BCB Thesis Seminar Haibo Liu March 9, 2017 Swine Blood Transcriptomics: Application and Advancement Home Department: Animal Science Major Professors: Christopher Tuggle, Animal Science and Peng Liu, Statistics

Abstract: The uses of transcriptomic analysis of blood to identify biomarkers predictive of quantitative phenotypes and to study immune responses are major fields of study. We are interested in improving swine feed efficiency by selection for low residual feed intake (RFI). However, whether this selection would compromise pigs’ immune response is not clear given reduced feed intake of low-RFI pigs.

In one study, transcriptomes of peripheral blood from pigs of two lines divergently selected for RFI and treated with lipopolysaccharide (LPS) were profiled by time-series RNA-seq. The lines were largely similar in most biological pathways and processes studied, though a lower level of inflammation in the low- vs high-RFI animals was suggested. A comparative analysis with similar data in humans showed that humans and pigs responded to LPS stimulation similarly at both gene and pathway levels.

In another study, candidate biomarkers for predicting RFI were identified by RNA-seq profiling post-weaning blood transcriptome of the two lines. In the last study, a high-quality annotated transcriptome of porcine peripheral blood was built via a hybrid assembly strategy. This thesis work provides evidence that selection for improved feed efficiency did not compromise pigs’ immune response, offers candidate biomarkers for predicting RFI to facilitate RFI-based selection, and advances the structural and functional annotation of the porcine blood transcriptome.