Methods and systems are provided for managing non-beef livestock subjects in order to maximize their individual potential performance and the value of a product from the non-beef livestock subjects, and to maximize profits obtained in marketing the non-beef livestock subjects. The methods and systems draw an inference of a trait of a non-beef livestock subject by determining the nucleotide occurrence of at least one non-beef livestock SNP that is determined to be associated with the trait. The inference is used in methods of the present invention to establish the economic value of a non-beef livestock subject, to improve profits related to selling beef from a non-beef livestock subject; to manage non-beef livestock subjects, to sort non-beef livestock subjects; to improve the genetics of a non-beef livestock population by selecting and breeding of non-beef livestock subjects, to clone a non-beef livestock subject with a specific trait, to track meat or another commercial product of a non-beef livestock subject; and to diagnose a health condition of a non-beef livestock subject. Certain embodiments of the present invention provide methods, systems, and kits are directed to inferences of a trait related to milk or a dairy product in a livestock subject.