Inferring the energy cost of resistance to parasitic infection and its link to a trade-off.

Background: In infected hosts, immune responses trigger a systemic energy reallocation away from energy storage and growth, to fuel a costly defense program. The exact energy costs of immune defense are however unknown in general. Life history theory predicts that such costs underpin trade-offs between host disease resistance and other fitness related traits, yet this has been seldom assessed.

Detection of genetic variability in dairy cattle infectivity for bovine tuberculosis.

This study investigated the genetics of bovine tuberculosis (bTB) infectivity in Holstein-Friesian dairy cows using British national data. The analyses included cows with recorded sires from herds affected by bTB outbreaks between 2000 and 2022. Animals were considered bTB-positive if they reacted positively to the skin test and/or had positive post-mortem findings.

Meat yields and primal cut weights from beef carcasses can be predicted with similar accuracies using in-abattoir 3D measurements or EUROP classification grade.

Three-dimensional (3D) measurements extracted from beef carcass images were used to predict the weight of four saleable meat yield (SMY) traits (total SMY and the SMY of the forequarter, flank, and hindquarter) and four primal cuts (sirloin, ribeye, topside and rump). Data were collected at two UK abattoirs using time-of-flight cameras and manual bone out methods. Predictions were made for 484 carcasses, using multiple linear regression (MLR) or machine learning (ML) techniques.

Assessing genotype-environment interactions in Atlantic salmon reared in freshwater loch and recirculating systems.

The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices.

Validating statistical properties of resilience indicators derived from simulated longitudinal performance measures of farmed animals.

Resilience is commonly defined as the ability of an individual to be minimally affected or to quickly recover from a challenge. Improvement of animals' resilience is a vital component of sustainable livestock production but has so far been hampered by the lack of established quantitative resilience measures. Several studies proposed that summary statistics of the deviations of an animal's observed performance from its target performance trajectory (i.

Applying genetic technologies to combat infectious diseases in aquaculture.

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden.

Using in-abattoir 3-dimensional measurements from images of beef carcasses for the prediction of EUROP classification grade and carcass weight.

Imaging technology can aid the automatic extraction of measurements from beef carcasses, which can be used for objective grading. Many abattoirs, however, rely on manual grading due to the required infrastructure and cost, making technology unfeasible. This study explores 3-dimensional (3D) imaging technology, requiring limited infrastructure, and its ability to predict carcass weight, conformation class and fat class for non-invasive, objective classification.

Animal board invited review: Quantification of resilience in farm animals.

Resilience, when defined as the capacity of an animal to respond to short-term environmental challenges and to return to the prechallenge status, is a dynamic and complex trait. Resilient animals can reinforce the capacity of the herd to cope with often fluctuating and unpredictable environmental conditions. The ability of modern technologies to simultaneously record multiple performance measures of individual animals over time is a huge step forward to evaluate the resilience of farm animals.

The WUR0000125 PRRS resilience SNP had no apparent effect on pigs' infectivity and susceptibility in a novel transmission trial.

Background: Porcine reproductive and respiratory syndrome (PRRS) remains one of the most important infectious diseases for the pig industry. A novel small-scale transmission experiment was designed to assess whether the WUR0000125 (WUR for Wageningen University and Research) PRRS resilience single nucleotide polymorphism (SNP) confers lower susceptibility and infectivity to pigs under natural porcine reproductive and respiratory syndrome virus (PRRSV-2) transmission.

Methods: Commercial full- and half-sib piglets (n = 164) were assigned as either Inoculation, Shedder, or Contact pigs.

Genetic differentiation following recent domestication events: A study of farmed Nile tilapia () populations.

Nile tilapia () is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish ().

Exploring the value of genomic predictions to simultaneously improve production potential and resilience of farmed animals.

Sustainable livestock production requires that animals have a high production potential but are also highly resilient to environmental challenges. The first step to simultaneously improve these traits through genetic selection is to accurately predict their genetic merit. In this paper, we used simulations of sheep populations to assess the effect of genomic data, different genetic evaluation models and phenotyping strategies on prediction accuracies and bias for production potential and resilience.

The cost of host genetic resistance on body condition: Evidence from divergently selected sheep.

Trade-offs between host resistance to parasites and host growth or reproduction can occur due to allocation of limited available resources between competing demands. To predict potential trade-offs arising from genetic selection for host resistance, a better understanding of the associated nutritional costs is required. Here, we studied resistance costs by using sheep from lines divergently selected on their resistance to a common blood-feeding gastro-intestinal parasite ().

Genetic Associations of Novel Behaviour Traits Derived from Social Network Analysis with Growth, Feed Efficiency, and Carcass Characteristics in Pigs.

Reducing harmful aggressive behaviour remains a major challenge in pig production. Social network analysis (SNA) showed the potential in providing novel behavioural traits that describe the direct and indirect role of individual pigs in pen-level aggression. Our objectives were to (1) estimate the genetic parameters of these SNA traits, and (2) quantify the genetic associations between the SNA traits and commonly used performance measures: growth, feed intake, feed efficiency, and carcass traits.

Ecological and evolutionary dynamics of multi-strain RNA viruses.

Potential interactions among co-circulating viral strains in host populations are often overlooked in the study of virus transmission. However, these interactions probably shape transmission dynamics by influencing host immune responses or altering the relative fitness among co-circulating strains. In this Review, we describe multi-strain dynamics from ecological and evolutionary perspectives, outline scales in which multi-strain dynamics occur and summarize important immunological, phylogenetic and mathematical modelling approaches used to quantify interactions among strains.

Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission.

Background: The spread of infectious diseases in populations is controlled by the susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection), and recoverability (propensity to recover/die) of individuals. Estimating genetic risk factors for these three underlying host epidemiological traits can help reduce disease spread through genetic control strategies. Previous studies have identified important 'disease resistance single nucleotide polymorphisms (SNPs)', but how these affect the underlying traits is an unresolved question.

Estimation of age-stratified contact rates during the COVID-19 pandemic using a novel inference algorithm.

Well parameterized epidemiological models including accurate representation of contacts are fundamental to controlling epidemics. However, age-stratified contacts are typically estimated from pre-pandemic/peace-time surveys, even though interventions and public response likely alter contacts. Here, we fit age-stratified models, including re-estimation of relative contact rates between age classes, to public data describing the 2020-2021 COVID-19 outbreak in England.

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.

Modeling suggests gene editing combined with vaccination could eliminate a persistent disease in livestock.

Recent breakthroughs in gene-editing technologies that can render individual animals fully resistant to infections may offer unprecedented opportunities for controlling future epidemics in farm animals. Yet, their potential for reducing disease spread is poorly understood as the necessary theoretical framework for estimating epidemiological effects arising from gene-editing applications is currently lacking. Here, we develop semistochastic modeling approaches to investigate how the adoption of gene editing may affect infectious disease prevalence in farmed animal populations and the prospects and time scale for disease elimination.

Animal Board Invited Review: Meta-analysis of genetic parameters for resilience and efficiency traits in goats and sheep.

Genetic selection focused purely on production traits has proven very successful in improving the productive performance of livestock. However, heightened environmental and infectious disease challenges have raised the need to also improve the resilience of animals to such external stressors, as well as their efficiency in utilising available resources. A better understanding of the relationship between efficiency and production and health traits is needed to properly account for it in breeding programmes and to produce animals that can maintain high production performance in a range of environmental conditions with minimal environmental footprint.

Once bitten, twice shy: Aggressive and defeated pigs begin agonistic encounters with more negative emotions.

Aggression between unfamiliar commercial pigs is common and likely invokes strong emotions in contestants. Furthermore, contest outcomes affect subsequent aggressive behaviour, suggesting a potential lasting influence on affective state. Here we used a combination of qualitative and quantitative methods to assess the emotional expression of pigs in agonistic encounters.

Development of a critical appraisal tool for models predicting the impact of 'test, trace, and protect' programmes on COVID-19 transmission.

Objectives: To develop a critical appraisal tool for non-computational-specialist public health professionals to assess the quality and relevance of modelling studies about Test and Trace (and Protect - TTP) programmes' impact on COVID-19 transmission.

Study Design: Decision-making tool development.

Methods: Using Tugwell et al.

Review: Livestock disease resilience: from individual to herd level.

Infectious diseases are a major threat to the sustainable production of high-producing animals. Control efforts, such as vaccination or breeding approaches often target improvements to individual resilience to infections, i.e.

Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States.

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S.

Estimating individuals' genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data.

Individuals differ widely in their contribution to the spread of infection within and across populations. Three key epidemiological host traits affect infectious disease spread: susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection to others) and recoverability (propensity to recover quickly). Interventions aiming to reduce disease spread may target improvement in any one of these traits, but the necessary statistical methods for obtaining risk estimates are lacking.

Genetic Diversity of Cameroon Cattle and a Putative Genomic Map for Resistance to Bovine Tuberculosis.

Bovine Tuberculosis (bTB) caused by is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurization of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding European taurine cattle, such as Holsteins for increased resistance to bTB is feasible.