Integrating Growth Performance and Pathogen Detection to Investigate Disease Resilience in Commercial Swine

Authors

• Emmalise Hope Marie Meyer, University of Nebraska-LincolnFollow

First Advisor

Daniel Ciobanu

Committee Members

Dustin Loy, Samodha C. Fernando

Date of this Version

5-2026

Document Type

Thesis

Citation

A thesis presented to the faculty of the Graduate College at the University of Nebraska in partial fulfillment of requirements for the degree of Master of Science

Major: Animal Science

Under the supervision of Professor Daniel Ciobanu

Lincoln, Nebraska, May 2026

Comments

Copyright 2026, Emmalise Hope Marie Meyer. Used by permission

Abstract

Disease resilience is an important trait in commercial swine production, influencing both animal health and growth performance under natural disease challenge. The primary objective of this study was to integrate growth performance data with longitudinal pathogen detection to better understand factors contributing to disease resilience in commercial pigs. A population of 1,014 pigs across four batches was monitored from weaning through the grow-finish phase, with body weights collected to calculate average daily gain (ADG). Genome-wide association analyses were conducted using BayesC and BayesIM approaches to identify genomic regions associated with growth performance. Longitudinal pathogen surveillance was performed using pen-level oral fluid sequencing, and individual-level RT-qPCR assays were used to evaluate atypical porcine pestivirus (APPV) status in a subset of pigs.

Several genomic regions, including loci on chromosomes 1, 3, and X, were consistently associated with variation in ADG across production phases. Pathogen detection in oral fluids revealed some viral abundance at the pen-level; however, RT-qPCR analysis demonstrated dynamic APPV status at the individual level. A subset of pigs tested positive only at one time point, and APPV status at weaning was associated with differences in ADG.

Advisor: Daniel Ciobanu