Genetic mapping of canine fear and aggression

High-throughput DNA sequence analysis elucidates novel insight into the genetic basis of adaptation in local sheep

Understanding how evolutionary factors related to climate adaptation and human selection have influenced the genetic architecture of domesticated animals is of great interest in biology. In the current study, by using 304 whole genomes from different geographical regions (including Europe, north Africa, Southwest Asia, east Asia, west Africa, south Asia, east Africa, Australia and Turkey), We evaluate global sheep population dynamics in terms of genetic variation and population structure. We further conducted comparative population analysis to study the genetic underpinnings of climate adaption to local environments and also morphological traits. In order to identify genomic signals under selection, we applied fixation index (FST) and also nucleotide diversity (θπ) statistical measurements. Our results revealed several candidate genes on different chromosomes under selection for local climate adaptation (e.g. HOXC12, HOXC13, IRF1, FGD2 and GNAQ), body size (PDGFA, HMGA2, PDE3A) and also morphological related traits (RXFP2). The discovered candidate genes may offer newel insights into genetic underpinning of regional adaptation and commercially significant features in local sheep.

Transposons in the Williams-Beuren Syndrome Critical Region are Associated with Social Behavior in Assistance Dogs

A strong signature of selection in the domestic dog genome is found in a five-megabase region of chromosome six in which four structural variants derived from transposons have previously been associated with human-oriented social behavior, such as attentional bias to social stimuli and social interest in strangers. To explore these genetic associations in more phenotypic detail-as well as their role in training success in a specialized assistance dog program-we genotyped 1001 assistance dogs from Canine Companions for Independence®, including both successful graduates and dogs released from the training program for behaviors incompatible with their working role. We collected phenotypes on each dog using puppy-raiser questionnaires, trainer questionnaires, and both cognitive and behavioral tests. Using Bayesian mixed models, we found strong associations (95% credibility intervals excluding zero) between genotypes and certain behavioral measures, including separation-related problems, aggression when challenged or corrected, and reactivity to other dogs. Furthermore, we found moderate differences in the genotypes of dogs who graduated versus those who did not; insertions in GTF2I showed the strongest association with training success (β = 0.23, CI95% = - 0.04, 0.49), translating to an odds-ratio of 1.25 for one insertion. Our results provide insight into the role of each of these four transposons in canine sociability and may inform breeding and training practices for working dog organizations. Furthermore, the observed importance of the gene GTF2I supports the emerging consensus that variation in GTF2I genotypes and expression have important consequences for social behavior broadly.

Ethical Concerns about Fashionable Dog Breeding

The historical relationship between humans and dogs has involved selective breeding for various purposes, such as hunting, guarding, and service roles. However, over time, there has been a shift in preferences from functionality to aesthetics, which has influenced the diverse sizes, shapes, and coats of dog breeds. This review looks at fashionable dog breeding and questions the ethics of prioritising looks over health and behaviour. It aims to alert potential owners, breeders, and regulators to the importance of considering a dog's overall well-being, not just its appearance, which has resulted in fad breeding, leading to genetic disorders, health issues, and a loss of biodiversity. Ethical concerns arise from breeding brachycephalic breeds with respiratory conditions, inbreeding causing inherited disorders, and overbreeding popular breeds while shelter dogs remain unadopted. Additionally, the impact of cosmetic surgeries on popular dog breeds, as well as the neglect of behavioural traits in favour of physical characteristics and strict breeding practices are also considered. The current breeding model can have a negative impact on the emotional and cognitive well-being of dogs, resulting in issues such as aggression, anxiety, and other behavioural problems that can significantly reduce their overall quality of life. Unregulated breeding practices and the demand for rare breeds can lead to illegal breeding, compromising animal welfare. Prospective owners, veterinarians, kennel clubs, and legislators all need to play a responsible role in protecting animals.

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (π) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, Fst & π ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep.

The Relation between Plasma Nesfatin-1 Levels and Aggressive Behavior in Pit Bull Dogs

Aggression is a prevalent and concerning behavioral issue in dogs. Pit Bull dogs, known for their high levels of aggression, are recognized as a focus of concern in society. In our study, we aimed to investigate the behavioral characteristics of Pit Bull dogs and explore the potential roles of peptides involved in the neurobiology of aggression. Initially, female, and male dogs underwent aggression tests, and their aggression levels were categorized. Plasma nesfatin-1, serotonin, oxytocin, and dopamine levels were quantified using ELISA, with blood samples collected after a 24 h fasting period and 2 h post-refeeding. Our findings indicate that aggression in Pit Bull dogs correlates with decreased plasma nesfatin-1, serotonin, and oxytocin levels, while dopamine levels increase. The study's findings indicate that fasted dogs exhibited lower plasma levels of nesfatin-1, serotonin, and dopamine, while plasma oxytocin levels were higher. Furthermore, while the research findings do not suggest a significant relationship between the severity of aggression and the gender of the dog, male Pit Bull breeds appear to have higher plasma nesfatin-1 and serotonin levels compared to their female counterparts. The study's findings demonstrate that nesfatin-1, serotonin, oxytocin, and dopamine play pivotal roles in Pit Bull dogs' aggression, indicating potential interactions among these neuropeptides at the central nervous system level.

The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development

Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.

Multitrait meta-analyses identify potential candidate genes for growth-related traits in Holstein heifers

Understanding the underlying pleiotropic relationships among growth and body size traits is important for refining breeding strategies in dairy cattle for optimal body size and growth rate. Therefore, we performed single-trait GWAS for monthly-recorded body weight (BW), hip height, body length, and chest girth from birth to 12 mo of age in Holstein animals, followed by stepwise multiple regression of independent or lowly-linked markers from GWAS loci using conditional and joint association analyses (COJO). Subsequently, we conducted a multitrait meta-analysis to detect pleiotropic markers. Based on the single-trait GWAS, we identified 170 significant SNPs, in which 59 of them remained significant after the COJO analyses. The most significant SNP, located at BTA7:3,676,741, explained 2.93% of the total phenotypic variance for BW6 (BW at 6 mo of age). We identified 17 SNPs with potential pleiotropic effects based on the multitrait meta-analyses, which resulted in 3 additional SNPs in comparison to those detected based on the single-trait GWAS. The identified quantitative trait loci regions overlap with genes known to influence human growth-related traits. According to positional and functional analyses, we proposed HMGA2, HNF4G, MED13L, BHLHE40, FRZB, DMP1, TRIB3, and GATAD2A as important candidate genes influencing the studied traits. The combination of single-trait GWAS and meta-analyses of GWAS results improved the efficiency of detecting associated SNPs, and provided new insights into the genetic mechanisms of growth and development in Holstein cattle.

A purebred South American breed showing high effective population size and independent breed ancestry: The Chilean Terrier

The Chilean Terrier is a known breed in Chile that has not been genetically assessed despite its distinctive color patterns, agility, and hardiness across the diversity of climates encountered within the Chilean landscape. The population structure and its relatedness with other breeds, as well as the actual origin of the breed, remain unknown. We estimated several population parameters using samples from individuals representing the distribution of the Chilean Terrier across the country. By utilizing the Illumina HD canine genotyping array, we computed the effective population size (Ne ), individual inbreeding, and relatedness to evaluate the genetic diversity of the breed. The results show that linkage disequilibrium was relatively low and decayed rapidly; in fact, Ne was very high when compared to other breeds, and similar to other American indigenous breeds (such as the Chihuahua with values of Ne near 500). These results are in line with the low estimates of genomic inbreeding and relatedness and the relatively large number of effective chromosome segments (Me  = 2467) obtained using the properties of the genomic relationship matrix. Between population analysis (cross-population extended haplotype homozygosity, di ) with other breeds such as the Jack Russell Terrier, the Peruvian-Inca Orchid, and the Chihuahua suggested that candidate regions harboring FGF5, PAX3, and ASIP, probably explained some morphological traits, such as the distinctive color pattern characteristic of the breed. When considering Admixture estimates and phylogenetic analysis, together with other breeds of American and European origin, the Chilean Terrier does not have a recent European ancestry. Overall, the results suggest that the breed has evolved independently in Chile from other terrier breeds, from an unknown European terrier ancestor.

Veterinary education and experience shape beliefs about dog breeds. Part 2: Trust

Dog breed stereotypes are frequently used to inform people's expectations about canine behavior, despite evidence that breed is largely uninformative in predicting individual dog behavior. Further, these beliefs differ among populations. However, it remains unknown how ratings of warmth toward a breed are associated with ratings of other social behavioral domains, and whether differences exist between populations with varying experience with dogs. The purpose of this study was to evaluate ratings of trust and warmth among survey respondents including veterinary students, veterinary faculty and staff, undergraduates in animal-health related majors and members of the general public. Using an online survey, respondents rated their likelihood to trust a dog in varying scenarios for 10 different dog breeds. Additionally, respondents used a feelings thermometer to rate how warm or cool they felt towards each breed. Findings revealed differences in feelings thermometer and trust ratings across populations. All ratings were lower among the veterinary academic respondents compared to the general public and undergraduates. Veterinary students further along in their training, as well as undergraduates with clinical experience, reflected perceptions similar to those of the veterinary faculty and staff providing support for cultural transmission of beliefs during veterinary education and training.

Machine learning prediction and classification of behavioral selection in a canine olfactory detection program

There is growing interest in canine behavioral research specifically for working dogs. Here we take advantage of a dataset of a Transportation Safety Administration olfactory detection cohort of 628 Labrador Retrievers to perform Machine Learning (ML) prediction and classification studies of behavioral traits and environmental effects. Data were available for four time points over a 12 month foster period after which dogs were accepted into a training program or eliminated. Three supervised ML algorithms had robust performance in correctly predicting which dogs would be accepted into the training program, but poor performance in distinguishing those that were eliminated (~ 25% of the cohort). The 12 month testing time point yielded the best ability to distinguish accepted and eliminated dogs (AUC = 0.68). Classification studies using Principal Components Analysis and Recursive Feature Elimination using Cross-Validation revealed the importance of olfaction and possession-related traits for an airport terminal search and retrieve test, and possession, confidence, and initiative traits for an environmental test. Our findings suggest which tests, environments, behavioral traits, and time course are most important for olfactory detection dog selection. We discuss how this approach can guide further research that encompasses cognitive and emotional, and social and environmental effects.

Enrichment of self-domestication and neural crest function loci in the heritability of neurodevelopmental disorders

Self-domestication could contribute to shaping the biology of human brain and consequently the predisposition to neurodevelopmental disorders. Leveraging genome-wide data from the Psychiatric Genomics Consortium, we tested the enrichment of self-domestication and neural crest function loci with respect to the heritability of autism spectrum disorder, schizophrenia (SCZ in East Asian and European ancestries, EAS and EUR, respectively), attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, and Tourette's syndrome (TS). Considering only self-domestication and neural-crest-function annotations in the linkage disequilibrium score regression (LDSC) model, our partitioned heritability analysis revealed statistically significant enrichments across all disorders investigated. The estimates of the heritability enrichments for self-domestication loci were similar across neurodevelopmental disorders, ranging from 0.902 (EAS SCZ, p = 4.55 × 10-20) to 1.577 (TS, p = 5.85 × 10-5). Conversely, a wider spectrum of heritability enrichment estimates was present for neural crest function with the highest enrichment observed for TS (enrichment = 3.453, p = 2.88 × 10-3) and the lowest for EAS SCZ (enrichment = 1.971, p = 3.81 × 10-3). Although these estimates appear to be strong, the enrichments for self-domestication and neural crest function were null once we included additional annotations related to different genomic features. This indicates that the effect of self-domestication on the polygenic architecture of neurodevelopmental disorders is not independent of other functions of human genome.

The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds

Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: FST, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.

An Assessment of Scientific Evidence Relating to the Effect of Early Experience on the Risk of Human-Directed Aggression by Adult Dogs

Human-directed aggression by domestic dogs is a major worldwide public health problem. The causes of aggression are complex, and research in this area often has to balance ecological validity with pragmatic controls; accordingly, it often does not meet the thresholds for quality typically used in reviews applying a classical "evidence-based" approach. Here, we propose a method of literature assessment that makes the "best use" of available evidence to identify and synthesise evidence relating to the most likely risk factors reported in the scientific literature. We used a systematic review process to initially identify relevant literature relating to potential early life experience (i.e., in the first six months of life) risk factors in the dog for human-directed aggression in the adult animal. Fourteen papers met our initial screening process and were subsequently analysed in detail, with data extracted and effect sizes calculated where possible. This highlighted the potential importance of the source of the animal, the age at which it was rehomed, the reason for the acquisition, the experience level of the owner, the animal's socialisation experiences, the consistent husbandry and management practices, the training, the sex ratio of the litter and the history of dogs that display aggression in the pedigree as risk factors. Taken together, it seems that early experiences which limit the ability to develop effective coping strategies and routines may be particularly important. We provide guidance for the future standardised reporting of risk related to human-directed aggression by dogs to allow greater synthesis of the literature in the future.

Would You Detour with Me? Association between Functional Breed Selection and Social Learning in Dogs Sheds Light on Elements of Dog-Human Cooperation

Interspecific social learning is a main synchronizing mechanism that enables dogs to adapt to the anthropogenic niche. It is not known whether dogs in general possess the capacity of learning from humans or whether more recent selective events have affected their ability to learn from humans. We hypothesized that cooperative and independent working dog breeds may behave differently in a social learning task. Dogs (N = 78 from 16 cooperative and 18 independent breeds) had to detour a transparent, V-shaped wire mesh fence. The experiment consisted of three one-minute-long trials. The control condition did not include a demonstration. In the demonstration condition, the experimenter placed a reward in the inside corner by walking around the fence. Cooperative dogs reached the target significantly faster, while independent dogs did not detour faster in trials 2 and 3 after the human demonstration. Detour latencies were not associated with the keeping conditions and training level of the subjects. As we assembled both test groups from several genetically distantly related breeds, we can exclude the explanation that higher cooperativity emerged only in particular clades of dogs; instead, functional selection for particular working tasks could enhance capacities that affect a wide range of socio-cognitive traits in dogs.

Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

BACKGROUND

In light of previous studies that profiled breed-specific traits or used genome-wide association studies to refine loci associated with characteristic morphological features in dogs, the field has gained tremendous genetic insights for known dog traits observed among breeds. Here we aim to address the question from a reserve perspective: whether there are breed-specific genotypes that may underlie currently unknown phenotypes. This study provides a complete set of breed-specific genetic signatures (BSGS). Several novel BSGS with significant protein-altering effects were highlighted and validated.

RESULTS

Using the next generation whole-genome sequencing technology coupled with unsupervised machine learning for pattern recognitions, we constructed and analyzed a high-resolution sequence map for 76 breeds of 412 dogs. Genomic structures including novel single nucleotide polymorphisms (SNPs), SNP clusters, insertions, deletions (INDELs) and short tandem repeats (STRs) were uncovered mutually exclusively among breeds. We also partially validated some novel nonsense variants by Sanger sequencing with additional dogs. Four novel nonsense BSGS were found in the Bernese Mountain Dog, Samoyed, Bull Terrier, and Basset Hound, respectively. Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. A total of 15 genomic regions containing three types of BSGS (SNP-clusters, INDELs and STRs) were identified in the Akita, Alaskan Malamute, Chow Chow, Field Spaniel, Keeshond, Shetland Sheepdog and Sussex Spaniel, in which Keeshond and Sussex Spaniel each carried one amino-acid changing BSGS in such regions.

CONCLUSION

Given the strong relationship between human and dog breed-specific traits, this study might be of considerable interest to researchers and all. Novel genetic signatures that can differentiate dog breeds were uncovered. Several functional genetic signatures might indicate potentially breed-specific unknown phenotypic traits or disease predispositions. These results open the door for further investigations. Importantly, the computational tools we developed can be applied to any dog breeds as well as other species. This study will stimulate new thinking, as the results of breed-specific genetic signatures may offer an overarching relevance of the animal models to human health and disease.

Psychological Stress Is Associated with Increased Cancer Risk in Dogs

Although there is evidence that psychological stress may be associated with increased cancer risk, the effect of stress on cancer risk is difficult to study, both in humans, due to socioeconomic factors, and in animal models, due to questionable biological relevance. Here, we test whether heritable canine temperament that increases psychological stress is associated with cancer risk. The study data are breed-specific averages of incidences of multiple cancer types and of temperament classes. The latter are derived from a latent class analysis of behavioral questionnaires completed by owners (C-BARQ). We thus classified the dogs according to whether they are calm vs. reactive within and across breeds. Using meta-analysis approaches, we modeled the risk of multiple cancer types in calm vs. reactive dogs. We adjusted for breed averages of body mass and lifespan, which are common confounders that impact cancer. Our study confirms that body size has a significant effect of on risk of multiple types of cancers in dogs and shows for the first time that temperament also has a moderate effect. These findings suggest dog models of heritable psychological stress are suitable for molecular epidemiological and translational studies on its effects on cancer risk.

Genetic dissection of behavioral traits related to successful training of drug detection dogs

Drug detection dogs play integral roles in society. However, the interplay between their behaviors and genetic characteristics underlying their performance remains uninvestigated. Herein, more than 120,000 genetic variants were evaluated in 326 German Shepherd or Labrador Retriever dogs to profile the genetic traits associated with various behavioral traits related to the successful training of drug detection dogs. Behavioral breed differences were observed in 'friendliness to humans' and 'tolerance to dogs.' A genome-wide association study within both breeds identified 11 regions potentially associated with drug detection dog characteristics as well as 'interest in the target' and 'friendliness to humans,' which are related to drug detection abilities. Among them, 63 protein-coding genes, including Atat1 and Pfn2 known to be associated with anxiety-related or exploration behavior in mice, respectively, were located surrounding the identified candidate polymorphisms. This study highlights genetic characteristics associated with behavioral traits that are important for the successful training of drug detection dogs. Thus, these findings may facilitate improved breeding and training of these dogs.

Genomic analysis of firework fear and noise reactivity in standard poodles

BACKGROUND

Fear of firework noises and other loud, sudden noises (noise reactivity) is a significant problem for many dogs and may have a negative effect on both welfare and, in severe cases, the life expectancy of dogs. A wide range of behavior traits, including fear-related behaviors, have high heritability estimates in dogs. The aim of this study was to estimate genomic heritability for fear of fireworks and loud noises in dogs.

RESULTS

A genomic heritability estimate was performed based on genome-wide SNPs from standard poodles with records of fear of fireworks and noise reactivity. The study was based on questionnaires answered by owners, who also volunteered to return a cheek swab from their dog for DNA analyses. SNP-based heritability was estimated to be 0.28 for firework fear and 0.16 for noise reactivity. We also identified an interesting region on chromosome 17 that was weakly associated with both traits.

CONCLUSIONS

We have estimated low to medium genomic heritabilities for fear of fireworks and noise reactivity in standard poodles. We have also identified an interesting region on chromosome 17, which harbors genes that have been shown to be involved in different psychiatric traits with anxiety components in humans. The region was associated with both traits; however, the association was weak and need further verification from other studies.

Association of DNA methylation with energy and fear-related behaviors in canines

Introduction

Behavioral traits are influenced by gene by environment interactions. To study the genetic and epigenetic components of behavior, we analyzed whether dog behavioral traits could be predicted by their DNA methylation and genotypes.

Methods

We conducted an analysis on dog behaviors such as sociability, trainability and energy as measured by Canine Behavioral and Research Assessment Questionnaire (C-BARQ) behavioral surveys paired with buccal swabs from 46 dogs. Previously we used targeted bisulfite sequencing to analyze DNA methylation and collected genotype data from over 1,500 single nucleotide polymorphisms (SNPs). Owner-reported C-BARQ responses were used to quantify 14 behavioral trait values.

Results

Using Partial Least Squares (PLS) Regression analysis we found behavioral traits such as energy, attachment/attention-seeking, non-social fear, and stranger-directed fear to be significantly associated with DNA methylation across 3,059 loci. After we adjusted for age as a confounding variable, energy and stranger-directed fear remained significantly associated with methylation. We found that most behavioral traits were not predictable by our limited set of SNPs.

Discussion

By identifying individual genes whose methylation is significantly associated with behavioral traits, we generate hypotheses about possible mechanisms involved in behavioral regulation. Overall, our study extends previous work in behavioral epigenetics, shows that canine behaviors are predictable by DNA methylation, and serves as a proof of concept for future studies in behavioral epigenetics.

Domestic dog lineages reveal genetic drivers of behavioral diversification

Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing a framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral, and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.

Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing

Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.

Latent class analysis of behavior across dog breeds reveal underlying temperament profiles

Latent class analysis (LCA) is a type of modeling analysis approach that has been used to identify unobserved groups or subgroups within multivariate categorical data. LCA has been used for a wide array of psychological evaluations in humans, including the identification of depression subtypes or PTSD comorbidity patterns. However, it has never been used for the assessment of animal behavior. Our objective here is to identify behavioral profile-types of dogs using LCA. The LCA was performed on a C-BARQ behavioral questionnaire dataset from 57,454 participants representing over 350 pure breeds and mixed breed dogs. Two, three, and four class LCA models were developed using C-BARQ trait scores and environmental covariates. In our study, LCA is shown as an effective and flexible tool to classify behavioral assessments. By evaluating the traits that carry the strongest relevance, it was possible to define the basis of these grouping differences. Groupings can be ranked and used as levels for simplified comparisons of complex constructs, such as temperament, that could be further exploited in downstream applications such as genomic association analyses. We propose this approach will facilitate dissection of physiological and environmental factors associated with psychopathology in dogs, humans, and mammals in general.

Genome scanning of behavioral selection in a canine olfactory detection breeding cohort

Research on working dogs is growing rapidly due to increasing global demand. Here we report genome scanning of the risk of puppies being eliminated for behavioral reasons prior to entering the training phase of the US Transportation Security Administration's (TSA) canine olfactory detection breeding and training program through 2013. Elimination of dogs for behavioral rather than medical reasons was based on evaluations at three, six, nine and twelve months after birth. Throughout that period, the fostered dogs underwent standardized behavioral tests at TSA facilities, and, for a subset of tests, dogs were tested in four different environments. Using methods developed for family studies, we performed a case-control genome wide association study (GWAS) of elimination due to behavioral observation and testing results in a cohort of 528 Labrador Retrievers (2002-2013). We accounted for relatedness by including the pedigree as a covariate and maximized power by including individuals with phenotype, but not genotype, data (approximately half of this cohort). We determined genome wide significance based on Bonferroni adjustment of two quasi-likelihood score tests optimized for either small or nearly-fully penetrant effect sizes. Six loci were significant and five suggestive, with approximately equal numbers of loci for the two tests and frequencies of loci with single versus multiple mapped markers. Several loci implicate a single gene, including CHD2, NRG3 and PDE1A which have strong relevance to behavior in humans and other species. We briefly discuss how expanded studies of canine breeding programs could advance understanding of learning and performance in the mammalian life course. Although human interactions and other environmental conditions will remain critical, our findings suggest genomic breeding selection could help improve working dog populations.

Large scale across-breed genome-wide association study reveals a variant in HMGA2 associated with inguinal cryptorchidism risk in dogs

Cryptorchidism is the most common congenital sex development disorder in dogs. Despite this, little progress has been made in understanding its genetic background. Extensive genetic testing of dogs through consumer and veterinary channels using a high-density SNP genotyping microarray coupled with links to clinical records presents the opportunity for a large-scale genome-wide association study to elucidate the molecular risk factors associated with cryptorchidism in dogs. Using an inter-breed genome-wide association study approach, a significant statistical association on canine chromosome 10 was identified, with the top SNP pinpointing a variant of HMGA2 previously associated with adult weight variance. In further analysis we show that incidence of cryptorchidism is skewed towards smaller dogs in concordance with the identified variant’s previous association with adult weight. This study represents the first putative variant to be associated with cryptorchidism in dogs.

Genetics and Brain Transcriptomics of Completed Suicide

OBJECTIVE

The authors sought to study the transcriptomic and genomic features of completed suicide by parsing the method chosen, to capture molecular correlates of the distinctive frame of mind of individuals who die by suicide, while reducing heterogeneity.

METHODS

The authors analyzed gene expression (RNA sequencing) from postmortem dorsolateral prefrontal cortex of patients who died by suicide with violent compared with nonviolent means, nonsuicide patients with the same psychiatric disorders, and a neurotypical group (total N=329). They then examined genomic risk scores (GRSs) for each psychiatric disorder included, and GRSs for cognition (IQ) and for suicide attempt, testing how they predict diagnosis or traits (total N=888).

RESULTS

Patients who died by suicide by violent means showed a transcriptomic pattern remarkably divergent from each of the other patient groups but less from the neurotypical group; consistently, their genomic profile of risk was relatively low for their diagnosed illness as well as for suicide attempt, and relatively high for IQ: they were more similar to the neurotypical group than to other patients. Differentially expressed genes (DEGs) associated with patients who died by suicide by violent means pointed to purinergic signaling in microglia, showing similarities to a genome-wide association study of Drosophila aggression. Weighted gene coexpression network analysis revealed that these DEGs were coexpressed in a context of mitochondrial metabolic activation unique to suicide by violent means.

CONCLUSIONS

These findings suggest that patients who die by suicide by violent means are in part biologically separable from other patients with the same diagnoses, and their behavioral outcome may be less dependent on genetic risk for conventional psychiatric disorders and be associated with an alteration of purinergic signaling and mitochondrial metabolism.

Genetic testing of dogs predicts problem behaviors in clinical and nonclinical samples

BACKGROUND

Very little is known about the etiology of personality and psychiatric disorders. Because the core neurobiology of many such traits is evolutionarily conserved, dogs present a powerful model. We previously reported genome scans of breed averages of ten traits related to fear, anxiety, aggression and social behavior in multiple cohorts of pedigree dogs. As a second phase of that discovery, here we tested the ability of markers at 13 of those loci to predict canine behavior in a community sample of 397 pedigree and mixed-breed dogs with individual-level genotype and phenotype data.

RESULTS

We found support for all markers and loci. By including 122 dogs with veterinary behavioral diagnoses in our cohort, we were able to identify eight loci associated with those diagnoses. Logistic regression models showed subsets of those loci could predict behavioral diagnoses. We corroborated our previous findings that small body size is associated with many problem behaviors and large body size is associated with increased trainability. Children in the home were associated with anxiety traits; illness and other animals in the home with coprophagia; working-dog status with increased energy and separation-related problems; and competitive dogs with increased aggression directed at familiar dogs, but reduced fear directed at humans and unfamiliar dogs. Compared to other dogs, Pit Bull-type dogs were not defined by a set of our markers and were not more aggressive; but they were strongly associated with pulling on the leash. Using severity-threshold models, Pit Bull-type dogs showed reduced risk of owner-directed aggression (75th quantile) and increased risk of dog-directed fear (95th quantile).

CONCLUSIONS

Our association analysis in a community sample of pedigree and mixed-breed dogs supports the interbreed mapping. The modeling shows some markers are predictive of behavioral diagnoses. Our findings have broad utility, including for clinical and breeding purposes, but we caution that thorough understanding is necessary for their interpretation and use.

Hmga2 deficiency is associated with allometric growth retardation, infertility, and behavioral abnormalities in mice

The high mobility group AT-hook 2 (HMGA2) protein works as an architectural regulator by binding AT-rich DNA sequences to induce conformational changes affecting transcription. Genomic deletions disrupting HMGA2 coding sequences and flanking noncoding sequences cause dwarfism in mice and rabbits. Here, CRISPR/Cas9 was used in mice to generate an Hmga2 null allele that specifically disrupts only the coding sequence. The loss of one or both alleles of Hmga2 resulted in reduced body size of 20% and 60%, respectively, compared to wild-type littermates as well as an allometric reduction in skull length in Hmga2-/- mice. Both male and female Hmga2-/- mice are infertile, whereas Hmga2+/- mice are fertile. Examination of reproductive tissues of Hmga2-/- males revealed a significantly reduced size of testis, epididymis, and seminal vesicle compared to controls, and 70% of knock-out males showed externalized penis, but no cryptorchidism was observed. Sperm analyses revealed severe oligospermia in mutant males and slightly decreased sperm viability, increased DNA damage but normal sperm chromatin compaction. Testis histology surprisingly revealed a normal seminiferous epithelium, despite the significant reduction in testis size. In addition, Hmga2-/- mice showed a significantly reduced exploratory behavior. In summary, the phenotypic effects in mouse using targeted mutagenesis confirmed that Hmga2 is affecting prenatal and postnatal growth regulation, male reproductive tissue development, and presents the first indication that Hmga2 function is required for normal mouse behavior. No specific effect, despite an allometric reduction, on craniofacial development was noted in contrast to previous reports of an altered craniofacial development in mice and rabbits carrying deletions of both coding and noncoding sequences at the 5' part of Hmga2.

Study of Behavioural Traits in Can de Palleiro (Galician Shepherd Dog)

Simple Summary

The Can de Palleiro or Galician shepherd is a canine breed that was in danger of extinction but is currently growing rapidly in popularity. In this study, different behavioural traits of the breed were evaluated in order to assess breeds, select the best breeding animals and identify behaviour problems. This is the first study carried out in the Can de Palleiro breed using different scientifically validated tests. Questionnaires filled by the owners (C_BARQ) were collected, and a behavioural test (SAB) was conducted to evaluate the response of the dogs to a specific stimulus at a certain time and in a certain environment. In addition, the results from the Can de Palleiro breed were compared with those obtained from the general canine population of Galicia. Thereby, the Can de Palleiro breed showed less owner-directed aggression, dog-directed fear, excitability, non-social fear and separation-related problems and better trainability.

Abstract

The Can de Palleiro (CP) is an autochthonous canine breed from Galicia (NW Spain). Interestingly, no previous research has been published about the behaviour of this breed. Thus, the aim of the present study was to obtain a deeper understanding of CP behavioural and temperamental traits and detect any potentially problematic behaviour by using the Canine Behavioural Assessment and Research Questionnaire (C-BARQ) and the Socially Acceptable Behaviour (SAB) test. Behavioural information was obtained from 377 dogs—177 CPs and 200 general population (GP) dogs—using the C-BARQ. Additionally, 32 dogs were enrolled to perform the SAB test (19 CPs and 13 GP dogs) in order to directly evaluate their temperament. Our results indicated that CP dogs had a lower tendency to show aggressiveness towards their owners (0.18 times lower, p = 0.033) and less fear of other dogs (by 0.43 times, p = 0.001), as well as higher trainability levels (2.56 times higher, p < 0.001) when compared to GP dogs. CP dogs also had increased odds of showing chasing behaviour (3.81 times higher, p < 0.001). Conversely, CPs had reduced odds of non-social fear, separation-related problems and excitability (by 0.42, 0.35 and 0.48 times, respectively; p < 0.001, p < 0.001 and p = 0.002). The current research represents a starting point for the study of the behaviour of CPs, which appear to be a working breed, with guarding and, especially, herding characteristics.

CyberGenomics: Application of Behavioral Genetics in Cybersecurity

Cybersecurity (CS) is a contemporary field for research and applied study of a range of aspects from across multiple disciplines. A cybersecurity expert has an in-depth knowledge of technology but is often also recognized for the ability to view technology in a non-standard way. This paper explores how CS specialists are both a combination of professional computing-based skills and genetically encoded traits. Almost every human behavioral trait is a result of many genome variants in action altogether with environmental factors. The review focuses on contextualizing the behavior genetics aspects in the application of cybersecurity. It reconsiders methods that help to identify aspects of human behavior from the genetic information. And stress is an illustrative factor to start the discussion within the community on what methodology should be used in an ethical way to approach those questions. CS positions are considered stressful due to the complexity of the domain and the social impact it can have in cases of failure. An individual risk profile could be created combining known genome variants linked to a trait of particular behavior using a special biostatistical approach such as a polygenic score. These revised advancements bring challenging possibilities in the applications of human behavior genetics and CS.

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

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

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

Belyaev's concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized in commercial colors of the domesticated fox that never occur in the wild and has been confirmed in a wide variety of pet breeds. Many human disease models involving animals allow to test drugs before human testing. Perhaps this is why investigators doing transcriptomic profiling of domestic versus wild animals have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes of tame and aggressive rats, identified their differentially expressed genes (DEGs), and, for the first time, applied principal component analysis to compare them with all the known DEGs of domestic versus wild animals that we could find. Two principal components, PC1 and PC2, respectively explained 67% and 33% of differential-gene-expression variance (hereinafter: log2 value) between domestic and wild animals. PC1 corresponded to multiple orthologous DEGs supported by homologs; these DEGs kept the log2 value sign from species to species and from tissue to tissue (i.e., a common domestication pattern). PC2 represented stand-alone homologous DEG pairs reversing the log2 value sign from one species to another and from tissue to tissue (i.e., representing intraspecific and interspecific variation).

Neurodevelopmental scaling is a major driver of brain-behavior differences in temperament across dog breeds

Behavioral traits like aggression, anxiety, and trainability differ significantly across dog breeds and are highly heritable. However, the neural bases of these differences are unknown. Here we analyzed structural MRI scans of 62 dogs in relation to breed-average scores for the 14 major dimensions in the Canine Behavioral Assessment and Research Questionnaire, a well-validated measure of canine temperament. Several behavior categories showed significant relationships with morphologically covarying gray matter networks and regional volume changes. Networks involved in social processing and the flight-or-fight response were associated with stranger-directed fear and aggression, putatively the main behaviors under selection pressure during wolf-to-dog domestication. Trainability was significantly associated with expansion in broad regions of cortex, while fear, aggression, and other "problem" behaviors were associated with expansion in distributed subcortical regions. These results closely overlapped with regional volume changes with total brain size, in striking correspondence with models of developmental constraint on brain evolution. This suggests that the established link between dog body size and behavior is due at least in part to disproportionate enlargement of later-developing regions in larger brained dogs. We discuss how this may explain the known correlation of increasing reactivity with decreasing body size in dogs.

Genome-Wide Association Studies Reveal Neurological Genes for Dog Herding, Predation, Temperament, and Trainability Traits

Genome-wide association study (GWAS) using dog breed standard values as phenotypic measurements is an efficient way to identify genes associated with morphological and behavioral traits. As a result of strong human purposeful selections, several specialized behavioral traits such as herding and hunting have been formed in different modern dog breeds. However, genetic analyses on this topic are rather limited due to the accurate phenotyping difficulty for these complex behavioral traits. Here, 268 dog whole-genome sequences from 130 modern breeds were used to investigate candidate genes underlying dog herding, predation, temperament, and trainability by GWAS. Behavioral phenotypes were obtained from the American Kennel Club based on dog breed standard descriptions or groups (conventional categorization of dog historical roles). The GWAS results of herding behavior (without body size as a covariate) revealed 44 significantly associated sites within five chromosomes. Significantly associated sites on CFA7, 9, 10, and 20 were located either in or near neuropathological or neuronal genes including THOC1, ASIC2, MSRB3, LLPH, RFX8, and CHL1. MSRB3 and CHL1 genes were reported to be associated with dog fear. Since herding is a restricted hunting behavior by removing killing instinct, 36 hounds and 55 herding dogs were used to analyze predation behavior. Three neuronal-related genes (JAK2, MEIS1, and LRRTM4) were revealed as candidates for predation behavior. The significantly associated variant of temperament GWAS was located within ACSS3 gene. The highest associated variant in trainability GWAS is located on CFA22, with no variants detected above the Bonferroni threshold. Since dog behaviors are correlated with body size, we next incorporate body mass as covariates into GWAS; and significant signals around THOC1, MSRB3, LLPH, RFX8, CHL1, LRRTM4, and ACSS3 genes were still detected for dog herding, predation, and temperament behaviors. In humans, these candidate genes are either involved in nervous system development or associated with mental disorders. In conclusion, our results imply that these neuronal or psychiatric genes might be involved in biological processes underlying dog herding, predation, and temperament behavioral traits.

Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis

BACKGROUND AND AIM

Human evolution resulted from changes in our biology, behaviour, and culture. One source of these changes has been hypothesised to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times.

METHODS

In this paper, we compare whole-genome data between the Late Neolithic/Bronze Age individuals and modern Europeans.

RESULTS

We show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups.

CONCLUSION

We hypothesise that these changes might account for the increased features of self-domestication in modern humans and, ultimately, for subtle recent changes in human cognition and behaviour, including language.

Socialization in Commercial Breeding Kennels: The Use of Novel Stimuli to Measure Social and Non-Social Fear in Dogs

Simple Summary

Owner-based reports of dogs presumed to come from commercial breeding kennels (CBKs) suggest high levels of fear in this population. Fear in kenneled dogs is a serious behavioral welfare concern as it may lead to both acute and chronic stress. Novel social and non-social stimuli have been shown to elicit behaviors associated with fear in animals. New knowledge on the levels of fear in dogs from CBKs could be used to further refine protocols intended for assessment of welfare in CBKs and to improve breeders’ management practices. The aim of this study, therefore, was to evaluate how dogs from CBKs reacted to social (i.e., a person approaching) and non-social (i.e., a traffic cone and a dog statue) stimuli, and to perform a preliminary evaluation of how these responses might be used as indicators of dogs’ overall socialization levels in kennels. Results revealed that dogs had primarily mildly fearful responses to the stimuli presented. These findings are encouraging as extreme fearful reactions were rarely recorded. Nevertheless, there is a clear margin for commercial breeders to improve the socialization protocols in their kennels to better incorporate both social and non-social stimuli.

Abstract

Understanding the behavioral welfare of dogs in commercial breeding kennels (CBKs) is important for improving breeders’ management practices as well as dog welfare. In the current study, breeding dogs from CBKs were exposed to novel stimuli to evaluate their behavioral responses, with emphasis on indicators of fear. Subjects were presented with a standard stranger-approach test, a traffic cone, and a realistic dog statue. Sixty dogs were exposed to the three stimuli and behavioral responses were scored using an ethogram developed for this study. Dogs spent significantly more time investigating the environment, staying further away from the stimulus, and they took longer to approach and investigate when presented with the cone than with the dog statue or stranger (p < 0.01). These findings suggest that the cone elicited more fear-related behaviors than the dog statue and stranger. Given these results, in addition to socializing their dogs to unfamiliar people and other dogs within their kennels, commercial breeders should be encouraged to increase the exposure of their dogs to more diverse novel stimuli to reduce non-social fear and support the welfare of dogs while they reside in the kennel and when they transition to new homes.

A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes

Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq data to compare the effect of co-directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common ancestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene-markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson’s χ² test p < 0.001, Fisher’s exact test p < 0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial distribution), thus enforcing the norm (wild type).

The influence of X chromosome variants on trait neuroticism

Autosomal variants have successfully been associated with trait neuroticism in genome-wide analysis of adequately powered samples. But such studies have so far excluded the X chromosome from analysis. Here, we report genetic association analyses of X chromosome and XY pseudoautosomal single nucleotide polymorphisms (SNPs) and trait neuroticism using UK Biobank samples (N = 405,274). Significant association was found with neuroticism on the X chromosome for 204 markers found within three independent loci (a further 783 were suggestive). Most of the lead neuroticism-related X chromosome variants were located in intergenic regions (n = 397). Involvement of HS6ST2, which has been previously associated with sociability behaviour in the dog, was supported by single SNP and gene-based tests. We found that the amino acid and nucleotide sequences are highly conserved between dogs and humans. From the suggestive X chromosome variants, there were 19 nearby genes which could be linked to gene ontology information. Molecular function was primarily related to binding and catalytic activity; notable biological processes were cellular and metabolic, and nucleic acid binding and transcription factor protein classes were most commonly involved. X-variant heritability of neuroticism was estimated at 0.22% (SE = 0.05) from a full dosage compensation model. A polygenic X-variant score created in an independent sample (maximum N ≈ 7,300) did not predict significant variance in neuroticism, psychological distress, or depressive disorder. We conclude that the X chromosome harbours significant variants influencing neuroticism, and might prove important for other quantitative traits and complex disorders.

DNA methylation in canine brains is related to domestication and dog-breed formation

Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. During domestication, dogs have evolved an unprecedented between-breed variation in morphology and behavior in an evolutionary short period. In the present study, we explore DNA methylation differences in brain, the most relevant tissue with respect to behavior, between wolf and dog breeds. We optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and three wolves was used. GBS and GBS-MeDIP libraries were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 ± 0.4% of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 ± 4,042,106 unique base pairs. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors may have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding but are also useful to further understanding of epigenetic involvement.

The Development of a Novel Questionnaire Approach to the Investigation of Horse Training, Management, and Behaviour

Simple Summary

The way horses are trained and managed influences their behaviour. The Equine Behaviour Assessment and Research Questionnaire (E-BARQ) was developed to gather information on the training, management, and behaviour of domestic horses. An international panel was established to assist with the questionnaire development and the pilot questionnaire collected data on 1320 horses. Statistical analysis revealed the E-BARQ to be a suitable representation of relevant features of horse training and management and the objective reporting of horse behaviour.

Abstract

The Equine Behaviour Assessment and Research Questionnaire (E-BARQ) is a questionnaire instrument developed to obtain quantitative data on the domestic equine triad of training, management, and behaviour of horses. The E-BARQ was developed to identify how changes in training and management impact behaviour over time, to define normal behaviour in horses, and to discover how to improve rider safety and horse welfare, leading to ethical equitation. During the development of the E-BARQ, we also investigated how best to motivate stakeholders to engage with this citizen science project. The pilot version of the E-BARQ collected qualitative data on respondents’ experience of the questionnaire. The pilot questionnaire was developed with the assistance of an international panel (with professional expertise in horse training, equitation science, veterinary science, equestrian coaching, welfare, animal behaviour, and elite-level riding), and was used to collect data on 1320 horses from approximately 1194 owner/caregiver respondents, with an option for respondents to provide free-text feedback. A Rotated Principal Component Analysis of the 218 behavioural, management, and training questionnaire items extracted a total of 65 rotated components. Thirty-six of the 65 rotated components demonstrated high internal reliability. Of the 218 questionnaire items, 43 items failed to reach the Rotated Principal Component Analysis criteria and were not included in the final version of the E-BARQ. Survey items that failed the Rotated Principal Component Analysis inclusion criteria were discarded if found to have a less than 85% response rate, or a variance of less than 1.3. Of those that survived the Rotated Principal Component Analysis, items were further assigned to horse temperament (17 rotated components), equitation (11 rotated components), and management and equipment (8 rotated components) groups. The feedback from respondents indicated the need for further items to be added to the questionnaire, resulting in a total of 214 items for the final E-BARQ survey. Many of these items were further grouped into question matrices, and the demographic items for horse and handler included, giving a final total of 97 questions on the E-BARQ questionnaire. These results provided content validity, showing that the questionnaire items were an acceptable representation of the entire horse training, management, and behavioural domain for the development of the final E-BARQ questionnaire.

Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome

Background

In population ecology, the concept of reproductive potential denotes the most vital indicator of chances to produce and sustain a healthy descendant until his/her reproductive maturity under the best conditions. This concept links quality of life and longevity of an individual with disease susceptibilities encoded by his/her genome. Female reproductive potential has been investigated deeply, widely, and comprehensively in the past, but the male one has not received an equal amount of attention. Therefore, here we focused on the human Y chromosome and found candidate single-nucleotide polymorphism (SNP) markers of male reproductive potential.

Results

Examining in silico (i.e., using our earlier created Web-service SNP_TATA_Z-tester) all 1206 unannotated SNPs within 70 bp proximal promoters of all 63 Y-linked genes, we found 261 possible male-reproductive-potential SNP markers that can significantly alter the binding affinity of TATA-binding protein (TBP) for these promoters. Among them, there are candidate SNP markers of spermatogenesis disorders (e.g., rs1402972626), pediatric cancer (e.g., rs1483581212) as well as male anxiety damaging family relationships and mother’s and children’s health (e.g., rs187456378). First of all, we selectively verified in vitro both absolute and relative values of the analyzed TBP–promoter affinity, whose Pearson’s coefficients of correlation between predicted and measured values were r = 0.84 (significance p <  0.025) and r = 0.98 (p <  0.025), respectively. Next, we found that there are twofold fewer candidate SNP markers decreasing TBP–promoter affinity relative to those increasing it, whereas in the genome-wide norm, SNP-induced damage to TBP–promoter complexes is fourfold more frequent than SNP-induced improvement (p <  0.05, binomial distribution). This means natural selection against underexpression of these genes. Meanwhile, the numbers of candidate SNP markers of an increase and decrease in male reproductive potential were indistinguishably equal to each other (p <  0.05) as if male self-domestication could have happened, with its experimentally known disruptive natural selection. Because there is still not enough scientific evidence that this could have happened, we discuss the human diseases associated with candidate SNP markers of male reproductive potential that may correspond to domestication-related disorders in pets.

Conclusions

Overall, our findings seem to support a self-domestication syndrome with disruptive natural selection by male reproductive potential preventing Y-linked underexpression of a protein.

Active and social life is associated with lower non-social fearfulness in pet dogs

Behavioural problems are leading welfare issues in domestic dogs. In particular, anxiety-related behavioural problems, such as fearfulness and noise sensitivity are highly prevalent conditions that cause distress to fearful dogs. To better understand the environmental factors associated with non-social fear, including noise sensitivity, fear of novel situations, and fear of surfaces and heights, a large online survey including data on 13,700 Finnish pet dogs was performed by the dog owners. After fulfilling inclusion criteria, this data consisted of 9,613 dogs with fear of fireworks, 9,513 dogs with fear of thunder, 6,945 dogs with fear of novel situations, and 2,932 dogs with fear of surfaces and heights. Logistic regression analyses revealed that dogs with frequent non-social fear had experienced less socialisation during puppyhood, were more often neutered, had inexperienced owners, lived without conspecifics, participated less frequently in activities or training, and lived in more urban environments. In addition, we identified several breed differences, and a tendency of more common non-social fear in small dog breeds, which suggests a genetic background. Non-social fearfulness has a negative effect on well-being of the dogs. Our findings suggest that the socialisation and the living environment and the value of other dogs' company and owner interaction via activities and training may improve the well-being of the dogs.

Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioral traits

Strong selection has resulted in substantial morphological and behavioral diversity across modern dog breeds, which makes dogs interesting model animals to study the underlying genetic architecture of these traits. However, results from between-breed analyses may confound selection signatures for behavior and morphological features that were coselected during breed development. In this study, we assess population genetic differences in a unique resource of dogs of the same breed but with systematic behavioral selection in only one population. We exploit these different breeding backgrounds to identify signatures of recent selection. Selection signatures within populations were found on chromosomes 4 and 19, with the strongest signals in behavior-related genes. Regions showing strong signals of divergent selection were located on chromosomes 1, 24, and 32, and include candidate genes for both physical features and behavior. Some of the selection signatures appear to be driven by loci associated with coat color (Chr 24; ASIP) and length (Chr 32; FGF5), while others showed evidence of association with behavior. Our findings suggest that signatures of selection within dog breeds have been driven by selection for morphology and behavior. Furthermore, we demonstrate that combining selection scans with association analyses is effective for dissecting the traits under selection.

Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions

Given their remarkable phenotypic diversity, dogs present a unique opportunity for investigating the genetic bases of cognitive and behavioral traits. Our previous work demonstrated that genetic relatedness among breeds accounts for a substantial portion of variation in dog cognition. Here, we investigated the genetic architecture of breed differences in cognition, seeking to identify genes that contribute to variation in cognitive phenotypes. To do so, we combined cognitive data from the citizen science project Dognition.com with published breed-average genetic polymorphism data, resulting in a dataset of 1654 individuals with cognitive phenotypes representing 49 breeds. We conducted a breed-average genome-wide association study to identify specific polymorphisms associated with breed differences in inhibitory control, communication, memory, and physical reasoning. We found five single nucleotide polymorphisms (SNPs) that reached genome-wide significance after Bonferroni correction, located in EML1, OR52E2, HS3ST5, a U6 spliceosomal RNA, and a long noncoding RNA. When we combined results across multiple SNPs within the same gene, we identified 188 genes implicated in breed differences in cognition. This gene set included more genes than expected by chance that were (1) differentially expressed in brain tissue and (2) involved in nervous system functions including peripheral nervous system development, Wnt signaling, presynapse assembly, and synaptic vesicle exocytosis. These results advance our understanding of the genetic underpinnings of complex cognitive phenotypes and identify specific genetic variants for further research.

The molecular effect of a polymorphic microRNA binding site of Wolfram syndrome 1 gene in dogs

Background

Although the molecular function of wolframin remains unclear, the lack of this protein is known to cause stress in the endoplasmic reticulum. Some variants in the Wolfram Syndrome 1 gene (WFS1) were associated with various neuropsychiatric disorders in humans, such as aggressiveness, impulsivity and anxiety.

Results

Here we present an in silico study predicting a single nucleotide polymorphism (rs852850348) in the canine WFS1 gene which was verified by direct sequencing and was genotyped by a PCR-based technique. We found that the rs852850348 polymorphism is located in a putative microRNA (cfa-miR-8834a and cfa-miR-1838) binding site. Therefore, the molecular effect of allelic variants was studied in a luciferase reporter system that allowed assessing gene expression. We demonstrated that the variant reduced the activity of the reporter protein expression in an allele-specific manner. Additionally, we performed a behavioral experiment and investigated the association with this locus to different performance in this test. Association was found between food possessivity and the studied WFS1 gene polymorphism in the Border collie breed.

Conclusions

Based on our findings, the rs852850348 locus might contribute to the genetic risk of possessivity behavior of dogs in at least one breed and might influence the regulation of wolframin expression.

A novel genomic region on chromosome 11 associated with fearfulness in dogs

The complex phenotypic and genetic nature of anxieties hampers progress in unravelling their molecular etiologies. Dogs present extensive natural variation in fear and anxiety behaviour and could advance the understanding of the molecular background of behaviour due to their unique breeding history and genetic architecture. As dogs live as part of human families under constant care and monitoring, information from their behaviour and experiences are easily available. Here we have studied the genetic background of fearfulness in the Great Dane breed. Dogs were scored and categorised into cases and controls based on the results of the validated owner-completed behavioural survey. A genome-wide association study in a cohort of 124 dogs with and without socialisation as a covariate revealed a genome-wide significant locus on chromosome 11. Whole exome sequencing and whole genome sequencing revealed extensive regions of opposite homozygosity in the same locus on chromosome 11 between the cases and controls with interesting neuronal candidate genes such as MAPK9/JNK2, a known hippocampal regulator of anxiety. Further characterisation of the identified locus will pave the way for molecular understanding of fear in dogs and may provide a natural animal model for human anxieties.

Genome wide association study of 40 clinical measurements in eight dog breeds

The domestic dog represents an ideal model for identifying susceptibility genes, many of which are shared with humans. In this study, we investigated the genetic contribution to individual differences in 40 clinically important measurements by a genome-wide association study (GWAS) in a multinational cohort of 472 healthy dogs from eight breeds. Meta-analysis using the binary effects model after breed-specific GWAS, identified 13 genome-wide significant associations, three of them showed experimental-wide significant associations. We detected a signal at chromosome 13 for the serum concentration of alanine aminotransferase (ALT) in which we detected four breed-specific signals. A large proportion of the variance of ALT (18.1–47.7%) was explained by this locus. Similarly, a single SNP was also responsible for a large proportion of the variance (6.8–78.4%) for other measurements such as fructosamine, stress during physical exam, glucose, and morphometric measurements. The genetic contribution of single variant was much larger than in humans. These findings illustrate the importance of performing meta-analysis after breed-specific GWAS to reveal the genetic contribution to individual differences in clinically important measurements, which would lead to improvement of veterinary medicine.

Prevalence, comorbidity, and breed differences in canine anxiety in 13,700 Finnish pet dogs

Behaviour problems and anxieties in dogs decrease their quality of life and may lead to relinquishment or euthanasia. Considering the large number of pet dogs and the commonness of these problematic behaviours, a better understanding of the epidemiology and related molecular and environmental factors is needed. We have here studied the prevalence, comorbidity, and breed specificity of seven canine anxiety-like traits: noise sensitivity, fearfulness, fear of surfaces and heights, inattention/impulsivity, compulsion, separation related behaviour and aggression with an online behaviour questionnaire answered by dog owners. Our results show that noise sensitivity is the most common anxiety-related trait with a prevalence of 32% in 13,700 Finnish pet dogs. Due to the high prevalence of noise sensitivity and fear, they were the most common comorbidities. However, when comparing the relative risk, the largest risk ratios were seen between hyperactivity/inattention, separation related behaviour and compulsion, and between fear and aggression. Furthermore, dog breeds showed large differences in prevalence of all anxiety-related traits, suggesting a strong genetic contribution. As a result, selective breeding focusing on behaviour may reduce the prevalence of canine anxieties. Anxious animals may suffer from chronic stress and thus, modified breeding policies could improve the welfare of our companion dogs.