Identifying The Underlying Molecular Basis of Three Deleterious Phenotypes in Hereford Cattle

Hereford cattle are among the most popular breeds of beef cattle in the United States. As with any breeding population, traits or phenotypes may arise that are less desirable and/or have negative economic consequences. In Herefords, three such phenotypes have been observed throughout the history of the breed and remain concerns in the current population. These phenotypes include. In Herefords, ocular squamous cell carcinoma, commonly called cancer eye, scurs, and ocular dermoid are three phenotypes observed throughout the history of the breed and remains a concern in the current population. This project was conducted in an effort to define the potential underlying molecular genetic basis of these traits using 95 animals affected with at least one of the phenotypes. Samples of these 95 animals were submitted by Hereford breeders and received either as whole blood, tissue, or semen. The case group of 95 animals representing cases of each phenotype, consisted of 57 with cancer eye, 18 scurred female individuals, and 19 with ocular dermoid. Genomic DNA was isolated, and all samples were whole-genome sequenced (WGS) to an average depth of coverage of 9.93 following quality control and pruning of the sequences using Plink. The American Hereford Association provided WGS information from 105 individuals to be used as unaffected control samples. Analysis from the WGS, showed significant associations with numerous variants on multiple chromosomes. Variants were considered significant if exceeding the genome-wide significance (p