German and Belgian shepherd dogs are more susceptible to chronic superficial keratitis (CSK), an autoimmune-related eye disease, due to genetic risk factors. Our objective is to identify the genomic regions and candidate variants responsible for this disease by conducting genome-wide association studies (GWAS) and direct sequencing of the major histocompatibility complex (MHC) class II genes, which are known to play a role in autoimmune diseases. We will then evaluate the risk across all the identified loci to determine the genotype combinations that pose low-to-high risk for developing CSK.