Sequence variants associated with resilient responses in growing pigs

Abstract

The current work aimed to identify genomic regions and candidate genes associated with resilience in pigs. In previous work, we proposed the body weight deviation from the expected growth curve (ΔBW) and the increase of the positive acute-phase protein haptoglobin (ΔHP) after a vaccine challenge as resilience indicators which may be improved through selective breeding in pigs. Individuals with steady growth rate and minor activation of haptoglobin (high ΔBW and low ΔHP values) were considered resilient. In contrast, pigs with perturbed growth rate and high activation of haptoglobin (low ΔBW and high ΔHP values) were considered susceptible. Both ∆BW and ∆HP were simultaneously considered to select the most resilient (N = 40) and susceptible (N = 40) pigs. A genome-wide association study was carried out for the pigs' response classification to the challenge test using whole-genome sequence data (7,760,720 variants). Eleven associated genomic regions were identified, harbouring relevant candidate genes related to the immune response (such as pro- and anti-inflammatory responses) and growth pathways. These associated genomic regions harboured 41 potential functional mutations (frameshift, splice donor, splice acceptor, start loss and stop loss/gain) in candidate genes. Overall, this study advances our knowledge about the genetic determinism of resilience, highlighting its polygenic nature and strong relationship with immunity and growth.

FIGURE 1

Manhattan plot for the whole‐genome association study for the pigs' response to the challenge. The black dashed line indicates the p‐value threshold of 10⁻⁵. [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 2

Relevant candidate genes for pigs' response to the challenge are mainly involved in the immune response pathway. Positional candidate genes identified in the genomic regions associated with the response to the challenge are highlighted. [Colour figure can be viewed at wileyonlinelibrary.com]