Collections of polynucleotides useful estimating breeding value or detecting likelihood of an increased susceptibility to contracting paratuberculosis are disclosed. The polynucleotides are used to detect genomic sequences quantitatively associated with an increased susceptibility to contracting paratuberculosis trait. Methods for using the collections to estimate breeding value or predict likelihood of an increased susceptibility to contracting paratuberculosis are also provided. Kits comprising the collection of polynucleotides are also provided.