Genetic parameter estimates for the use of an aviary with winter garden by laying hens.

The behavioral activity of laying hens in an aviary is indicative of their welfare and health. Furthermore, hens' usage of the different locations within an aviary has been shown to influence laying performance and egg quality. For example, hens that spent a longer duration of time in the nest during laying were observed to have lower laying performance. Therefore, understanding genetics of laying hens' usage of the aviary could be important for predicting egg quality, production traits and health and welfare. The objectives of this study were to estimate genetic parameters for duration of time spent at different locations within the aviary and an adjacent winter garden using a multivariate repeatability model and to compare correlations between time spent in these locations. For this study, a total of 1,106 Dekalb white laying hens (Hendrix Genetics) were genotyped using a proprietary 60K SNP array. These hens had access to 5 different zones within the aviary, which included the top level tier, nest box tier, lower level tier, floor littered area and a winter garden. Hens were in the aviary for a total of 290 d and daily records of duration were collected for each hen visit to any location in the aviary, culminating in a total of 937,740 records. Heritability estimates ranged from 0.05 (0.01) to 0.28 (0.03) for the duration of time spent in the different zones. The lowest heritability was estimated for time spent at the lower level tier, while a higher heritability was estimated for time spent in the floor littered area. A moderately high negative genetic correlation of -0.59 (0.08) was observed between time spent in the top level tier and time spent in the floor littered area, while a favorable correlation of 0.37 (0.14) was found between time spent in the lower level tier and time spent in the winter garden. The findings of this study show that the duration of time spent at different zones within an aviary has genetic basis and could be used for selecting animals for better performance and higher welfare.

Intra-individual variation of hen movements is associated with later keel bone fractures in a quasi-commercial aviary.

Measuring intra- and inter-individual variation in movement can bring important insights into the fundamental ecology of animals and their welfare. Although previous studies identified consistent differences in movements of laying hens within commercial aviaries, the level of consistency was not quantified, limiting our capacity to understand the importance of individual movements for welfare. We aimed to quantify the scope of intra- and inter-individual differences in movements of commercial laying hens and examined their associations with indicators of welfare at the end of production. We quantified individual differences in one composite daily movement score for 80 hens over 54 days post-transfer to a quasi-commercial aviary. Results showed consistent inter-individual differences in movement averages, explaining 44% of the variation, as well as individual variation in predictability and temporal plasticity (at the population-level, hens increased their movements for 39 days). Hens that were more predictable in their daily movements had more severe keel bone fractures at the end of production while we found no such correlation between daily movement averages (individual intercept) and welfare indicators. Our findings highlight the importance of inter-individual difference in intra-individual variation of movements to improve poultry welfare.

High resolution parallel sequencing reveals multistrain Campylobacter in broiler chicken flocks testing 'negative' by conventional culture methods: implications for control of Campylobacter infection.

Contaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR, Campylobacter is typically detected amongst broiler flocks from 3 wk of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of the Campylobacter outer membrane protein, encoded by the porA gene, to test for presence of Campylobacter DNA amongst fresh fecal samples collected from broiler flocks aged 23 to 28 d. Campylobacter DNA was detected in all of the 290 samples tested using the porA target, and in 48% of samples using 16S bacterial profiling, irrespective of whether or not Campylobacter could be detected using conventional qPCR thresholds. A single porAf2 variant was predominant among flocks that would be determined to be Campylobacter 'positive' by conventional means, but a diverse pattern was seen among flocks that were Campylobacter 'negative'. The ability to routinely detect low levels of Campylobacter amongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why single Campylobacter variants proliferate in some broiler flocks and not others.

Similarity in Temporal Movement Patterns in Laying Hens Increases with Time and Social Association.

We explored the relationship between social associations and individual activity patterns in domestic hens. Out of 1420 laying hens, 421 hens were equipped with RFID tags attached to RFID-specific leg bands (leg bands from Company Roxan, Selkirk, Scotland) to continuously track their change in location across four different areas (one indoor and three outdoor areas). Using a combination of social network analysis for quantifying social relationships and dynamic time warping for characterizing the movement patterns of hens, we found that hens were consistent in their individual variation in temporal activity and maintained stable social relationships in terms of preferred association partners. In addition to being consistent, social associations correlated with movement patterns and this correlation strengthened over the period of observation, suggesting that the animals aligned their activity patterns with those of their social affiliates. These results demonstrate the importance of social relationships when considering the expression of individual behaviour. Notably, differences in temporal patterns emerge despite rather homogeneous rearing conditions, same environment, and low genetic diversity. Thus, while variation in behavioural phenotypes can be observed across isolated individuals, this study shows that the social environment within a group can shape and enhance variation in general movement patterns of individual animals.

Groups and Individuals: Optical Flow Patterns of Broiler Chicken Flocks Are Correlated with the Behavior of Individual Birds.

Group level measures of welfare flocks have been criticized on the grounds that they give only average measures and overlook the welfare of individual animals. However, we here show that the group-level optical flow patterns made by broiler flocks can be used to deliver information not just about the flock averages but also about the proportion of individuals in different movement categories. Mean optical flow provides information about the average movement of the whole flock while the variance, skew and kurtosis quantify the variation between individuals. We correlated flock optical flow patterns with the behavior and welfare of a sample of 16 birds per flock in two runway tests and a water (latency-to-lie) test. In the runway tests, there was a positive correlation between the average time taken to complete the runway and the skew and kurtosis of optical flow on day 28 of flock life (on average slow individuals came from flocks with a high skew and kurtosis). In the water test, there was a positive correlation between the average length of time the birds remained standing and the mean and variance of flock optical flow (on average, the most mobile individuals came from flocks with the highest mean). Patterns at the flock level thus contain valuable information about the activity of different proportions of the individuals within a flock.

Cell Proliferation in the Adult Chicken Hippocampus Correlates With Individual Differences in Time Spent in Outdoor Areas and Tonic Immobility.

Access to outdoor areas is provided as a means of enhancing welfare in commercial systems for laying hens (Gallus gallus domesticus), but substantial individual differences exist in their proportional use. Baseline cell proliferation levels of Adult Hippocampal Neurogenesis (AHN) have been associated with individual differences in reactive vs. proactive coping style, and in both mammals and birds, AHN is upregulated by positive experiences including environmental enrichment and exercise. We thus sought to explore whether individual differences in use of outdoor areas and in tonic immobility responses (indicative of fearfulness) were associated with hippocampal cell proliferation and neuronal differentiation. Radio frequency identification technology was used to track the ranging behavior of 440 individual focal hens within a commercially-relevant system over a 72-days period, after which tonic immobility durations were measured. Following hippocampal tissue collection from 58 focal hens, proliferation and neuronal differentiation were measured through quantitative PCR for proliferating cell nuclear antigen (PCNA) and doublecortin mRNA, respectively. Individual differences in tonic immobility duration positively correlated with PCNA expression over the whole hippocampal formation, while greater time spent in outdoor areas (the grassy range and stone yard) was associated with higher proliferation in the rostral subregion. Basal proliferation in the chicken hippocampal formation may thus relate to reactivity, while levels in the rostral region may be stimulated by ranging experience. Doublecortin expression in the caudal hippocampus negatively co-varied with time on the grassy range, but was not associated with tonic immobility duration. This suggests that ranging outside may be associated with stress. Within laying hen flocks, individual differences in hippocampal plasticity thus relate to coping style and use of external areas.

DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns.

Domesticated animals are unique to investigate the contribution of genetic and non-genetic factors to specific phenotypes. Among non-genetic factors involved in phenotype formation are epigenetic mechanisms. Here we aimed to identify whether relative DNA methylation differences in the nidopallium between groups of individuals are among the non-genetic factors involved in the emergence of differential behavioral patterns in hens. The nidopallium was selected due to its important role in complex cognitive function (i.e., decision making) in birds. Behavioral patterns that spontaneously emerge in hens living in a highly controlled environment were identified with a unique tracking system that recorded their transitions between pen zones. Behavioral activity patterns were characterized through three classification schemes: (i) daily specific features of behavioral routines (Entropy), (ii) daily spatio-temporal activity patterns (Dynamic Time Warping), and (iii) social leading behavior (Leading Index). Unique differentially methylated regions (DMRs) were identified between behavioral patterns emerging within classification schemes, with entropy having the higher number. Functionally, DTW had double the proportion of affected promoters and half of the distal intergenic regions. Pathway enrichment analysis of DMR-associated genes revealed that Entropy relates mainly to cell cycle checkpoints, Leading Index to mitochondrial function, and DTW to gene expression regulation. Our study suggests that different biological functions within neurons (particularly in the nidopallium) could be responsible for the emergence of distinct behavior patterns and that epigenetic variation within brain tissues would be an important factor to explain behavioral variation.

Improving intra- and inter-observer repeatability and accuracy of keel bone assessment by training with radiographs.

Assessing keel bone damage reliably and accurately is a requirement for all research on this topic. Most commonly, assessment is done on live birds by palpation and is therefore prone to bias. A 2-day Training School of the COST Action "Identifying causes and solutions of keel bone damage in laying hens" with 16 participants of variable experience was held where palpation of live hens was followed by consulting corresponding radiographic images of keel bones. We hypothesized that the inter-observer and intra-observer repeatabilities as well as the agreement between palpation and assessment from the radiograph (considered as the accuracy) would increase from day 1 to 2. Repeatability estimates were calculated using the R-package rptR and the change in level of accuracy on day 1 and 2 was analyzed with generalized linear models. As predicted, the inter-observer repeatabilities of the assessments of the fractures and deviations were improved by training, but this improvement differed for fractures and deviations between the cranial, middle, and caudal parts of the keel bone. Intra-observer repeatabilities before training also differed between the different parts of the keel bone and were highest for fractures at the caudal part of the keel bone. The training affected the accuracy of palpation to different degrees for the different parts of the keel bone. A training effect was found for the caudal part of the keel bone in regard to fractures and deviations, but for fractures the training effect was missing for the cranial part and for deviations it was missing for the middle part of the keel bone. In conclusion, the training school involving radiographs improved inter-observer repeatabilities in the diagnosis of fractures and deviations of keel bones and thus had the potential to lead to more comparable results among research groups.

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review.

There is increasing evidence of a pivotal role of the gut microbiota (GUT-M) in key physiological functions in vertebrates. Many studies discuss functional implications of the GUT-M not only on immunity, growth, metabolism, but also on brain development and behavior. However, while the influence of the microbiota-gut-brain axis (MGBA) on behavior is documented in rodents and humans, data on farm animals are scarce. This review will first report the well-known influence of the MGBA on behavior in rodent and human and then describe its influence on emotion, memory, social and feeding behaviors in farm animals. This corpus of experiments suggests that a better understanding of the effects of the MGBA on behavior could have large implications in various fields of animal production. Specifically, animal welfare and health could be improved by selection, nutrition and management processes that take into account the role of the GUT-M in behavior.

A Systematic Review of Precision Livestock Farming in the Poultry Sector: Is Technology Focussed on Improving Bird Welfare?

Precision livestock farming (PLF) systems have the potential to improve animal welfare through providing a continuous picture of welfare states in real time and enabling fast interventions that benefit the current flock. However, it remains unclear whether the goal of PLF development has been to improve welfare or increase production efficiency. The aims of this systematic literature review are to provide an overview of the current state of PLF in poultry farming and investigate whether the focus of PLF research has been to improve bird welfare. The study characteristics extracted from 264 peer-reviewed publications and conference proceedings suggest that poultry PLF has received increasing attention on a global scale, but is yet to become a widespread commercial reality. PLF development has most commonly focussed on broiler farming, followed by laying hens, and mainly involves the use of sensors (environmental and wearable) and cameras. More publications had animal health and welfare than production as either one of or the only goal, suggesting that PLF development so far has focussed on improving animal health and welfare. Future work should prioritise improving the rate of commercialisation of PLF systems, so that their potential to improve bird welfare might be realised.

Improving intra- and inter-observer repeatability and accuracy of keel bone assessment by training with radiographs.

Assessing keel bone damage reliably and accurately is a requirement for all research on this topic. Most commonly, assessment is done on live birds by palpation and is therefore prone to bias. A 2-day Training School of the COST Action "Identifying causes and solutions of keel bone damage in laying hens" with 16 participants of variable experience was held where palpation of live hens was followed by consulting corresponding radiographic images of keel bones. We hypothesized that the inter-observer and intra-observer repeatabilities as well as the agreement between palpation and assessment from the radiograph (considered as the accuracy) would increase from day 1 to 2. Repeatability estimates were calculated using the R-package rptR and the change in level of accuracy on day 1 and 2 was analyzed with generalized linear models. As predicted, the inter-observer repeatabilities of the assessments of the fractures and deviations were improved by training, but this improvement differed for fractures and deviations between the cranial, middle, and caudal parts of the keel bone. Intra-observer repeatabilities before training also differed between the different parts of the keel bone and were highest for fractures at the caudal part of the keel bone. The training affected the accuracy of palpation to different degrees for the different parts of the keel bone. A training effect was found for the caudal part of the keel bone in regard to fractures and deviations, but for fractures the training effect was missing for the cranial part and for deviations it was missing for the middle part of the keel bone. In conclusion, the training school involving radiographs improved inter-observer repeatabilities in the diagnosis of fractures and deviations of keel bones and thus had the potential to lead to more comparable results among research groups.

Progression and risk factors of pododermatitis in part-time group housed rabbit does in Switzerland.

In rabbits (Oryctolagus cuniculus L.), pododermatitis is a chronic multifactorial skin disease that appears mainly on the plantar surface of the hind legs. This presumably progressive disease can cause pain leading to poor welfare, yet the progression of this disease has not been thoroughly assessed on the level of individual animals. The aim of this longitudinal study thus was to investigate the possible risk factors and the progression of pododermatitis in group housed breeding does in Switzerland on litter and plastic slats. Three commercial rabbit farms with part-time group housing on litter and plastic slats were visited every four weeks throughout one year. During every visit, the same 201 adult female breeding rabbits (67 does per farm) were evaluated for the presence and severity of pododermatitis. Additionally, the does' age, parity, body weight, reproductive state, hybrid, claw length, cleanliness and moisture of the paws and the temperature and humidity inside the barns were recorded as potential risk factors. The risk factors were analysed through general linear models and additive Bayesian network (ABN) modelling using a directed acyclic graph (DAG) for visualising associations between potential risk factors. The progression of pododermatitis was analysed with a transition matrix. Relative humidity inside the barns, body weight, number of kindlings, age, and claw length were the most important risk factors, all being positively associated with pododermatitis. In contrast to expectations, the cleanliness of the left hind paw was negatively associated with the occurrence of pododermatitis, but the effect was small. In young does, the severity of pododermatitis quickly increased and in some rabbits proceeded to ulcerated spots. It was shown that 60.00%, 14.17% and 3.33% of ulcerated lesions recovered to a state without ulceration within 4, 8 or >12 weeks, respectively.

Pododermatitis in group housed rabbit does in Switzerland-Prevalence, severity and risk factors.

In rabbits (Oryctolagus cuniculus L.), pododermatitis is a chronic multifactorial skin disease that appears mainly on the plantar surface of the hind legs. In later stages, it causes pain leading to poor welfare of affected animals. Pododermatitis is commonly observed in commercial rabbit production in breeding does housed with wire mesh flooring. However, the prevalence in breeding does that are housed in groups on litter and plastic slats is not known. The aim of this cross-sectional study was to investigate the frequency, the severity and possible risk factors of pododermatitis in group housed breeding does in Switzerland on litter and plastic slats. Between June and September 2016 about 30% of all adult female breeding rabbits (1090 animals in total) were evaluated for the presence and the severity of pododermatitis on 17 commercial rabbit farms with group housing. The latter was done with a tagged visual-analogue-scale. Additionally, various animal-related (e.g. hybrid, age or body weight) and environmental risk factors (e.g. temperature, relative humidity or wet area per pen) known from the literature were recorded. The risk factors were analysed with generalized linear models, additive Bayesian network (ABN) models resulting in directed acyclic graphs (DAGs) and random forests with variable importance plots. On average, 25% of the rabbits displayed ulcerative pododermatitis likely to be painful on at least one hind leg, while the prevalence varied between farms from 4 to 49%. The age, body weight and claw-length of the animals were positively associated with pododermatitis as the most important risk factors. The best model explained 37.4% of the observed variance in the primary outcome measure for pododermatitis. These findings demonstrate that pododermatitis is prevalent in female breeding does even in group housing systems with litter and plastic slats. However, the results of this cross-sectional study also indicate that important risk factors may have been missed or were not recorded precisely enough. Thus, more in-depth research is needed to assess risk factors of pododermatitis in view of effectively preventing the occurrence of this painful disease.

Ranging behavior relates to welfare indicators pre- and post-range access in commercial free-range broilers.

Little is known about the effect of accessing an outdoor range on chicken welfare. We tracked individual ranging behavior of 538 mixed-sex Ross 308 chickens on a commercial farm across 4 flocks in winter and summer. Before range access, at 17 to 19 d of age, and post-range access, at 30 to 33 and 42 to 46 d of age in winter and summer flocks respectively, welfare indicators were measured on chickens (pre-range: winter N = 292; summer N = 280; post-range: winter N = 131; summer N = 140), including weight, gait score, dermatitis and plumage condition. Post-ranging autopsies were performed (winter: N = 170; summer: N = 60) to assess breast burn, leg health, and ascites. Fewer chickens accessed the range in winter flocks (32.5%) than summer flocks (82.1%). Few relationships between welfare and ranging were identified in winter, likely due to minimal ranging and the earlier age of post-ranging data collection compared to summer flocks. In summer flocks prior to range access, chickens that accessed the range weighed 4.9% less (P = 0.03) than chickens that did not access the range. Pre-ranging weight, gait score, and overall plumage cover predicted the amount of range use by ranging chickens in summer flocks (P < 0.01), but it explained less than 5% of the variation, suggesting other factors are associated with ranging behavior. In summer flocks post-range access, ranging chickens weighed 12.8% less than non-ranging chickens (P < 0.001). More range visits were associated with lower weight (P < 0.01), improved gait scores (P = 0.02), greater breast plumage cover (P = 0.02), lower ascites index (P = 0.01), and less pericardial fluid (P = 0.04). More time spent on the range was associated with lower weight (P < 0.01) and better gait scores (P < 0.01). These results suggest that accessing an outdoor range in summer is partly related to changes in broiler chicken welfare. Further investigations are required to determine causation.

Susceptibility to keel bone fractures in laying hens and the role of genetic variation.

Keel bone fractures are a well-known welfare problem in modern commercial laying hen systems. The present study sought to identify genetic variation in relation to keel bone fracture susceptibility of 4 distinct crossbred and one pure line, and by extension, possible breeding traits. Susceptibility to fractures were assessed using an ex vivo impact testing protocol in combination with a study design that minimized environmental variation to focus on genetic differences. The 5 crossbred/pure lines differed in their susceptibility to keel bone fractures with the greatest likelihood of fracture in one of the 3 commercial lines and the lowest susceptibility to fractures in one of the experimental lines. Egg production at the hen-level did not differ between the crossbred/pure lines (P > 0.05), though an increased susceptibility to keel bone fractures was associated with thinner eggshells and reduced egg breaking strength, a pattern consistent among all tested crossbred/pure lines. Our findings suggest an association between egg quality and bone strength which appeared to be independent of crossbred/pure line. The findings indicate the benefit of the impact methodology to identify potential breeding characteristics to reduce incidence of keel fracture as well as the potential relationship with eggshell quality.

Limited Associations between Keel Bone Damage and Bone Properties Measured with Computer Tomography, Three-Point Bending Test, and Analysis of Minerals in Swiss Laying Hens.

Keel bone damage is a wide-spread welfare problem in laying hens. It is unclear so far whether bone quality relates to keel bone damage. The goal of the present study was to detect possible associations between keel bone damage and bone properties of intact and damaged keel bones and of tibias in end-of-lay hens raised in loose housing systems. Bones were palpated and examined by peripheral quantitative computer tomography (PQCT), a three-point bending test, and analyses of bone ash. Contrary to our expectations, PQCT revealed higher cortical and trabecular contents in fractured than in intact keel bones. This might be due to structural bone repair after fractures. Density measurements of cortical and trabecular tissues of keel bones did not differ between individuals with and without fractures. In the three-point bending test of the tibias, ultimate shear strength was significantly higher in birds with intact vs. fractured keel bones. Likewise, birds with intact or slightly deviated keel bones had higher mineral and calcium contents of the keel bone than birds with fractured keel bones. Calcium content in keel bones was correlated with calcium content in tibias. Although there were some associations between bone traits related to bone strength and keel bone damage, other factors such as stochastic events related to housing such as falls and collisions seem to be at least as important for the prevalence of keel bone damage.

Ranging Behaviour of Commercial Free-Range Broiler Chickens 1: Factors Related to Flock Variability.

Little is known about the ranging behaviour of chickens. Understanding ranging behaviour is required to improve management and shed and range design to ensure optimal ranging opportunities. Using Radio Frequency Identification technology, we tracked 300 individual broiler chickens in each of four mixed sex ROSS 308 flocks on one commercial farm across two seasons. Ranging behaviour was tracked from the first day of range access (21 days of age) until 35 days of age in winter and 44 days of age in summer. Range use was higher than previously reported from scan sampling studies. More chickens accessed the range in summer (81%) than winter (32%; p < 0.05). On average, daily frequency and duration of range use was greater in summer flocks (4.4 ± 0.1 visits for a total of 26.3 ± 0.8 min/day) than winter flocks (3.2 ± 0.2 visits for a total of 7.9 ± 1.0 min/day). Seasonal differences were only marginally explained by weather conditions and may reflect the reduction in range exposure between seasons (number of days, hours per day, and time of day). Specific times of the day (p < 0.01) and pop-holes were favoured (p < 0.05). We provide evidence of relationships between ranging and external factors that may explain ranging preferences.

Ranging Behaviour of Commercial Free-Range Broiler Chickens 2: Individual Variation.

Little is known about broiler chicken ranging behaviour. Previous studies have monitored ranging behaviour at flock level but whether individual ranging behaviour varies within a flock is unknown. Using Radio Frequency Identification technology, we tracked 1200 individual ROSS 308 broiler chickens across four mixed sex flocks in two seasons on one commercial farm. Ranging behaviour was tracked from first day of range access (21 days of age) until 35 days of age in winter flocks and 44 days of age in summer flocks. We identified groups of chickens that differed in frequency of range visits: chickens that never accessed the range (13 to 67% of tagged chickens), low ranging chickens (15 to 44% of tagged chickens) that accounted for <15% of all range visits and included chickens that used the range only once (6 to 12% of tagged chickens), and high ranging chickens (3 to 9% of tagged chickens) that accounted for 33 to 50% of all range visits. Males spent longer on the range than females in winter (p < 0.05). Identifying the causes of inter-individual variation in ranging behaviour may help optimise ranging opportunities in free-range systems and is important to elucidate the potential welfare implications of ranging.

Individual Ranging Behaviour Patterns in Commercial Free-Range Layers as Observed through RFID Tracking.

In this exploratory study, we tracked free-range laying hens on two commercial flocks with Radio Frequency Identification (RFID) technology with the aim to examine individual hen variation in range use. Three distinct outdoor zones were identified at increasing distances from the shed; the veranda [0-2.4 m], close range [2.4-11.4 m], and far range [>11.4 m]. Hens' movements between these areas were tracked using radio frequency identification technology. Most of the hens in both flocks (68.6% in Flock A, and 82.2% in Flock B) accessed the range every day during the study. Of the hens that accessed the range, most hens accessed all three zones (73.7% in Flock A, and 84.5% in Flock B). Hens spent half of their time outdoors in the veranda area. Within-individual consistency of range use (daily duration and frequency) varied considerably, and hens which were more consistent in their daily range use spent more time on the range overall (p < 0.001). Understanding variation within and between individuals in ranging behaviour may help elucidate the implications of ranging for laying hens.