Empirical assessment of competitive hybridization and noise in ultra high density canine tiling arrays.

BACKGROUND: In addition to probe sequence characteristics, noise in hybridization array data is thought to be influenced by competitive hybridization between probes tiled at high densities. Empirical evaluation of competitive hybridization and an estimation of what other non-sequence related features might affect noisy data is currently lacking. RESULTS: A high density array was designed to a 1.5 megabase region of the canine genome to explore the potential for probe competition to introduce noise. Multivariate assessment of the influence of probe, segment and design characteristics on hybridization intensity demonstrate that whilst increased density significantly depresses fluorescence intensities, this effect is largely consistent when an ultra high density offset is applied. Signal variation not attributable to sequence composition resulted from the reduction in competition when large inter-probe spacing was introduced due to long repetitive elements and when a lower density offset was applied. Tiling of probes immediately adjacent to various classes of repeat elements did not generate noise. Comparison of identical probe sets hybridized with DNA extracted from blood or saliva establishes salivary DNA as a source of noise. CONCLUSIONS: This analysis demonstrates the occurrence of competitive hybridization between oligonucleotide probes in high density tiling arrays. It supports that probe competition does not generate random noise when it is maintained across a region. To prevent the introduction of noise from this source, the degree of competition should be regulated by minimizing variation in density across the target region. This finding can make an important contribution to optimizing coverage whilst minimizing sources of noise in the design of high density tiling arrays.

Mortality Resulting from Undesirable Behaviours in Dogs Aged Three Years and under Attending Primary-Care Veterinary Practices in Australia.

There is increasing evidence that undesirable behaviours (UBs) in dogs can compromise the welfare of both canine companions and their carers. Veterinarians are regularly consulted about affected animals and may be asked to euthanase the more severely affected individuals. A recent study of veterinary records showed that UBs were the predominant cause of mortality in young dogs in the UK. This companion study from Australia reports the proportion of mortality due to UBs among dogs aged three years and under that attended veterinary practices from 2013 to 2018. Deidentified patient records were extracted from the VetCompass Australia database and manually assessed to reveal the prevalence and type of UBs reported. The results reveal that 29.7% of the 4341 dogs that died at three years of age or under had deaths ascribed to at least one UB, and that the most commonly reported UB was aggression. Neutered dogs had 2.5× the odds of death due to an UB compared to intact dogs, and crossbred dogs were found to have 1.43× the odds of a UB related death compared to purebred dogs. The breeds at highest risk were Australian cattle dogs (odds ratio (OR) 4.77) and American Staffordshire terriers (OR 4.69). The attending veterinarian referred behaviour cases to a behaviourist or dog trainer in 11.0% of all UB cases, and attempted pharmacological therapy in 5.9% of cases. The results reveal how often UBs affect dogs and their owners in Australia, and infer the beneficial impact that educating dog owners and veterinary professionals in modifying and managing UBs may have.

Mental Health Disease or Preventable Problem? Australian Dog Trainers' Opinions about Canine Separation Anxiety Differ with Training Style.

Separation anxiety is common. Many dog owners do not seek help from a veterinarian but might consult a trainer. The objective of this study was to investigate Australian trainers' opinions about separation anxiety. An online survey was distributed via training organisations, resulting in 63 completed surveys. Descriptive statistics and Fisher's exact tests were applied. Respondents were grouped into reward-based (n = 41) and balanced (n = 22) trainers. Most trainers (82.5%) used multiple methods to identify separation anxiety but only 7.9% referred to a veterinarian for diagnosis. Reward-based trainers ranked assistance from a veterinarian and owner's willingness to try medication as more important than balanced trainers (p < 0.05). More balanced trainers reported that medication was rarely necessary in the cases they saw: 50% balanced compared with 4.9% reward-based trainers, with 95% CIs of [28.2, 71.8] and [0.6, 16.5], respectively. Almost all (95.5%) balanced trainers believed separation anxiety was preventable compared with 52.6% of reward-based trainers (p < 0.05). We conclude that opinions about separation anxiety varied between reward-based and balanced trainers. Trainers are not taught, expected, or legally allowed to diagnose anxiety disorders. This study showed that balanced trainers were less likely to recommend involvement of veterinarians who can make a diagnosis and rule out other causes of observed behaviours.

Association between coat colour and the behaviour of Australian Labrador retrievers.

BACKGROUND: Making assumptions regarding temperament and intelligence based on the physical appearance of dogs can be a conscious or unconscious human act. Labrador retrievers with chocolate-coloured coats are anecdotally considered to be less trainable and more hyperactive and aggressive than their black or yellow peers. To test these assertions, we analysed the owner-reported behavioural traits of Labradors in relation to both their observable coat colour, and their TYRP1 and MC1R genotypes. RESULTS: We used the results of an owner-based questionnaire to determine scores for 21 behavioural traits and test whether these scores varied with coat colour (n = 225). Familiar dog aggression was the only trait that was found to vary significantly with coat colour (P = 0.013). Yellow Labradors had a higher score than chocolate Labradors, even when corrected for multiple testing (P = 0.021).We repeated the analyses for a subset of 63 Labradors with available genotyping data for the genes (MC1R and TYRP1) that are known to determine the primary coat colours in Labradors. Familiar dog aggression scores varied with both the observed coat colour and MC1R genotype. Dogs homozygous for MC1R recessive allele (with yellow coat colour) scored higher for familiar dog aggression than either black or chocolate Labradors. However, no association maintained significance when incorporating Bonferroni correction. Dog trainability scores decreased additively as the number of recessive brown alleles for TYRP1 increased. This allelic association was independent of the observable coat colour. Dogs homozygous for the brown allele were considered less trainable than dogs with no brown alleles (P = 0.030). CONCLUSIONS: Our results do not support that chocolate-coloured Labradors are more hyperactive or aggressive than either black or yellow Labradors. Trainability scores varied with TYRP1 genotype but not the observable coat colour. Further validation is required.

Work-type influences perceived livestock herding success in Australian Working Kelpies.

BACKGROUND: Working dog handlers and breeders have very different behavioural requirements in the animals that they employ for managing livestock. The Australian Working Kelpie breed may be used in several working contexts, notably yards, paddocks and a combination of both. The working context influences the skillsets required and gives rise to three corresponding work-types: Yard, Paddock and Utility Kelpies. In particular, dogs used for working stock in the confines of yards and trucks interact with stock more forcefully than those mustering in larger areas (paddocks) where they can herd stock effectively from a greater distance. This article explores owner assessments of dog working quality and assessment of genomic similarity by multidimensional scaling, to ask whether it is sufficient for breeders to aim for a multipurpose breeding objective, or whether breeding only specialist lines maximises user satisfaction for yard and paddock work. RESULTS: Reported owner perceptions of 298 dogs assessed with the Livestock Herding Dog assessment tool showed that dog handlers across all working types were very happy with their dogs' level of general skills.Compared with both Yard and Utility Kelpies, Paddock Kelpies had significantly lower trait scores for force (pressure applied by the dog to move livestock), willingness to back the stock (run along a sheep's dorsum) and bite (frequency of using the mouth to grab or bite the livestock). Meanwhile, compared with both Paddock and Utility Kelpies, the Yard Kelpies had significantly higher scores for hyperactivity and excitability (both with and without stock) and impulsiveness without stock. As one would predict for all-rounders, Utility Kelpies had intermediate scores for all behaviours and working traits. CONCLUSIONS: Specialist characteristics were displayed by dogs in the Yard Kelpie and Paddock Kelpie groups. In particular, Yard Kelpies demonstrate higher excitability, willingness to back the stock, and a higher tendency to bark and bite the stock. Conversely, Paddock Kelpies rarely display these characteristics. Utility Kelpies, as the name suggests, are intermediate between the other two groups and display the characteristics of both. Genetic analysis suggests that the Yard, Utility and Paddock Kelpies are not distinguishable at a DNA level. In conclusion, at this time there is no suggestion of a breed split in the Australian Working Kelpie generated by selection for work type. A common breeding objective should enable dogs to be produced that fulfil all potential working requirements. This reinforces the importance of breeder skill in recognising the phenotypic potential of pups in order to place them in appropriate working contexts.

Holding back the genes: limitations of research into canine behavioural genetics.

Canine behaviours that are both desirable and undesirable to owners have a demonstrable genetic component. Some behaviours are breed-specific, such as the livestock guarding by maremmas and flank sucking seen in Dobermanns. While the identification of genes responsible for common canine diseases is rapidly advancing, those genes underlying behaviours remain elusive. The challenges of accurately defining and measuring behavioural phenotypes remain an obstacle, and the use of variable phenotyping methods has prevented meta-analysis of behavioural studies. International standardised testing protocols and terminology in canine behavioural evaluations should facilitate selection against behavioural disorders in the modern dog and optimise breeding success and performance in working dogs. This review examines the common hurdles faced by researchers of behavioural genetics and the current state of knowledge.