Genetic analysis of the modern Australian labradoodle dog breed reveals an excess of the poodle genome

Longevity of companion dog breeds: those at risk from early death

The companion dog is one of the most phenotypically diverse species. Variability between breeds extends not only to morphology and aspects of behaviour, but also to longevity. Despite this fact, little research has been devoted to assessing variation in life expectancy between breeds or evaluating the potential for phylogenetic characterisation of longevity. Using a dataset of 584,734 unique dogs located within the UK, including 284,734 deceased, we present variation in longevity estimates within the following: parental lineage (purebred = 1 breed, crossbred ≥ 2 breeds), breed (n = 155), body size (large, medium, small), sex (male, female) and cephalic index (brachycephalic, mesocephalic, dolichocephalic). Survival estimates were then partitioned amongst phylogenetic clades: providing evidence that canine evolutionary history (via domestication and associated artificial selection) is associated with breed lifespan. This information provides evidence to inform discussions regarding pedigree health, whilst helping current/prospective owners, breeders, policy makers, funding bodies and welfare organisations improve decision making regarding canine welfare.

Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases

Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.

Whole genome resequencing reveals the genetic contribution of Kazakh and Swiss Brown cattle to a population of Xinjiang Brown cattle

Xinjiang Brown cattle is characterized by wide environmental adaptation from its female parent (Kazakh cattle) and good production performance from its male parent (Swiss Brown cattle). However, the genetic basis underlying these characteristics hasnotbeenexplored. Here we compared 50 genomes of Xinjiang Brown cattle to the genomes of other eight breeds worldwide to analyze patterns of genetic variation in the Xinjiang Brown cattle. We found canonical genomic characteristics of cross breed with the lowest linkage disequilibrium and the highest effective population size. At the global level, Xinjiang Brown cattle had 9.88% Kazakh cattle and 90.12% Swiss Brown cattle inheritance. Our local ancestry inference revealed the segments with the excess of Kazakh cattle blood enriched in genes or pathways involved in digestion,absorption,metabolism and disease. More importantly, we also observed the completely fixed haplotypes inherited from Swiss Brown cattle harboring genes (LCORL, GHR, MEF2D, PCSK1 and MSRB3), KEGG pathways, cattle QTLs or human NHGRIGWAS catalog related to body measurement and growth traits. Our findings will not only help understand the process of cross breeding but can provide basic materials for further QTL mapping and improvement of important traits in Xinjiang Brown cattle.

How much is that doodle in the window? Exploring motivations and behaviours of UK owners acquiring designer crossbreed dogs (2019-2020)

Background

Demand for intentional crosses of purebred dog breeds, often labelled ‘designer crossbreeds’ (e.g., Labrador Retriever X Poodle, the ‘Labradoodle’), has recently increased in the UK. This study aimed to explore this phenomenon by comparing pre-purchase motivations, pre-purchase and purchase behaviours of UK owners of designer crossbred puppies purchased during 2019-2020 with those of owners of purebred puppies purchased during the same period.

Results

Data were collected in an online cross-sectional survey between November-December 2020. Responses from n = 6293 puppies (designer crossbred puppies: n = 1575; purebred puppies: n = 4718) were analysed. Perceived hypoallergenicity was cited as a motivator for breed/crossbreed choice by almost half of designer crossbreed owners (47.1%), six times more than purebred dog owners (7.86%; odds ratio [OR]: 9.12, 95% CI: 7.70-10.8). Designer crossbred puppies were more likely to have been acquired via a general selling website (e.g., Gumtree; 13.8%) compared to purebred puppies (7.67%; OR: 2.19, 95% CI: 1.77-2.71), or an animal-specific selling websites (e.g., Pets4Homes; 55.7%) compared to purebred puppies (37.4%; OR: 1.89, 95% CI: 1.65-2.17). Designer crossbreed owners were less likely to see their puppy in person prior to purchase than purebred owners (60.4% vs. 67.0%, respectively; OR: 0.74, 95% CI: 0.64-0.85), and at purchase, designer crossbred puppies were less likely to be seen with their mother (73.1% vs. 79.8%, respectively; OR: 0.82, 95% CI: 0.70-0.95), and littermates (67.7% vs. 78.1%, respectively; OR: 0.63, 95% CI: 0.55-0.73). Designer crossbreeds had a significantly higher purchase price, with 25.7% of designer crossbreed puppies costing £2000-£2999 compared to 15.1% of purebred puppies (X² = 207.31, p <  0.001).

Conclusions

The recent boom in designer crossbreeds in the UK has been fuelled by a desire for perceived hypoallergenic and generally healthy dogs that fit the lifestyles of households with children and limited experience with dogs. Some sought-after traits in designer crossbreeds are misconceptions that risk canine welfare, including relinquishment risk, if owner expectations are not met. Purchasing practices fuelling this boom support irresponsible breeding and selling practices, which combined with reduced pressure for health testing from buyers, may result in a higher disease burden and poorer future welfare for this growing designer dog population.

Grooming-Related Concerns Among Companion Animals: Preliminary Data on an Overlooked Topic and Considerations for Animals' Access to Health-Related Services

Grooming is an essential health maintenance activity that is fundamental to the welfare of many companion animals. Despite the potentially serious consequences of inadequate grooming for pets and their caregivers, few studies have examined the role of access to pet grooming services and supplies in promoting and maintaining companion animal health and welfare. The goal of this paper was 2-fold: (1) To provide preliminary findings demonstrating the scope of grooming and matting concerns among animals served by a large, non-profit animal welfare organization and (2) to provide a call for research to guide effective prevention of and responses to grooming-related omissions of care. We retrospectively extracted data from five American Society for the Prevention of Cruelty to Animals (ASPCA) programs serving the New York City area: ASPCA Animal Hospital (AAH), Community Medicine (CM), One ASPCA Fund, ASPCA-NYPD (New York City Police Department) Partnership, and the Community Engagement (CE) Program. The prevalence of grooming–related concerns was relatively consistent across all three veterinary service programs (AAH: 6%; CM: 4%; One ASPCA Fund: 6%). Thirteen percent of the ASPCA-NYPD Partnership's cruelty cases involved general hair matting concerns and/or strangulating hair mat wounds (93% were long-haired dog breed types). Five percent of CE cases received grooming-related supplies to support pet caregivers' in-home grooming capabilities. Our findings underscore the need to understand the scope of grooming-related concerns among animals served by veterinarians and other community programs to improve animals' access to health-related services.

Breed and conformational predispositions for prolapsed nictitating membrane gland (PNMG) in dogs in the UK: A VetCompass study

Background

Prolapsed nictitating membrane gland (PNMG) is the most common disorder of the third eyelid in dogs. However, the epidemiology of PNMG in the wider dog population remains understudied.

Methods

Using de-identified clinical data from the VetCompass Programme, this cohort study aimed to report the prevalence, demographic and breed-related risk factors of PNMG in dogs attending UK primary care veterinary practices in 2016.

Results

There were 1,802 PNMG cases identified from 905,543 dogs, yielding an annual prevalence of 0.20% (95% confidence interval (CI) 0.19–0.21). The median age at first diagnosis was 0.63 years (IQR 0.33–1.98, range 0.11–18.00). Dogs aged under 1 year had 10.82 times the odds (95% CI 9.17–12.76) compared with dogs aged from 2 to under 4 years. Neutered animals had higher odds than entire animals within both sexes. Breeds with the highest odds of PNMG compared with crossbred dogs included Neapolitan Mastiff (odds ratio (OR) 34.26, 95%CI 15.92–73.75), English Bulldog (OR 24.08, 95% CI 20.62–28.13), Cane Corso (OR 14.66, 95% CI 8.18–26.28), Lhasa Apso (OR 12.37, 95% CI 10.26–14.92) and American Cocker Spaniel (OR 11.57, 95% CI 5.59–23.96). Purebred dogs had 1.43 times the odds (95% CI 1.26–1.63) of PNMG compared with crossbreed dogs. Breeds with brachycephalic skull conformation had 6.71 times the odds (95%CI 5.89–7.64) compared with breeds with mesocephalic skull conformation. Insured dogs had 1.89 times the odds (95% CI 1.65–2.16) compared with uninsured dogs.

Conclusions

This study reports the largest cohort of primary-care PNMG cases assembled to date. The results showing young age at diagnosis along with the breed, purebred and brachycephalic skull conformation predispositions suggest a hereditary involvement in PNMG development. These results may help to guide breeding strategies to reduce the prevalence of PNMG and improve welfare in predisposed individuals.

Best practices for analyzing imputed genotypes from low-pass sequencing in dogs

Although DNA array-based approaches for genome-wide association studies (GWAS) permit the collection of thousands of low-cost genotypes, it is often at the expense of resolution and completeness, as SNP chip technologies are ultimately limited by SNPs chosen during array development. An alternative low-cost approach is low-pass whole genome sequencing (WGS) followed by imputation. Rather than relying on high levels of genotype confidence at a set of select loci, low-pass WGS and imputation rely on the combined information from millions of randomly sampled low-confidence genotypes. To investigate low-pass WGS and imputation in the dog, we assessed accuracy and performance by downsampling 97 high-coverage (> 15×) WGS datasets from 51 different breeds to approximately 1× coverage, simulating low-pass WGS. Using a reference panel of 676 dogs from 91 breeds, genotypes were imputed from the downsampled data and compared to a truth set of genotypes generated from high-coverage WGS. Using our truth set, we optimized a variant quality filtering strategy that retained approximately 80% of 14 M imputed sites and lowered the imputation error rate from 3.0% to 1.5%. Seven million sites remained with a MAF > 5% and an average imputation quality score of 0.95. Finally, we simulated the impact of imputation errors on outcomes for case-control GWAS, where small effect sizes were most impacted and medium-to-large effect sizes were minorly impacted. These analyses provide best practice guidelines for study design and data post-processing of low-pass WGS-imputed genotypes in dogs.