Uncovering the Genetic Basis of Porcine Resilience Through GWAS of Feed Intake Data

TL;DR

This study identifies genetic factors linked to resilience in pigs using feed intake data, offering insights for breeding more adaptable livestock.

Contribution

The study introduces new candidate genes for porcine resilience and provides a framework for genomic selection in swine breeding.

Findings

Candidate genes CD74, CSF1R, and HTR4 are associated with resilience traits in pigs.

Resilience traits show moderate to high genetic correlations with production traits.

188 SNPs were identified and linked to 44 candidate genes through GWAS.

Abstract

Recent climatic variability driven by global warming has introduced new challenges for livestock production, motivating the swine industry to breed animals with enhanced adaptability to extreme environments. Using daily feed-intake records collected by automated feeding systems, we estimated the genetic parameters of porcine resilience traits. A genome-wide association study further identified candidate genes associated with resilience, including CD74, CSF1R, and HTR4. These findings provide a biological basis for understanding resilience in livestock and inform genomic selection strategies.

Resilience usually refers to the ability of an animal to be minimally affected by disturbance or to quickly return to its pre-disturbance state. Pigs with strong resilience usually have better production performance and higher tolerance to common diseases. This study utilized feed intake records collected by a Feed Intake Recording Equipment from three pig breeds (Duroc: 823; Landrace: 582; and Yorkshire: 2032). Six resilience traits were constructed using the root mean square error (RMSE) of daily feed intake and feeding duration, cumulative feed intake, and cumulative feeding duration derived from ordinary least squares (OLS) regression, along with quantile regression (QR) estimates of daily feed intake and feeding duration. The correlations between these resilience traits and production traits were subsequently estimated. Single-trait genome-wide association studies (GWASs) were performed using imputed resequencing data to identify key genomic regions and candidate genes associated with resilience traits. The estimated heritability ranged from 0.103 to 0.267 for resilience traits and 0.293 to 0.560 for production traits. Moderate genetic correlations were observed among the resilience traits, while moderate to high genetic correlations were found between resilience traits and production traits. In particular, the traits RMSEFI, RMSECFI, QRFI, and QRFD exhibited significant moderate to high correlations with most production traits. A genome-wide association study (GWAS) based on imputed whole-genome sequencing data was conducted to identify genomic regions associated with resilience traits in pigs. Using single-trait mixed linear models, 188 SNPs were identified and annotated to 44 candidate genes. Several of these genes (CD74, CSF1R, and HTR4) are involved in host immune responses and signal transduction pathways. These findings contribute to a better understanding of the genetic mechanisms underlying resilience in pigs and provide insights for enhancing genomic selection in pig breeding.

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