L, and N), to be ranked in terms of their relative footrot susceptibility or resistance. The G allele appeared to be most strongly associated with resistance (P ≤ 0.01), whilst the I allele appeared to be most strongly associated with susceptibility (P ≤ 0.01). Additional variation was detected at the ovine DQA₂ locus by cloning and sequencing a number of DQA₂ alleles, with sub-division of the G, C and F alleles into G1, G2, C1, C2, C3, F1 and F2. A total of fourteen different DQA₂ sequences were obtained. Alignment of all the sequences revealed that the E, G2 and H allelic sequences were conserved across different breeds. Sequences obtained from the F allele did however, show breed-specific differences, with two F allele sequences being identified. F1 came from a mixed breed, which was a Coopworth x Perendale cross, while F2 came from a Romney. In addition, the sequence data provided evidence of a DQA₂ duplication in some sheep, with the G 1 allele sharing closer homology to a putative bovine DQA₃gene, than with other ovine DQA₂ sequences. The putative DQA₃ gene appeared to associate with a DQA₁-null haplotype. Sequence analysis also suggested that DQA₂ alleles E and C2 may not be expressed because of the lack of a splice site at the end of exon 2. From the sequence information obtained the structure of the ovine DQA₂ antigen-binding groove could be predicted. This enabled the antigen-peptide binding ability of different alleles to be compared