Methods of analyzing a biological sample obtained from the canine subject for the presence of one or two copies one or two copies of minor allele T of SNP Affx-206229307; or one or two copies of minor allele A of SNP Affx-206560187; or one or two copies of minor allele T of SNP Affx-206229307 and one or two copies of minor allele A of SNP Affx-206560187 are disclosed. The methods are used in methods to identify a canine subject that has an increased likelihood or risk of hypothyroidism and in methods of treating a canine subject to reduce risk of hypothyroidism or to treat a canine subject that has hypothyroidism. The treatments comprise administering to the canine subject a low arginine diet and/or comprising an effective amount of a composition comprising a protein source, a carbohydrate source, a vegetable source, and a fruit source. Canine food compositions are disclosed.