Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Animal Science


Bioinformatics and Computational Biology

First Advisor

Christopher K. Tuggle

Second Advisor

Peng Liu


Improving swine feed efficiency (FE) by selection for low residual feed intake (RFI) is of practical interest. However, whether selection for low RFI compromises a pig’s immune response is not clear. In addition, current RFI-based selection for improving feed efficiency was expensive and time-consuming. Seeking alternative tools to facilitate selection, such as predictive biomarkers for RFI, is of great interest. The objectives of this thesis are as follows: (1) to investigate whether selection for low RFI compromise a pig’s immune response; (2) to develop candidate biomarkers applicable at early growth stage for predicting RFI at late growth stage; (3) to improve the annotation of the porcine blood transcriptome.

In Chapter 2, pigs of two lines divergently selected for RFI were injected with lipopolysaccharide (LPS). Transcriptomes of peripheral blood at baseline and multi-time points post injection were profiled by RNA-seq. LPS injection induced systemic inflammatory response in both RFI lines. However, no significant differences were detected in dynamics of body temperature, blood cell count and cytokine levels during the time course. Only a very small number of differentially expressed genes (DEGs) were detected between the lines over all time points, though ~ 50% of blood genes were differentially expressed post LPS injection compared to baseline for each line. The two lines were largely similar in most biological pathways and processes studied. Minor differences included a slightly lower level of inflammatory response in the low- versus high-RFI animals. Cross-species comparison showed that humans and pigs responded to LPS stimulation similarly at both the gene and pathway levels, though pigs are more tolerant to LPS than humans.

In Chapter 3, post-weaning blood transcriptomic differences between the two lines were studied by RNA-seq. DEGs between the lines significantly overlapped gene sets associated with human diseases, such as eating disorders, hyperphagia and mitochondrial disease. Genes functioning in the mitochondrion and proteasome, and signaling had lower and higher expression in the low-RFI group relative to the high-RFI group, respectively. Expression levels of five differentially expressed genes between the two groups were significantly associated with individual animal’s RFI values. These five genes were candidate biomarkers for predicting RFI.

Given limitations of current annotation of the porcine reference genome, a high-quality annotated transcriptome of porcine peripheral blood was built in the last study via a hybrid assembly strategy with a large amount of blood RNA-seq data from studies mentioned above and public databases.

Taken together, this work provides evidence that selection for low RFI did not significantly compromise pigs’ immune response to systemic inflammation, offers a few candidate biomarkers for predicting RFI to facilitate RFI-based selection, and significantly advances the structural and functional annotation of porcine blood transcriptome.


Copyright Owner

Haibo Liu



File Format


File Size

230 pages