Exploration of Genetic Factors Influencing Gut Health in Pigs

PhD Student: Emil Ibragimov
Thesis defended 3 November 2023

Post-weaning diarrhea (PWD) poses a significant challenge in pig farming leading to diminished animal well-being, decreased meat yield and often necessitating antimicrobial intervention. While considerable efforts have been directed towards identifying preventive measures for PWD, a critical aspect that remains underexplored is the mechanisms of resistance to this condition. It this thesis we are addressing this knowledge gap by focusing on the genetic factors associated with maintaining a healthy gut. The study takes a dual perspective: one aspect concentrates on identifying genetic factors that can prevent common gut infections causing PWD, while the other focus on determining factors linked to a pig's resilience—measured through essential traits for pig production—in the face of prevalent stressors during the post-weaning period.

A primary objective of this study is to uncover the genetic foundations of PWD resistance in pigs. Additionally, the research delves into the genetic factors influencing production and carcass traits, serving as crucial benchmarks for evaluating gut resilience against pathogenic influences.

The thesis is grounded in one published paper and two manuscripts, which are currently under review for publication.

In Paper 1, we performed a detailed genome-wide association study (GWAS) on a closely monitored cohort, identifying a marker on SSC16 linked to PWD susceptibility. Additionally, serum metabolomics analysis revealed a significant association between PWD and altered pantothenic acid levels. A subsequent GWAS on a separate cohort highlighted a distinct quantitative trait locus (QTL) on SSC16 associated with diarrhea resistance.

Papers 2 and 3 focused on identifying genetic determinants of pig gut resilience through key production traits: feed efficiency (FE) and lean meat percentage (LMP). In Paper 2, an integrated genomics and transcriptomic analysis identified candidate genes for FE modulation in pigs. By combining GWAS results with RNA-seq analyses on colon epithelium, we prioritized genes within the QTL region. The GWAS we performed in Paper 3 on LMP revealed two distinct QTLs. Prioritizing candidate genes through publicly available genotype-gene expression association studies provided insights into the genetic factors influencing LMP in pigs. These studies collectively contribute to understanding genetic mechanisms related to PWD susceptibility, diarrhea resistance, and gut resilience in pigs.