Poultry Science

IntroductionAntimicrobial Resistance (AMR) presents a critical public health challenge, particularly in smallholder broiler farming, where antibiotics are often used preventively in the absence of effective biosecurity measures. ObjectiveThis study investigates the adoption of biosecurity practices as a sustainable alternative to antibiotics through Participatory Systems Mapping and Experimental Games. MethodsA participatory mixed-methods study was conducted in southern Bangladesh (September 2024-June 2025). Causal Loop Diagrams (CLDs) were co-created with farmers, dealers, and veterinary officers. Ten broiler farmers from single village were selected via purposive and snowball sampling. Experimental games simulated four production cycles where farmers chose Option A (biosecurity, adopters) or Option B (antibiotics, non-adopters) after several interactive trainings. Key metrics including biosecurity compliance (0-12 scale), mortality, FCR, antibiotic use, outbreak history, and economic outcomes were recorded. ResultsCLD analysis revealed a reinforcing loop of increased antibiotic reliance driven by fear of mortality, and balancing loops involving training, biosecurity practices, and consumer incentives to reduce use. Five farmers chose Option A, and both groups remained stable until Round 4. Adopters had flock sizes of 800-2000 birds (non-adopters, 600-1000; mean for both = 1000), were younger, and more educated compared to non-adopters. At baseline, both groups had similar biosecurity scores (0). Adopters had higher mean outbreaks (2 vs. 1.4), mortality (5.6 vs. 4.2), antibiotic use (3.6 vs. 3), and FCR (1.8 vs. 1.6) compared to non-adopters. By Round 4, adopters improved biosecurity scores by 125%, eliminated outbreaks, reduced mortality by 52.6%, stopped antibiotic use, improved FCR by 13.3%, and gained 71.72% profit per bird compared to non-adopters. Non-adopters, influenced by adopters, increased biosecurity scores by 25%, reducing outbreaks, mortality, antibiotic use, and FCR. Adopters also increased direct sales to consumers, yielding a 10%-16% profit gain per bird each round. ConclusionThis study highlights the successful adoption of biosecurity practices by farmers, replacing antibiotics and improving production outcomes. Farmer-driven adoption of these practices fosters long-term sustainability and supports a healthier planet within the One Health framework.

Restlessness is a symptom of chronic boredom in humans and a behavioural phenomenon anecdotally described as a concern in bulls raised for fattening purposes, but it has so far not been addressed in research. The two studies presented in this paper aimed to gain first insights into restlessness in bulls. We operationally defined restlessness by the number of transitions between behaviours in a given time period, and quantified restlessness in bulls of different weight classes (300, 400, 500 kg) on farms keeping bulls on fully-slatted floors (n=8, Study 1) as well as across three different husbandry systems (fully-slatted floor (FS, n=4), straw-based (SB, n=4) and organic pasture (OP, n=3), Study 2). All farms were visited twice, and the behaviour of different individuals was continuously recorded for 15 minutes each between 9 a.m. and 5 p.m. (Study 1) and for 8 minutes each between 6 a.m. and 10 p.m. (Study 2). The effects of weight class and husbandry system were analysed using generalised linear mixed-effects models, and we ran a sequence analysis to cluster observations by the sequence, frequency, and duration of bulls behaviours in Study 1. Bulls kept in fully-slatted floor systems in Study 1 changed their behaviour on average 48.3 times per 10 minutes, with high variability both within and across farms. Weight class did not have a statistically supported effect on the number of transitions, and the sequence analysis revealed four clusters that differed in sequence and in the number of transitions. In Study 2, OP bulls showed fewer transitions than SB and FS bulls (X22 = 23.6, p < 0.001), while SB and FS bulls did not differ. While SB pens were more structured and offered more space per animal, both SB and FS systems can be characterised by monotony, which may explain the similar level of restlessness in both systems. Alternatively, or in addition, the high feeding intensity in SB and FS systems may have caused the higher number of transitions compared to the OP system, potentially elicited by subacute ruminal acidosis and/or laminitis and the resulting pain. However, these explanations are speculative and require systematic disentanglement in future studies. This study provides initial insights into restlessness in bulls and lays the groundwork for future research to identify the causes underlying restlessness and investigate its association with bull welfare.

BackgroundBlack soldier fly larvae (Hermetia illucens, BSFL) efficiently bio-convert organic waste into high-value protein, which has significant potential in domesticated animal feed formulations. BSFL growth and bioconversion potential can be enhanced through selective breeding, which requires accurate estimates of genetic parameters and knowledge of genotype-by-diet (G x D) interactions. However, comprehensive knowledge of G x D interactions is limited, and reports of genetic parameters are sparse across genetic strains and production environments globally. ResultsThis study estimated heritabilities, dominance effects and genetic correlations for BSFL growth traits and quantified G x D interactions. Phenotypes of 2,097 fifth-instar larvae reared on three diets were recorded, including larval body weight (LBW), length (LL), width (LW), and surface area (LSA). All larvae were genotyped using a custom 6K Allegro SNP panel. Genetic parameters and G x D interactions were estimated by fitting an additive-dominance model in ASReml-R. Heritabilities for growth traits were low across diets (0.05-0.14), with diet-specific estimates ranging from low to moderate (0.06-0.36). Dominance effects were significant across the traits (0.09-0.19), and genetic correlations were high among growth traits (>0.81), except between LW and LL (0.51). G x D interactions were moderate across diets (-0.04-0.49). ConclusionResults suggest that moderate to high genetic gain is achievable over a long-term breeding programme, given the genetic basis of growth traits and BSFs short generation interval (38-45 days). However, G x D interactions must be considered, either through combined or diet-specific selection strategies, and the significant dominance effects suggest heterosis could accelerate improvement.

BackgroundThe emergence of the highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in North America, beginning in February 2022, has highlighted the dynamic, unpredictable, and regionally variable risk of infections. Studies are needed to assess the spatiotemporal clustering of HPAI H5 at the interface between wild waterfowl and commercial poultry to better understand and mitigate this risk. MethodsPublicly available data on HPAI H5 detections in wild birds and commercial poultry from January 2022 to January 2026 were analyzed at the county level. Retrospective space-time permutation models were used to identify and scan for clusters with higher than expected detection rates. ResultsA total of 17,091 HPAI H5 detections were reported in wild birds across 1,467 county-level locations. Four species, Mallard (Anas platyrhynchos) (2,848 detections, 16.66%), Canada goose (Branta canadensis) (1,496, 8.75%), Green-winged teal (Anas carolinensis) (1,364, 7.98%), and Snow goose (Anser caerulescens) (1,084, 6.34%), accounted for 39.73% of detections. In commercial poultry, 532 outbreaks in turkey operations, 148 outbreaks in table-egg layer operations, 99 outbreaks in broiler chicken operations, and 89 outbreaks in commercial duck operations were reported, respectively. Several spillover events followed an east-to-west expansion. In early 2022, mallard detections preceded outbreaks in Northeast egg-layer and duck farms, while snow goose detections in the Upper Midwest coincided with turkey farm outbreaks. In the Pacific and Mountain West during summer 2022, detections in Canada geese overlapped with turkey farm outbreaks. A resurgence occurred in the Midwest (2025), with snow and Canada goose detections overlapping severe outbreaks in turkey and layer flocks. Additionally, in the Upper Midwest, Canada goose and mallard detections overlapped with outbreaks in commercial duck farms during fall-winter 2025. ConclusionsThe study findings demonstrate distinct vector-based transmission dynamics of HPAI H5 at the wild waterfowl-poultry interface. Farm biosecurity strategies must adapt to these recurrent, vector-specific risks.

Enteric methane emissions from ruminant livestock contribute to global warming, creating an urgent need for effective mitigation strategies that do not compromise animal productivity and welfare. Methanogenic archaea within the rumen microbiome drive enteric methane emissions. However, large-scale rumen-fluid sampling in commercial production systems is impractical, due to its invasive nature and the associated logistical challenges. This study hypothesised that rumination enables the capture of rumen microbial signals within the oral cavity and using oral microbiome profiles to provide a practical, non-invasive alternative method for proxy methane phenotyping in commercial production systems. To test the hypothesis, we estimated the oral microbiability, defined as the proportion of phenotypic variance in methane emissions explained by oral microbiome variation. Samples were collected from 209 animals across two trials in Queensland, Australia. Oral microbiome samples were obtained from all animals, with paired rumen samples in one trial, and methane emissions were measured using either the sulphur hexafluoride (SF6) tracer technique or the GreenFeed system. Microbial features were characterised using taxonomic and functional annotations, and microbiability was estimated using mixed linear models incorporating microbiome-based relationship matrices. Although the small sample size limited strong conclusions, the oral microbiability estimates reported in this study were comparable to those derived from rumen samples. Functional microbial profiles generally explained a greater proportion of methane variation than taxonomic profiles, suggesting that microbial function is more closely linked to methane production than community composition alone. However, these differences were not statistically significant due to large standard errors. These findings suggest that oral microbiome sampling potentially provides a practical, minimally invasive, scalable proxy method for methane emissions of individual cattle in grazing systems, where direct methane gas measurements are labour-intensive and difficult to implement. Integrating oral microbiome profiles in the existing breeding model with the host genetics, weight and environmental factors could provide a promising pathway for enabling selection for low emissions and advancing reduced emissions livestock farming under real-world production conditions. Lay summaryCattle produce methane as part of their normal digestion and this contributes to climate change. Reducing methane emission in grazing livestock systems is therefore important. However, measuring methane from individual grazing animals is difficult, costly, and often impractical under commercial conditions. The rumen microbiome has been used as a proxy for estimating methane emissions, but collecting rumen samples is invasive and impractical for large-scale use. Because rumination transfers material from the rumen to the mouth, we investigated whether microbes found in cattle mouths could also be used to estimate how much methane an individual animal produced. We suggest that mouth-swab sampling method can be an alternative to rumen fluid sampling because it was less invasive, relatively quick and practically applicable in commercial conditions. Importantly, the microbiome explained a meaningful proportion of the between-animal variation for methane emission. This suggests that collection of mouth swabs is a potentially scalable alternative proxy method to identify cattle that naturally produce less methane. Overall, our findings support the potential use of oral ruminant microbial information to improve breeding and management strategies aimed at reducing methane emissions while maintaining productive livestock systems. Teaser TextThis study demonstrates that collecting oral swabs from the mouths of grazing beef cattle could provide a scalable method to estimate individual methane emissions in commercial production systems, offering a practical alternative to invasive rumen sampling and complex gas measurement systems. These findings support the development of scalable breeding and management strategies for methane mitigation in large-scale livestock production systems.

Trichomonas gallinae is a protozoan parasite of major concern in avian medicine, particularly in domestic pigeons (Columba livia). This study investigated the risk factors associated with the frequency of nitroimidazole resistance and T. gallinae prevalence in domesticated pigeons from Eastern Spain, kept for different competitions. A total of 220 pigeons from 11 lofts were sampled and examined by microscopy and culture, revealing a 63.6% infection prevalence. Genotyping identified genotype C as predominant, with occasional detection of genotype A, mixed A/C infections, and one isolate of Lineage III. In vitro susceptibility testing of 42 isolates showed a high prevalence (81%) of metronidazole resistance (MIC values [&ge;] 20 {micro}g/ml), with minimum inhibitory concentrations (MICs) ranging from 5 to >100 {micro}g/mL in 9/11 pigeon lofts examined. Resistance was significantly associated with the use of metronidazole and was more frequent in young and non-reproductive birds. Biannual treatments and the combination of ronidazole and dimetridazole at higher doses were associated with lower infection rates than monotherapies or annual treatments. No significant associations were found between resistance and environmental or loft management parameters, although poor hygiene and high bird density were common in lofts with resistant strains. These findings highlight the urgent need for regulated treatment protocols, improved biosecurity, and the development of alternative trichomonacidal agents to combat the emergence of drug-resistant T. gallinae in pigeon populations.

BackgroundAlthough the biological mechanism for heterosis has been debated for a long time, heterosis is widely utilized to increase the global productivity of crops and livestock. Recently, the mechanism has been well characterized in crops and livestock with a male-heterogametic XY system due to genomic assembly advancements, especially the availability of haploid genomes. However, the biological mechanism for heterosis remains unclear in poultry possessing the female-heterogametic ZW system. ResultsHere, we assembled chromosome-level diploid and haploid genomes of the Muscovy duck. We developed an efficient and cost-effective method to assemble 12 variation graph-haploid Muscovy duck genomes from three full-sibling pairs with high quality using short-read Illumina sequences. We further characterized genetic, expression and regulatory patterns of parental alleles at multiple scales. We found that maternal haploid genomes generally had more open chromatin organization and higher accessibility, and higher levels of gene expression, while showing similar DNA methylation levels when compared to paternal haploid genomes. In contrast, the female paternal Z chromosome showed the most, and the male paternal Z chromosome presented more, relaxed chromatin organization and chromatin accessibility, and gene expression compared to the male maternal Z chromosome. Thus, the ZW system largely relies on compensation and balance to regulate gene expression on the sex Z chromosome. Moreover, we identified non-Mendelian regions covering 0.26% of the genome ([~]3.18 Mb). These regions contained lower gene density, GC content, and repeat sequence frequency, but were enriched for DNA motifs bound by transcription factors, likely leading to a compacted chromatin structure and lower chromatin accessibility. ConclusionsOur work here provides a comprehensive profile of parental alleles genetic, expression and regulatory patterns in the female-heterogametic ZW system, and might be useful for the utilization of heterosis in poultry.

Proteomic profiling provides a framework for describing breed-specific growth, physiological and adaptive mechanisms in livestock. This study compared the plasma proteomic profiles of Red Sokoto (RS) and West African Dwarf (WAD) goats, with emphasis on growth-related proteins. Plasma samples from 20 goats (RS = 10; WAD = 10) collected across three locations in southwestern Nigeria were analysed using liquid chromatography-mass spectrometry (LC-MS). A total of 66 plasma proteins were identified in RS goats and 59 in WAD goats, of which 14 were associated with growth regulation. Distinct breed-specific expression patterns were evident. RS goats exhibited higher abundance of fibronectin and calmodulin, indicating enhanced tissue remodelling, muscle development, and calcium-mediated signaling. In contrast, WAD goats showed relatively higher expression of key metabolic and endocrine regulators, including insulin, leptin, ghrelin, glucagon, adiponectin, epidermal growth factor, erythropoietin, and thrombopoietin, reflecting greater metabolic efficiency and adaptive resilience. Gene ontology enrichment analysis revealed marked functional divergence between breeds: RS goats demonstrated stronger enrichment of GO terms related to signal transduction efficiency, cell-matrix adhesion, calcium ion binding, and growth-related morphogenetic processes, whereas WAD goats showed enrichment of GO categories associated with energy metabolism, stress adaptation, catabolic regulation, and hematopoietic support. These findings indicate that breed differences in growth potential are driven more by pathway efficiency and functional integration than hormone abundance. Plasma proteomic and GO-based functional profiles highlight coordinated anabolic and structural growth regulation in RS goats and a resilience-oriented metabolic strategy in WAD goats, with important implications for breed-specific selection, conservation, and sustainable goat production systems.

Cross-Fostering, i.e., the exchange of eggs or hatchlings, is a widely used technique, to disentangle genetic from environmental effects or to manipulate the clutch size. In most bird species, this manipulation is easily accepted by the social parents, leading to the conclusion that fostering has no detrimental effect. Using a dataset of four cohorts (N=298) of zebra finches (Taeniopygia castanotis), in which we fostered routinely a single egg into another nest of zebra finches, we explored potential short- and long-time effects of fostering. Noteworthy, these experiments were not designed to test this hypothesis. The objective of the egg fostering experiments was to test for parental recognition (Caspers et al. 2017) and mate choice decisions (Goluke 2018). Consequently, the aim of the present study is purely explorative. Our study confirmed previous findings that fostering has no short-term effects on the morphology and growth rates of the chicks, neither in males nor in females. However, we found that fostering has a sex-specific long-term effect. Females originating from fostered eggs had a significantly reduced lifespan compared to those from non-fostered eggs. Conversely, the lifespan of fostered males was similar to that of non-fostered males. All birds were housed in large groups, experiencing the same conditions after nutritional independence (day 35). Therefore, we can only speculate that fostering might result in early developmental stress, which may affect the individual fitness of females later in life, ultimately leading to shorter lifespans.

In the present study, we assessed the pathogenicity of H5N8 avian influenza viruses belongs to the clade 2.3.4.4b in chicken. Birds of three different dose groups, 102, 104, and 106 EID50 were used in the study. No mortality was observed in 102 EID0 group. Percent cumulative mortality of 104 and 106 EID50 group was 66.67 and 100 %, respectively. Varying duration of MDT of 3.2 and 2 days was observed in 104 and 106 EID50 group, respectively. The CID50 of virus was found to be 104.5 EID50. High no. of viral RNA copies were found both in oropharyngeal and cloacal swabs and in various organs of birds infected in 104 and 106 EID50 group. Significant gross and histological changes and presence of viral antigen in various organs were observed in 104 and 106 EID50 group. So, the study concludes that Indian HPAI, H5N8 isolates are highly pathogenic in nature to chicken by affecting most organs systemically. CID50 of this H5N8 virus indicates poor adaption in chicken and it implies poor transmission possibility of this virus for host species in field condition. Though this virus is highly pathogenic in nature as that of HPAI, H5N1 viruses, absence of endothelial staining in most organ attributes variation in replication process and pathogenesis from HPAI, H5N1 viruses. Hence, further studies need to be done to elucidate the pathobiology of this virus in various bird species. HighlightsO_LIH5N8 virus belong to the clade 2.3.4.4b, Indian isolate is highly pathogenic in nature as that of HPAIV, H5N1. C_LIO_LIThe dose inocula, 102 EID50 is noninfectious to chicken. C_LIO_LIThe dose inocula, 104 and 106 EID50 had caused significant mortality in the inoculated chicken with MDT of 2 and 3.2 days, respectively. C_LIO_LIH5N8 virus was detected with high viral titres in clocal and oral shedding and in multiple organ with the dose inocula, 104 and 106 EID50. C_LIO_LI104 and 106 EID50 of H5N8 inocula virus caused significant gross and histological changes in multiple organs and viral antigens were detected in respective organs. C_LI

Reported avocado dietary fiber (DF) content and composition are inconsistently reported, particularly during ripening. Thus, this study aimed to characterize the amount and type of DF in Hass avocados and evaluate DF changes during ripening. Unripe (day 0), ripe (day 5), and overripe (day 12) Hass avocados were freeze-dried and defatted. DF was analyzed using non-starch polysaccharide (NSP) enzymatic-chemical methods. Per 100g of as-is avocado, unripe contained 3.96g total DF, ripe 3.68g, and overripe 3.26g. In ripe avocados, DF comprised 43% soluble (SDF) and 57% insoluble dietary fiber (IDF). SDF consisted primarily of rhamnogalacturonan-1 and arabinan pectins, while IDF was predominantly cellulose (32%), hemicelluloses (23%), and lignin (2%). Total DF decreased with ripening, with pectin undergoing solubilization and depolymerization, while cellulose and hemicelluloses remained stable. These findings are important as dietary fibers differentially influence intestinal microbial fermentation and health benefits.

Managing post-weaning diarrhoea (PWD) in piglets is difficult due to limits on antibiotics and zinc. Chitosan is emerging as a potential feed additive. We analysed a chito-oligosaccharide hydrochloride (COS-HCl), a low molecular weight (LMW) chitosan, and a medium molecular weight (MMW) chitosan, and assessed their effects on growth, faecal consistency, microbiota, and potential interference with enterotoxigenic Escherichia coli (ETEC). The three chitosans were characterised using {superscript 1}H-NMR, SEC-RI-MS, and SEC-RI-MALLS. COS-HCl had an Mw of 0.824 kDa; LMW and MMW showed Mw ranges of 14.4 kDa (0.3-30 kDa) and 116 kDa (15-600 kDa). Degrees of acetylation were 9.5%, 6.5%, and 15%. Two 42-day field studies evaluated average daily gain (ADG), faecal consistency, and microbiota. In the first trial, COS-HCl at 0.025-0.1% did not significantly affect ADG (-33 to - 12 g/d). In the second, LMW and MMW at 0.01% did not significantly change ADG (-7 and +3 g/d). Faecal consistency, ETEC shedding, and microbiota composition were similar to controls. An enzymatic HPLC-MS method enabled quantification of MMW chitosan in premix. Our results highlight the importance of advanced chitosan characterisation for precision nutrition and suggest that a threshold dosemay be needed to benefit growth and gut health in PWD management. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/714014v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@19c9e23org.highwire.dtl.DTLVardef@152461aorg.highwire.dtl.DTLVardef@7886e0org.highwire.dtl.DTLVardef@df0d9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

Monitoring and improving animal health and welfare is a pressing need. Technological advances are increasing our ability to do so in a range of settings but currently, there are limited uses in experimental settings for less common model animals. Red foxes (Vulpes vulpes) are maintained by the French National Agency for Food, Environmental, and Occupational Health and Safety (ANSES) for regulatory and research purposes, primarily related to its role as a European Union and French Reference Laboratory for rabies and Echinococcus spp. In 2022, four foxes were surgically fitted with internal implants that recorded body temperature and activity levels and subsequently inoculated with rabies virus (RABV). Retrospectively, we tested the potential of these two variables to provide an early warning for the onset of rabies symptoms. We applied two anomaly detection algorithms (Shewhart and EWMA) with varying confidence levels to the data sets and compared how early the different models could detect significant changes while limiting false alarms during the calibration period. We hypothesized that body temperatures would rise significantly and foxes would significantly alter their activity levels at the beginning of infection, both at an earlier stage than is detectable through direct observation. We found that foxes significantly changed their activity during infection. We were best able to detect these changes using the EWMA algorithm, in some cases producing consecutive alarms up to two weeks before the death of an animal, while limiting false alarms. We found no evidence of fever in any of the infected foxes and body temperature did not appear to be a reliable indicator of foxes health. While here we applied our methods to a particularly severe and rarely implemented model with a very small sample size, this proof of concept illustrates the potential of these methods for a wide range of other situations that would benefit from similar long-term monitoring, including experimental protocols with milder clinical signs and routine monitoring for unexpected declines in health or welfare.

Sentinel behaviour occurs when individuals use raised positions to scan for predators while the rest of the group forages. Here, we investigated whether a colonial cooperatively breeding species that forages in large groups, the sociable weaver, Philetairus socius, displays sentinel behaviour. This behaviour has been reported in species with similar ecology, behaviour and foraging habits, (e.g. ground foraging in open habitats where aerial predators are common) and, hence, we expected that it could occur in sociable weavers. On the other hand, sentinel behaviour appears to be less common in species that live in very large groups. We used an experimental set-up consisting of an artificial feeding station and perches to assess occurrence of sentinel related behaviours: (i) perching events > 30s on an elevated position, (ii) head-movements and (iii) alarm calling. Birds were seldom observed perching while others fed, and those that did, perched for periods that were too short to be considered as sentinel behaviour (less than 5s on average). Our results suggest that this behaviour is uncommon or even absent in sociable weavers. We discuss whether other factors such as foraging in very large groups, or interspecific foraging associations might make sentinel behaviour less important in this species.

Sleep plays a key role in both physical recovery and welfare. However, sleep patterns remain poorly documented in animals, particularly in athletic horses. This study aimed to provide a detailed description of sleep quantity and quality in training Thoroughbred racehorses and to investigate their relationships with age, abnormal behaviours, and cortisol. Thirteen Thoroughbreds (2-7 years old) were continuously monitored in their home environment over three consecutive days. An ethogram was used to quantify the two main phases of sleep: Non Rapid Eye Movement sleep (NREM) and Rapid Eye Movement sleep (REM), as well as sleep interruptions (from day 1 at 12:00 a.m. to day 3 at 12:00 a.m.). Sleep Quality Indices (SQI), defined as the quantity of sleep divided by the number of sleep interruptions (SI), were calculated. Behavioural observations of four indicators of poor welfare (alertness, stereotypies, inactivity, aggressiveness towards humans) were performed using scan sampling, and salivary cortisol was measured each morning. Linear models were used to assess the links between sleep quantity and quality, age, mean cortisol, and abnormal behaviours. Sleep quantity was significantly associated with age: positively for total NREM sleep (ANOVA: {chi}{superscript 2} = 5.26, p < 0.05) and, negatively for total REM sleep (ANOVA: {chi}{superscript 2} = 4.46, p <0.05) and total recumbency duration (ANOVA: {chi}{superscript 2} = 5.68, p < 0.05), suggesting an age-related shift favouring NREM over REM. Morning cortisol concentrations and the frequency of abnormal behaviours were significantly higher in horses with lower sleep quality (cortisol: Total SQI, ANOVA: F = 5.26, p < 0.05; Combined SQI, ANOVA: F = 5.40, p < 0.05; abnormal behaviours: Total SQI, ANOVA: F = 4.07, p = 0.074), pointing to a potential link between stress or altered welfare and poorer sleep quality. These findings suggest that, whilst the type and duration of equine sleep may be mainly affected byage, sleep quality is associated with both cortisol levels and the expression of abnormal behaviours, indicating that poor sleep quality may be linked to poor welfare in this population of horses. Thus, sleep appears to be closely linked with racehorse welfare, highlighting the need for further investigation into how it is influenced by factors such as husbandry, training load, recovery, and performance.

Linkage disequilibrium (LD) and haplotype block structure govern the resolution and utility of genomic selection, marker-assisted selection, and genome-wide association studies (GWAS) in livestock. We performed a comprehensive genome-wide characterization of LD decay, haplotype block architecture, and population diversity across all 24 autosomes in Nili-Ravi buffalo (Bubalus bubalis; n = 85), using 43,543 post-quality-control SNPs. Mean genome-wide r2 was 0.124 (median 0.074) and mean D was 0.540 (median 0.481), with LD half-decay at {approx}70 kb. A total of 133 haplotype blocks encompassing 721 SNPs were identified (Gabriel et al., 2002). Haploview analysis of nine chromosomes harbouring bTB resistance candidate genes revealed contrasting selection signatures: directional selection at innate immune loci (IFNG, TLR1; H < 0.55) versus balancing selection at adaptive immune loci (BoLA-DRB3, SP110; H > 1.0). Critically, BBU15 Block 3 (28.6 kb; OR52E5/NCR1 locus, 47.16 Mb) showed a genome-wide significant integrated haplotype score (iHS; -log1 0 p = 5.408), directly co-localising with the published bTB susceptibility QTL (Bermingham et al., 2014). The TAA haplotype (frequency 53.3%) at this block represents a candidate resistance-associated haplotype for marker-assisted selection. These findings provide essential parameters for SNP panel design and bTB resistance breeding in South Asian buffalo.

Island endemic birds are under greater threat than their mainland counterparts. Sedentary living and historically reduced predation may affect island bird sociality and inform their conservation and management. However, detailed studies on their sociality are uncommon. The federally- endangered koloa maoli (Anas wyvilliana, Hawaiian duck, or koloa) is primarily threatened by hybridization with feral mallards and avian botulism outbreaks. We used capture-mark-recapture and genetic data on koloa on the island of Kaua i, a stronghold of remaining koloa, to construct social networks and examine their associations (inferred from co-occurrence in traps) and spatial genetic structure. Information on associations might shed light on preferences for or against mallards and hybrids, and inform planned translocation efforts. Microgeographic spatial genetic structuring where relatedness among individuals scales with geographic distance is a potential liability for maintaining koloa genetic diversity, and would particularly be detrimental during highly localized outbreaks of botulism that could result in the removal of entire lineages. While we found persistent social associations among adult koloa, they were not apparently influenced by plumage traits or body mass, suggesting a lack of social preference for mallard-like individuals. Importantly, we found no spatial patterns of relatedness within the largest refuge. Therefore, botulism outbreaks remain a demographic threat but are unlikely to remove correlated genetic diversity. There were no sex differences in spatial genetic structure and both sexes moved within a refuge. The lack of spatial genetic structure and the presence of many unrelated conspecifics may enable koloa to limit inbreeding and retain genetic diversity without sex-biased dispersal. In the context of future translocations, our results suggest that translocating koloa captured in the same trap together will reduce disruption of preferred associations while also retaining genetic diversity among translocated individuals. LAY SUMMARYO_LIThe koloa maoli (Hawaiian duck, or koloa) is a federally-endangered, island endemic bird. Like other Hawaiian waterbirds, koloa are threatened by introduced predators and habitat loss, but also specifically by hybridization with feral mallards and localized avian botulism outbreaks. Currently, the island of Kaua i has the largest population of non-admixed koloa. We used capture-mark-recapture and genetic data of koloa at two wetland sites on Kaua i to examine their sociality and spatial genetic structure. C_LIO_LIKoloa formed preferential social associations, but they were not based on plumage traits, body mass or genetic relatedness. C_LIO_LIThere was no spatial genetic structure for males and females within a wetland site. Our results suggested that 1) koloa have no preference for mallard-like plumage that might increase hybrid pairing, 2) localized (within-refuge) botulism outbreaks are unlikely to remove close relatives and unique genetic lineages, and 3) translocation of groups could maintain social associations without limiting genetic diversity. C_LI

Breeding programs are essential in aquaculture, improving economically and environmentally important traits. In aquaculture systems, animals are raised in large groups, where social interactions are frequent and can influence individual performance. In these circumstances, indirect genetic effects can play an important role in the response to selection, and consequently, their effects on selection outcomes must be analyzed. This study aimed to evaluate the implications of heterogeneous social interaction effects on fish breeding programs using stochastic simulations. We simulated a fish breeding program with 2000 selection candidates from 1000 families formed by a partial mating design of 100 males and 100 females. Social interactions were simulated, affected by the target phenotype and two latent-personality traits. We investigated how genetic gains and phenotypic variances are affected by the magnitude and direction of social interaction effects on the target phenotype, different selection strategies, and the genetic correlations between the target phenotype and personality traits. Our results showed that increased social interaction effects lead to greater phenotypic variability in the target trait. Under mass selection, the genetic means of personality traits change, and these changes depend on the strength and direction of genetic correlations between the focal and personality traits. Conversely, group selection did not increase phenotypic variability but reduced genetic gain for the focal trait compared to mass selection. Moreover, group selection did not alter the genetic means of personality traits. However, this approach increased the rate of inbreeding per generation, which could be mitigated by optimizing the number of families per group.

Precision-cut lung slices (PCLS) have emerged as a powerful tool for studying the biology of viable human lung tissue. However, the presence of agarose impurities compromises RNA yield and integrity during the extraction process. We tested whether using an alternative Plant kit RNA extraction method to wash agarose impurities or pre-dissolving agarose from PCLS implementing a dissolving buffer for routine RNA isolation in gel-electrophoresis would improve RNA quantity, quality, and integrity. Our results show that RNA quantity and integrity are highly compromised when using a conventional method of RNA extraction. The plant kit and dissolution of agarose increased the RNA quantity to 0.42{+/-}0.11 and 0.65{+/-}0.17 {micro}g/PCLS (measured by the Qubit) and integrity number to 6.60{+/-}0.59 and 9.13{+/-}0.39 (measured by the Bioanalyzer), respectively. The presence of impurities in conventional and Plant kit extractions misled to an overestimation of the RNA quantity and quality using the NanoDrop. The Plant kit and agarose dissolution showed a significant transcript integrity increase in GUSB (p<0.0001) and COL1A1 (p<0.05) expression, validating these methods over conventional extraction. We encourage laboratories applying PCLS experimentation to implement alternative methods to remove agarose impurities during RNA extraction, as well as to rely on sensitive quantitative techniques, such as the Qubit and Bioanalyzer, for RNA quantification and integrity measurements.

Honeybee breeding plans are relatively recent in most countries. In France, diverse small-scale breeding groups are emerging. Beekeepers are highly diverse in their motivations, farm productions and services, practices and management techniques. Yet, little is known about what beekeepers would consider as relevant breeding goals in the design of breeding plans. We therefore conducted an online survey answered by about 250 French beekeepers, mostly professionals, to assess their perceived importance of including 20 pre-defined traits in breeding goals and to identify how beekeeping profiles might influence these priorities. Respondents rated each trait as essential, useful, or useless, and indicated if they wished useful or essential traits to be genetically improved or merely maintained at their current level. Results indicated a strong preference for multi-trait selection, with a median of 13 traits considered useful or essential. Honey yield, disease resistance, swarming tendency, gentleness, and summer feed autonomy, emerged as the main traits of interest with about 90% of beekeepers finding them at least useful. About 40% or more only wished to maintain these traits at their current level rather than to directionally improve them. A major exception to this was disease resistance, that 75% wanted to improve. Bees genetic background influenced the most the importance attributed to breeding goal traits, while other beekeeping profile characteristics only had a marginal effect on breeding goal trait priorities. Some poorly studied traits, such as summer and winter feed autonomy, winter diapause, and longevity, were considered at least useful in a breeding goal by over 70% of beekeepers. Future research is needed to explore possible selection criteria for these traits and estimate the potential for their genetic improvement. ImplicationsOur survey shows that French beekeepers wish to improve or maintain through selective breeding usual colony production and behavioral traits, but also colony resilience, especially disease resistance and feed autonomy. However, trait priorities differ depending on the genetic background of the bees used. This knowledge is essential for designing breeding programs that truly match beekeeper needs and for identifying which traits deserve research attention. In France, beekeepers are increasingly starting breeding efforts to adapt their bees to current conditions, facing growing pressures from climate change, diseases, invasive species, and pesticides. Well-designed breeding programs can support sustainable beekeeping and essential pollination services.