Behavioural genetic differences between Chinese and European pigs

Old breeds, new solutions? Effects of two different traditional sire breeds on skin lesions, tail lesions, tail losses, performance and behaviour of rearing pigs

Some studies indicated a relationship between modern, fast-growing, lean-meat-producing hybrid pigs and the occurrence of tail-biting, one of the major issues of conventional pig husbandry. Therefore, this study investigated the effects of different local, traditional sire breeds on the behaviour and performance of rearing pigs. Between December 2019 and November 2020, a total of 1 561 piglets were weaned from hybrid sows (Bundes Hybrid Zucht Programm (BHZP) Landrace × BHZP Large White) that were paired with either Swabian-Hall (SH), Bentheim Black Pied (BB) or BHZP-Piétrain (Pi) boars. Tails of the piglets were left intact (43.5%) or docked (56.5%), and male piglets were castrated. Piglets were conventionally reared on fully slatted plastic flooring in mixed-sex groups. Starting one day after weaning, skin lesions were scored once per pig, and tail lesions and losses were scored weekly until the end of rearing. The average daily gain was documented for the suckling and rearing period. The activity behaviour of eight focal pens was analysed using video recordings. Differences between modern and traditional breeds were found in this study for so-called aggressive and non-aggressive biting pronounced by skin and tail lesions and tail losses. Significantly fewer BB pigs had severe skin lesions on the front body than SH or Pi pigs (P < 0.05). Additionally, piglets that were classified as light (<5.6 kg) at weaning showed skin lesion scores of 0 more often than piglets that were classified with a medium (≥5.6-≤8.3 kg) or heavy (>8.3 kg) weaning weight (P < 0.05). In the first half of the rearing period, significantly more BB pigs were assessed as having no tail lesions and tail losses than SH and Pi pigs (P < 0.01). However, these differences disappeared in the second half of rearing. Either docked or undocked Pi pigs had significantly higher average daily gains than SH and BB pigs (P < 0.05). The activity of the focal pens was not influenced by the sire breed or tail lesion class, which might be due to the limited sample size of eight pens. To conclude, the use of the traditional sire breed BB has the potential to reduce injurious behaviour in the offspring. However, adjustments to the housing and feeding should be taken to further reduce the incidence of tail lesions and losses and to enhance performance.

Analysis of image-based sow activity patterns reveals several associations with piglet survival and early growth

An activity pattern describes variations in activities over time. The objectives of this study are to automatically predict sow activity from computer vision over 11 days peripartum and estimate how sow behavior influences piglet's performance during early lactation. The analysis of video images used the convolutional neural network (CNN) YOLO for sow detection and posture classification of 21 Large White and 22 Meishan primiparous sows housed in individual farrowing pens. A longitudinal analysis and a clustering method were combined to identify groups of sows with a similar activity pattern. Traits under study are as follows: (i) the distribution of time spent daily in different postures and (ii) different activities while standing. Six postures were included along with three classes of standing activities, i.e., eating, drinking, and other, which can be in motion or not and root-pawing or not. They correspond to a postural budget and a standing-activity budget. Groups of sows with similar changes in their budget over the period (D-3 to D-1; D0 and D1-D7) were identified with the k-means clustering method. Next, behavioral traits (time spent daily in each posture, frequency of postural changes) were used as explanatory variables in the Cox proportional hazards model for survival and in the linear model for growth. Piglet survival was influenced by sow behavior on D-1 and during the period D1-D7. Piglets born from sows that were standing and doing an activity other than drinking and eating on D-1 had a 26% lower risk of dying than other piglets. Those born from sows that changed posture more frequently on D1-D7 had a 44% lower risk of dying. The number of postural changes, which illustrate sow restlessness, influenced piglet growth in the three periods. The average daily gain of piglets born from sows that were more restless on D1-D7 and that changed posture more frequently to hide their udder on D0 decreased by 22 and 45 g/d, respectively. Conversely, those born from sows that changed posture more frequently to hide their udder during the period of D1-D7 grew faster (+71 g/d) than the other piglets. Sow restlessness at different time periods influenced piglet performance.

Differential expression of 10 genes in the hypothalamus of two generations of rats selected for a reaction to humans

Individual behavioral differences are due to an interaction of the genotype and the environment. Phenotypic manifestation of aggressive behavior depends on the coordinated expression of gene ensembles. Nonetheless, the identification of these genes and of combinations of their mutual influence on expression remains a difficult task. Using animal models of aggressive behavior (gray rats that were selected for a reaction to humans; tame and aggressive rat strains), we evaluated the expression of 10 genes potentially associated with aggressiveness according to the literature: Cacna1b, Cacna2d3, Drd2, Egr1, Gad2, Gria2, Mapk1, Nos1, Pomc, and Syn1. To identify the genes most important for the manifestation of aggressiveness, we analyzed the expression of these genes in two generations of rats: 88th and 90th. Assessment of gene expression levels was carried out by real-time PCR in the hypothalamus of tame and aggressive rats. This analysis confirmed that 4 out of the 10 genes differ in expression levels between aggressive rats and tame rats in both generations. Specifically, it was shown that the expression of the Cacna1b, Drd2, Egr1, and Gad2 genes does not differ between the two generations (88th vs 90th) within each strain, but significantly differs between the strains: in the tame rats of both generations, the expression levels of these genes are significantly lower as compared to those in the aggressive rats. Therefore, these genes hold promise for further studies on behavioral characteristics. Thus, we confirmed polygenic causes of phenotypic manifestation of aggressive reactions.

The Evidence for a Causal Link Between Disease and Damaging Behavior in Pigs

Damaging behaviors (DB) such as tail and ear biting are prevalent in pig production and reduce welfare and performance. Anecdotal reports suggest that health challenges increase the risk of tail-biting. The prevalence of tail damage and health problems show high correlations across batches within and between farms. There are many common risk factors for tail-biting and health problems, notably respiratory, enteric and locomotory diseases. These include suboptimal thermal climate, hygiene, stocking density and feed quality. The prevalence of tail damage and health problems also show high correlations across batches within and between farms. However, limited evidence supports two likely causal mechanisms for a direct link between DB and health problems. The first is that generalized poor health (e.g., enzootic pneumonia) on farm poses an increased risk of pigs performing DB. Recent studies indicate a possible causal link between an experimental inflammation and an increase in DB, and suggest a link between cytokines and tail-biting. The negative effects of poor health on the ingestion and processing of nutrients means that immune-stimulated pigs may develop specific nutrient deficiencies, increasing DB. The second causal mechanism involves tail-biting causing poor health. Indirectly, pathogens enter the body via the tail lesion and once infected, systemic spread of infection may occur. This occurs mainly via the venous route targeting the lungs, and to a lesser extent via cerebrospinal fluid and the lymphatic system. In carcasses with tail lesions, there is an increase in lung lesions, abscessation, arthritis and osteomyelitis. There is also evidence for the direct spread of pathogens between biters and victims. In summary, the literature supports the association between poor health and DB, particularly tail-biting. However, there is insufficient evidence to confirm causality in either direction. Nevertheless, the limited evidence is compelling enough to suggest that improvements to management and housing to enhance pig health will reduce DB. In the same way, improvements to housing and management designed to address DB, are likely to result in benefits to pig health. While most of the available literature relates to tail-biting, we suggest that similar mechanisms are responsible for links between health and other DB.

The association of C789A polymorphism in the dopamine beta-hydroxylase gene (DBH) and aggressive behaviour in dogs

The genetic basis of aggressive behaviour has been examined extensively, including analysis of genes encoding neurotransmitters, signalling molecules and regulatory enzymes, as well as their synthesis and degradation. Dopamine beta-hydroxylase, an enzyme catalysing the conversion of dopamine into norepinephrine in synaptic endings, significantly affects the modulation of emotional states and behaviour. The aim of this study was to determine the association of C789A polymorphism in the canine dopamine beta-hydroxylase gene (DBH) and aggressive behaviour in dogs. A total of 110 dogs of different breeds were analysed. All animals were classified according to their individual behavioural characteristics, defined by a veterinary interview and observation. Polymorphism was analysed using ACRS-PCR (amplification created restriction site-polymerase chain reaction) method. Significant differences in DBH genotypes and allele frequency between aggressive and non-aggressive dogs were observed (χ2 = 16,232, P = 0.0003). In aggressive dogs, the CC genotype (0.788) and C allele (0.815) were most frequent while in non-aggressive dogs, their frequencies were significantly lower (0.361 and 0.404, respectively). The obtained results indicate that DBH is a promising candidate gene for canine behavioural study.

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating 47 human genome-wide association studies, we demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases.

How to Improve Meat Quality and Welfare in Entire Male Pigs by Genetics

Simple Summary

Successful breeding of entire male pigs needs a better understanding of factors driving meat quality and behavior traits as entire male pigs have lower meat quality, including an occasional strong defect known as boar taint, and more aggressive and sexual behavior. The review provides an update on how genetic factors affecting boar taint compounds and aggressive behavior in male pigs with emphasis on application in selection.

Abstract

Giving up surgical castration is desirable to avoid pain during surgery but breeding entire males raises issues on meat quality, particularly on boar taint, and aggression. It has been known for decades that boar taint is directly related to sexual development in uncastrated male pigs. The proportion of tainted carcasses depends on many factors, including genetics. The selection of lines with a low risk of developing boar taint should be considered as the most desirable solution in the medium to long term. It has been evidenced that selection against boar taint is feasible, and has been set up in a balanced way in some pig populations to counterbalance potential unfavorable effects on reproductive performances. Selection against aggressive behaviors, though theoretically feasible, faces phenotyping challenges that compromise selection in practice. In the near future, new developments in modelization, automatic recording, and genomic data will help define breeding objectives to solve entire male meat quality and welfare issues.

The Role of Genetic Selection on Agonistic Behavior and Welfare of Gestating Sows Housed in Large Semi-Static Groups

Simple Summary

Group-housing of gestating sows is becoming increasingly common worldwide as it offers the sows the opportunity to exercise, display exploratory behaviors, and develop social relationships. Despite its advantages, group-housing as it stands in modern industries also presents several welfare issues such as overt aggression between pen-mates and resulting stress and injuries. To date, breeding companies often largely focused their efforts on genetic selection based on individual production characteristics (e.g., litter size, piglets’ growth, and meat quality) and traditionally ignored the social behaviors and the ability to establish a dominance hierarchy without exacerbated aggression. Hence, the extent to which agonistic behavior differs according to new genetic lines is unknown. The objective of this study was to compare and investigate the influence of two genetic lines on the welfare and performance of sows housed in large semi-static groups (up to 91 animals). While the first genetic line was more aggressive toward pen-mates during gestation, the second had piglets with a lower robustness and survivability. This study raises the difficulty of finding an optimal genetic line, including both positive welfare and productivity outcomes, and points to the urgent need of considering social aspects when developing genetic lines for group-housing.

Abstract

Confinement of gestating sows is becoming banished in favor of group-housing in countries worldwide, forcing breeding companies to develop genetic lines adapted for social living. This study aimed at assessing the influence of two genetic lines selected for high performance (HP1, HP2, derived from Landrace × Yorkshire) on welfare and reproductive performance of sows housed in large semi-static groups (20 groups of 46–91 animals) across several parities. To address this, agonistic behaviors were recorded on d0, d2, d27, and d29 post-mixing while body lesions were scored on d1, d26, and d84. Sows’ individual and reproductive performances were also recorded. HP2 sows were more aggressive than HP1 sows since they fought (p = 0.028) and bullied (p = 0.0009) pen-mates more frequently on d0–d2. HP2 sows had more total body lesions throughout gestation than HP1 sows at higher parities (p < 0.0001). Regarding reproductive performance, HP2 sows lost less piglets (p < 0.0001) and tended to wean more piglets (p = 0.067) than HP1 sows. In conclusion, while HP2 sows were the most aggressive, HP1 sows had piglets with lower survivability, which raises ethical issues in both cases and points to the need of considering social aspects when developing genetic lines for group-housing.

Reestablishment of Social Hierarchies in Weaned Pigs after Mixing

Pigs are animals that live in groups and have social hierarchies within the group. After mixing, they can re-establish social hierarchies within several days through fighting. Dominance hierarchical indices, such as I&SI, Elo rating, and Glicko rating, have been used to analyze social hierarchies of some social animals but not pigs. I&SI index involves iterative calculations that first minimize the number of inconsistencies (I) in a dominance matrix, and then minimize the strength of those inconsistencies (SI). Elo rating and Glicko rating indices are based on the sequence in which interactions occur, and continuously update ratings by looking at interactions sequentially. To study the temporal dynamics of social hierarchy formation and maintenance in weaned pigs after mixing, a total of 102 pigs (47 females and 55 barrows) were selected by similar body weight and mixed in 10 pens (10 or 11 females or barrows per pen). Their behavior was recorded and observed for 72 h after mixing. Results showed that hierarchical indices I&SI, Elo rating, and Glicko rating were associated with each other (|r| = 0.681 ~ 0.942, p < 0.001). I&SI was associated with logarithms of frequency of active attack (|r| = 0.65, p < 0.05) and tended to associated with logarithms of frequency of standoff (|r| = 0.48, p < 0.1). Elo rating, and Glicko rating were associated with the logarithms of duration of being bullied (|r| = 0.393~0.401, p < 0.05). In addition, Glicko rating tended to be associated with the logarithms of duration of active attack and frequency of active attack (|r| = 0.416~0.439, p < 0.1). Multiple linear regression analyses of logarithms of dyadic behavior indicators for three hierarchical indices indicated the same effects. The time (hours) to achieve social stability of pigs after mixing was lower for females than barrows (23.06 ± 4.15 vs. 40.55 ± 4.71 h; p < 0.001). The most dominant pig (the first ranked) in each pen quickly appeared within a few hours after mixing and remained stable. Overall, our study demonstrated that the ranks calculated by the three dominance hierarchical indices: I&SI, Elo rating, and Glicko rating, were consistent and partially associated with part of the dyadic behavioral indicators in weaned pigs after mixing.

Identification of Single Nucleotide Polymorphisms in Porcine MAOA Gene Associated with Aggressive Behavior of Weaned Pigs after Group Mixing

Simple Summary

Monoamine Oxidase A (MAOA) gene had been reported as a candidate gene of aggressive behavior in several species. In the present study, the most aggressive and docile weaned pigs in each pen after group mixing were selected to identify single nucleotide polymorphisms in porcine MAOA gene associated with aggressive behavior. Constructs containing variable lengths of truncated porcine MAOA promoter were used to determine the promoter activity by a dual luciferase reporter system. The core promoter region of porcine MAOA was located at −679 bp to −400 bp. A total of nine single nucleotide polymorphisms (SNPs) in the MAOA gene were genotyped, of which six SNPs had significant differences in allele frequency between the aggressive and docile pigs. Four linked SNPs in porcine MAOA gene were associated with aggressive behavior in weaned pigs after mixing, which can be used as candidate molecular markers for aggressive behavior in pigs.

Abstract

Understanding the genetic background underlying the expression of behavioral traits has the potential to fasten the genetic progress for reduced aggressive behavior of pigs. The monoamine oxidase A (MAOA) gene is known as the “warrior” gene, as it has been previously linked to aggressive behavior in humans and livestock animals. To identify single nucleotide polymorphisms in porcine MAOA gene associated with aggressive behavior of pigs, a total of 500 weaned pigs were selected and mixed in 51 pens. In each pen, two aggressive and two docile pigs (a total of 204 pigs) were selected based on their composite aggressive score (CAS). Ear tissue was sampled to extract genomic DNA. Constructs containing variable lengths of truncated porcine MAOA promoter were used to determine the promoter activity by a dual luciferase reporter system. The core promoter region was located at −679 bp to −400 bp. A total of nine single nucleotide polymorphisms (SNPs) in MAOA gene were genotyped, of which six SNPs had significant differences (p < 0.05) in allele frequency between the aggressive and docile pigs. Linkage disequilibrium and association analyses showed that the pigs inherited the wild genotypes showed more aggressive behavior (p < 0.05) than pigs with the mutant genotypes of the four linked SNPs, rs321936011, rs331624976, rs346245147, and rs346324437. In addition, pigs of GCAA haplotype were more (p < 0.05) aggressive than the pigs with GCGA or ATGG haplotype. The construct containing the wild genotype GG of rs321936011 had lower (p = 0.031) promoter activity compared to the mutant genotype AA. These results suggest that the four linked SNPs in MAOA gene could be considered as a molecular marker for behavioral trait selection in pigs.

Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds

The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by F_st within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.

A quantitative trait locus on chromosome 1 modulates intermale aggression in mice

Aggression between male conspecifics is a complex social behavior that is likely modulated by multiple gene variants. In this study, the BXD recombinant inbred mouse strains (RIS) were used to map quantitative trait loci (QTLs) underlying behaviors associated with intermale aggression. Four hundred and fifty-seven males from 55 strains (including the parentals) were observed at an age of 13 ± 1 week in a resident-intruder test following 10 days of isolation. Attack latency was measured directly within a 10-minute time period and the test was repeated 24 hours later. The variables we analyzed were the proportion of attacking males in a given strain as well as the attack latency (on days 1 and 2, and both days combined). On day 1, 29% of males attacked, and this increased to 37% on day 2. Large strain differences were obtained for all measures of aggression, indicating substantial heritability (intraclass correlations 0.10-0.18). We identified a significant QTL on chromosome (Chr) 1 and suggestive QTLs on mouse Chrs 1 and 12 for both attack and latency variables. The significant Chr 1 locus maps to a gene-sparse region between 82 and 88.5 Mb with the C57BL/6J allele increasing aggression and explaining about 18% of the variance. The most likely candidate gene modulating this trait is Htr2b which encodes the serotonin 2B receptor and has been implicated in aggressive and impulsive behavior in mice, humans and other species.