Advancing Genetic Selection and Behavioral Genomics of Working Dogs Through Collaborative Science.

The ancient partnership between people and dogs is struggling to meet modern day needs, with demand exceeding our capacity to safely breed high-performing and healthy dogs. New statistical genetic approaches and genomic technology have the potential to revolutionize dog breeding, by transitioning from problematic phenotypic selection to methods that can preserve genetic diversity while increasing the proportion of successful dogs. To fully utilize this technology will require ultra large datasets, with hundreds of thousands of dogs. Today, dog breeders struggle to apply even the tools available now, stymied by the need for sophisticated data storage infrastructure and expertise in statistical genetics. Here, we review recent advances in animal breeding, and how a new approach to dog breeding would address the needs of working dog breeders today while also providing them with a path to realizing the next generation of technology. We provide a step-by-step guide for dog breeders to start implementing estimated breeding value selection in their programs now, and we describe how genotyping and DNA sequencing data, as it becomes more widely available, can be integrated into this approach. Finally, we call for data sharing among dog breeding programs as a path to achieving a future that can benefit all dogs, and their human partners too.

Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions.

The underlying neurological events accompanying dog domestication remain elusive. To reconstruct the domestication process in an experimental setting, silver foxes (Vulpes vulpes) have been deliberately bred for tame vs aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. The hypothalamus is an essential part of the hypothalamic-pituitary-adrenal axis and regulates the fight-or-flight response, and thus, we hypothesized that selective breeding for tameness/aggressiveness has shaped the hypothalamic transcriptomic profile. RNA-seq analysis identified 70 differentially expressed genes (DEGs). Seven of these genes, DKKL1, FBLN7, NPL, PRIMPOL, PTGRN, SHCBP1L and SKIV2L, showed the same direction expression differences in the hypothalamus, basal forebrain and prefrontal cortex. The genes differentially expressed across the three tissues are involved in cell division, differentiation, adhesion and carbohydrate processing, suggesting an association of these processes with selective breeding. Additionally, 159 transcripts from the hypothalamus demonstrated differences in the abundance of alternative spliced forms between the tame and aggressive foxes. Weighted gene coexpression network analyses also suggested that gene modules in hypothalamus were significantly associated with tame vs aggressive behavior. Pathways associated with these modules include signal transduction, interleukin signaling, cytokine-cytokine receptor interaction and peptide ligand-binding receptors (eg, G-protein coupled receptor [GPCR] ligand binding). Current studies show the selection for tameness vs aggressiveness in foxes is associated with unique hypothalamic gene profiles partly shared with other brain regions and highlight DEGs involved in biological processes such as development, differentiation and immunological responses. The role of these processes in fox and dog domestication remains to be determined.

Behavioral predictors of subsequent respiratory illness signs in dogs admitted to an animal shelter.

Individual variability is evident in behavior and physiology of animals. Determining whether behavior at intake may predict subsequent illness in the animal shelter may influence the management of dogs housed at animal shelters and reduce overall disease. While normally associated with mild disease and low mortality rates, respiratory disease nevertheless poses significant challenges to the management of dogs in the stressful environment of animal shelters due to its highly infectious nature. Therefore, the aim of the study was to explore whether behavior at intake can predict subsequent occurrence and progression of upper respiratory disease in dogs at animal shelters. In a correlational study, 84 dogs were assessed throughout their stay at a city animal shelter. The dogs were subjected to a behavioral assessment, 1 min in-kennel behavioral observations across two observation periods, and the collection of urinary cortisol:creatinine (C:C) ratio. The occurrence and progression of upper respiratory disease was monitored through repeated clinical exams (rectal temperature and the occurrence of nasal and ocular discharge, and presence of coughing and sneezing). A basic PLS Path regression model revealed that time in the shelter (estimate = .53, p < .001), and sociability (estimate = .24, p < .001) and curiosity scores (estimate = .09, p = .026) were associated with increased illness. Activity and anxiety scores, however, were not associated with illness. Urinary C:C, taken on the first full day, did not predict subsequent illness when accounting for time. Limitations included attrition of dogs, a small percentage receiving vaccinations, and continuous and non-systematic rotation of dogs in the kennels. Understanding if behavior can predict subsequent illness may improve shelter management practices, and in turn, result in improved live-release outcomes.

Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.

In the version of this Article originally published, there were some errors in the affiliations: Stephen J. O'Brien's affiliations were incorrectly listed as 8,9; they should have been 7,9. Affiliation 3 was incorrectly named the Institute of Cytology and Genetics of the Russian Academy of Sciences; it should have read Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences. Affiliation 4 was incorrectly named the Institute of Molecular and Cell Biology of the Russian Academy of Sciences; it should have read Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences. These have now been corrected.

Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.

Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes the main trafficking protein for AMPA glutamate receptors and neurexins and suggests a role for synaptic plasticity in fox domestication. Other regions identified as likely to have been under selection in foxes include genes implicated in human neurological disorders, mouse behaviour and dog domestication. The fox represents a powerful model for the genetic analysis of affiliative and aggressive behaviours that can benefit genetic studies of behaviour in dogs and other mammals, including humans.

Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes.

Domesticated species exhibit a suite of behavioral, endocrinological, and morphological changes referred to as "domestication syndrome." These changes may include a reduction in reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and specifically reduced adrenocorticotropic hormone release from the anterior pituitary. To investigate the biological mechanisms targeted during domestication, we investigated gene expression in the pituitaries of experimentally domesticated foxes (Vulpes vulpes). RNA was sequenced from the anterior pituitary of six foxes selectively bred for tameness ("tame foxes") and six foxes selectively bred for aggression ("aggressive foxes"). Expression, splicing, and network differences identified between the two lines indicated the importance of genes related to regulation of exocytosis, specifically mediated by cAMP, organization of pseudopodia, and cell motility. These findings provide new insights into biological mechanisms that may have been targeted when these lines of foxes were selected for behavior and suggest new directions for research into HPA axis regulation and the biological underpinnings of domestication.

Transcriptome Analysis in Domesticated Species: Challenges and Strategies.

Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.

Psychogenic Stress in Hospitalized Dogs: Cross Species Comparisons, Implications for Health Care, and the Challenges of Evaluation.

Evidence to support the existence of health consequences of psychogenic stress has been documented across a range of domestic species. A general understanding of methods of recognition and means of mitigation of psychogenic stress in hospitalized animals is arguably an important feature of the continuing efforts of clinicians to improve the well-being and health of dogs and other veterinary patients. The intent of this review is to describe, in a variety of species: the physiology of the stress syndrome, with particular attention to the hypothalamic-pituitary-adrenal axis; causes and characteristics of psychogenic stress; mechanisms and sequelae of stress-induced immune dysfunction; and other adverse effects of stress on health outcomes. Following that, we describe general aspects of the measurement of stress and the role of physiological measures and behavioral signals that may predict stress in hospitalized animals, specifically focusing on dogs.

Salivary cortisol concentrations and behavior in a population of healthy dogs hospitalized for elective procedures.

Identification of severe stress in hospitalized veterinary patients may improve treatment outcomes and welfare. To assess stress levels, in Study 1, we collected salivary cortisol samples and behavioral parameters in 28 healthy dogs hospitalized prior to elective procedures. Dogs were categorized into two groups; low cortisol (LC) and high cortisol (HC), based on the distribution of cortisol concentrations (< or ≥ 0.6 µg/dL). We constructed a stress research tool (SRT) based on three behaviors, (head resting, panting and lip licking) that were most strongly related to salivary cortisol concentrations. In Study 2, we collected salivary cortisol samples from 39 additional dogs, evaluated behavior/cortisol relationships, assigned each dog to an LC or HC group, and tested the ability of the SRT to predict salivary cortisol. Median (interquartile range) salivary cortisol concentrations were not different between Study 1 (0.43 µg/dL, 0.33 to 1.00 µg/dL) and Study 2 dogs (0.41 µg/dL, 0.28 to 0.52 µg/dL). The median salivary cortisol concentration was significantly lower (P ≤ 0.001) in LC versus HC dogs in each study; (Study 1 LC: 0.38 µg/dL, (0.19 to 0.44), n = 19, HC: 2.0 µg/dL, (1.0 to 2.8), n = 9, and Study 2 LC: 0.35 µg/dL, (0.25 to 0.48), n = 28, HC: 0.89 µg/dL, (0.66 to 1.4), n = 7). In Study 1, three behaviors were found to be associated with salivary cortisol concentrations. Duration of head resting was negatively associated with salivary cortisol (ρ = -0.60, P = 0.001), panting and lip licking were positively associated with cortisol (ρ = 0.39, P = 0.04, and 0.30, P = 0.05, respectively), Head resting (p = 0.001) and panting (p = 0.003) were also associated with LC/HC group assignment. In Study 2 dogs, the three behaviors correlated (but not significantly) with salivary cortisol concentration; of the three, only head resting was significantly associated with LC/HC group assignment (P = 0.03). The SRT derived from Study 1 was effective at prediction of salivary cortisol concentrations when applied to 20 min but not 2 min of behavioral data from Study 2. Additionally, we note that dexmedetomidine and butorphanol sedation more than 6 h prior to measurement was found to be significantly (P = 0.05) associated with lower salivary cortisol concentrations when compared to unsedated dogs. Our work offers support for eventual construction of a rating tool that utilizes the presence or absence of specific behaviors to identify higher salivary cortisol concentrations in dogs subjected to hospitalization, which may be tied to greater psychogenic stress levels. Future work to investigate the effects of stress on dogs and its mitigation in clinical situations may be approached by studying a combination o f parameters, and should consider the possible beneficial effects of sedatives.