The bovine respiratory disease complex (BRDC) is a major concern for the beef industry throughout the United States of America and the rest of the world. In the USA, BRDC is estimated to cost more than $700 million dollars every year in losses due to reduced production of the beef cattle, loss of health, and increased rates of morbidity and mortality. To address this pressing concern, many producers use vaccines to provide protection within their herds. These vaccines have been developed and designed by many companies, all with a goal of reducing the incidence rate of BRDC in cattle herds and hopefully improving host protection against pathogens associated with BRDC. Viral pathogens are some of the most common, and standard, pathogens associated with BRDC. The following four viruses are often included in standard vaccines against BRDC due to their commonality within BRDC cases: bovine viral diarrhea virus 1 and 2 (BVDV1; BVDV2), bovine respiratory syncytial virus (BRSV), and bovine herpesvirus (BHV1). The objective of this thesis was to evaluate factors associated with response to vaccination and antibody titer traits, identify genomic regions of association, and investigate methods of detecting inter- and intrachromosomal interactions as well as epistatic networks. .

Serum samples were extracted from calves at up to four time points (pre-vaccination, initial vaccination, booster vaccination, and final titer) each at approximately three weeks apart each. These serum samples then underwent serial dilutions to quantify the amount of antigen binding antibodies present within the sample. Calculated titer scores at pre-vaccination, initial vaccination, and 3-weeks post booster vaccination were analyzed as individual titer traits, while initial vaccination response (booster vaccination – initial vaccination), booster vaccination response (final titer – booster vaccination), and overall vaccination response (final titer – initial vaccination) were analyzed as response to vaccination traits. Maternal decay (change of initial vaccination – pre-vaccination / number of days) was also analyzed, however this and pre-vaccination titer score were only analyzed for BVDV1 and BVDV2 due to availability of data. An effect of time of weaning (initial vaccination versus booster vaccination) and infection status (pink eye positive or negative) were identified, in addition to subsets of individuals who appear as non-responders. Genomic regions associated with antibody titer and response to vaccination traits were identified, although no potential genes of control could be identified within the regions.

Finally, detection of epistatic interactions was done with antibody titer and response to vaccination traits at 770k SNP genotype density. Interchromosomal interactions were identified within the initial titer and overall vaccination response traits for BRSV, but no significant interactions were identified in other traits. A tag SNP filter was applied to attempt identification of intrachromosomal interactions, but only a single previously undetected interaction was discovered. This tag SNP filtering was applied to the 50k SNP genotype used with previously studied fatty acid traits, but did not result in a reduction in SNP number. This allowed for the further detection of intrachromosomal interactions in fatty acid traits, and the characterization of epistatic networks through the use of WGCNA.