Pigs' skin lesions at weaning are primarily caused by standoff and being bullied instead of unilateral active attack at the individual level

Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs

Copy number variation (CNV) represents a significant reservoir of genetic diversity within the genome and exhibits a strong association with economically valuable traits in livestock. The manifestation of aggressive behavior in pigs has detrimental effects on production efficiency, immune competency, and meat quality. Nevertheless, the impact of CNV on the aggressive behavior of pigs remains elusive. In this investigation, we employed an integrated analysis of genome and transcriptome data to investigate the interplay between CNV, gene expression changes, and indicators of aggressive behavior in weaned pigs. Specifically, a subset of pigs comprising the most aggressive pigs (MAP, n = 12) and the least aggressive pigs (LAP, n = 11) was purposefully selected from a herd of 500 weaned pigs following a mixing procedure based on their composite aggressive score (CAS). Subsequently, we thoroughly analyzed copy number variation regions (CNVRs) across the entire genome using next-generation sequencing techniques, ultimately revealing the presence of 6869 CNVRs. Using genome-wide association study (GWAS) analysis and evaluating variance-stabilizing transformation (VST) values, we successfully identified distinct CNVRs that distinguished the MAP and LAP counterparts. Among the prioritized CNVRs, CNVR-4962 (designated as the top-ranked p-value and VST value, No. 1) was located within the Solute Carrier Organic Anion Transporter Family Member 3A1 (SLCO3A1) gene. The results of our analyses indicated a significantly higher (p < 0.05) copy number of SLCO3A1 in the MAP compared to the LAP. Furthermore, this increased copy number exhibited a positive correlation with the CAS of the pigs (p < 0.05). Furthermore, we integrated genomic data with transcriptomic data from the temporal lobe to facilitate the examination of expression quantitative trait loci (eQTL). Importantly, these observations were consistent with the mRNA expression pattern of SLCO3A1 in the temporal lobe of both MAP and LAP (p < 0.05). Consequently, our findings strongly suggest that CNVs affecting SLCO3A1 may influence gene expression through a dosage effect. These results highlight the potential of SLCO3A1 as a candidate gene associated with aggressive traits in pig breeding programs.

Assessment of slaughterhouse-based measures as animal welfare indicators in fattening pigs

In recent years, there has been growing interest in the assessment of animal welfare in slaughterhouses. The aim of this study was to determine the effectiveness of slaughter-based measures as animal welfare indicators and evaluate the relationships between these indicators and the sociodemographic characteristics of livestock drivers and transport conditions for fattening pigs in a commercial slaughterhouse. A total of 1,161 heavy pigs (105.6 ± 14.15 kg), from 22 commercial farms, were evaluated. Pigs were assessed ante mortem, during lairaging, by evaluating the number, location, and color of skin lesions, tail length, and the presence or absence of biting lesions, lameness, cough, rectal or vaginal prolapse, and umbilical hernia. Pulmonary lesions, pleuritis, pericarditis, and liver lesions were also recorded postmortem. A descriptive analysis was performed on antemortem and postmortem indicators to estimate their prevalence, and the relationships among antemortem and postmortem indicators were analyzed using two multilevel mixed-effects models—a linear regression and a logistic regression analysis— with the farm of origin as a fixed effect. Cough was present in 18.9% (n = 219) of pigs, whereas the prevalence of tail biting lesions (4.6%, n = 53), rectal prolapse (0.1%, n = 11), and vaginal prolapse (0.1%, n = 11) was low. As regards lesion shape, linear lesions accounted for the majority of skin lesions (55.8%, n = 648), followed by comma-shaped (34.7%, n = 403), diffuse (6.9%, n = 80), and rectangular lesions (2.5%, n = 29). Only 25.2% (n = 512) of lesions were bright red. At postmortem, pulmonary lesions were noted in 34.2 ± 13.5 (mean ± SEM) pigs, and were more prevalent in the cranial (11.9 ± 4.9) and medium lobes (12.2 ± 5.2); the caudal (5.3 ± 2.7) and accessory lobes (1.6 ± 1.6) were less affected. The number of skin lesions was significantly associated with drivers’ age, job experience (years), and marital status (p ≤ 0.001). The presence or absence of tail lesions was strongly associated with the number of skin lesions, scoring of pulmonary lesions, and animal live weight (p ≤ 0.001). Antemortem and postmortem indicators at slaughterhouses with low annual slaughter volumes can provide key information for disease monitoring and animal welfare.

Genetic Analysis of Novel Behaviour Traits in Pigs Derived from Social Network Analysis

Social network analysis (SNA) has provided novel traits that describe the role of individual pigs in aggression. The objectives were to (1) estimate the genetic parameters for these SNA traits, (2) quantify the genetic association between SNA and skin lesion traits, and (3) investigate the possible response to selection for SNA traits on skin lesion traits. Pigs were video recorded for 24 h post-mixing. The observed fight and bullying behaviour of each animal was used as input for the SNA. Skin lesions were counted on different body parts at 24 h (SL24h) and 3 weeks (SL3wk) post-mixing. A Bayesian approach estimated the genetic parameters of SNA traits and their association with skin lesions. SNA traits were heritable (h2 = 0.09 to 0.26) and strongly genetically correlated (rg > 0.88). Positive genetic correlations were observed between all SNA traits and anterior SL24h, except for clustering coefficient. Our results suggest that selection for an index that combines the eigenvector centrality and clustering coefficient could potentially decrease SL24h and SL3wk compared to selection for each trait separately. This study provides a first step towards potential integration of SNA traits into a multi-trait selection index for improving pigs’ welfare.