A genealogical survey of Australian registered dog breeds

Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis

There has been considerable interest in studying cancer in dogs and its potential as a model system for humans. One area of research has been the search for genetic risk variants in canine lymphoma, which is amongst the most common canine cancers. Previous studies have focused on a limited number of breeds, but none have included Border Collies. The aims of this study were to identify relationships between Border Collie lymphoma cases through an extensive pedigree investigation and to utilise relationship information to conduct genome-wide association study (GWAS) analyses to identify risk regions associated with lymphoma. The expanded pedigree analysis included 83,000 Border Collies, with 71 identified lymphoma cases. The analysis identified affected close relatives, and a common ancestor was identified for 54 cases. For the genomic study, a GWAS was designed to incorporate lymphoma cases, putative "carriers", and controls. A case-control GWAS was also conducted as a comparison. Both analyses showed significant SNPs in regions on chromosomes 18 and 27. Putative top candidate genes from these regions included DLA-79, WNT10B, LMBR1L, KMT2D, and CCNT1.

Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.

Genetic Diversity and Trends of Ancestral and New Inbreeding in Deutsch Drahthaar Assessed by Pedigree Data

Simple Summary

Deutsch Drahthaar (DD) is the most popular hunting dog in Germany, fulfilling all aspects of hunting including searching for trails. This breed was newly created at the beginning of the 20th century from a large number existing versatile hunting dog breeds. The aim of the breed was, and still is, to achieve the best performance in all aspects of hunting. We analyzed pedigrees of DD using demographic measures to quantify genetic diversity such as probabilities of gene origin and degrees of ancestral and individual inbreeding. A large number of genetically diverse founder dogs should open up the opportunity of creating a breed with a high genetic diversity and a low increase of inbreeding per generation. On the other hand, intense use of top sires and dams from a limited number of breeding lines may accelerate breeding progress in hunting abilities but reduce genetic diversity. Monitoring genetic diversity should help to maintain a high diversity of breeding populations. Our analysis of pedigree data from 101,887 DD dogs revealed inbreeding measures (coefficient of inbreeding F = 0.042, individual rate of inbreeding ΔF_i = 0.00551) and effective population size (Ne = 92) in the mean range compared to a wide range of other dog breeds. Ancestral inbreeding had a strong increasing trend, whereas trends in individual inbreeding and rate of individual inbreeding were slightly negative.

Abstract

Loss of genetic diversity and high inbreeding rates confer an increased risk of congenital anomalies and diseases and thus impacting dog breeding. In this study, we analyzed recent and ancestral inbreeding as well as other measures of genetic variability in the Deutsch Drahthaar (DD) dog population. Analyses included pedigree data from 101,887 animals and a reference population with 65,927 dogs born between 2000 and 2020. The mean equivalent complete generations was 8.6 with 69% known ancestors in generation 8. The mean realized effective population size was 92 with an increasing trend from 83 to 108 over birth years. The numbers of founders, effective founders and effective ancestors, as well as founder genomes, were 814, 66, 38 and 16.15, respectively. Thirteen ancestors explained 50% of the genetic diversity. The mean coefficient of inbreeding and individual rate of inbreeding (ΔF_i) were 0.042 and 0.00551, respectively, with a slightly decreasing trend in ΔF_i. Exposure of ancestors to identical-by-descent alleles explored through ancestral coefficients of inbreeding showed a strong increasing trend. Comparisons between new and ancestral inbreeding coefficients according to Kalinowski et al. showed an average relative contribution of 62% of new inbreeding to individual inbreeding. Comparisons among average coancestry within the parental population and average inbreeding in the reference population were not indicative of genetic substructures. In conclusion, the creation of the DD dog breed about 120 years ago resulted in a popular breed with considerable genetic diversity without substructuring into lines or subpopulations. The trend of new inbreeding was declining, while ancestral inbreeding through ancestors who were autozygous at least once in previous generations was increasing.

Genetics of canine myxomatous mitral valve disease

Myxomatous mitral valve disease (MMVD) is the most common heart disease and cause of cardiac death in domestic dogs. MMVD is characterised by slow progressive myxomatous degeneration from the tips of the mitral valves onwards with subsequent mitral valve regurgitation, and left atrial and ventricular dilatation. Although the disease usually has a long asymptomatic period, in dogs with severe disease, mortality is typically secondary to left-sided congestive heart failure. Although it is not uncommon for dogs to survive long enough in the asymptomatic period to die from unrelated causes; a proportion of dogs rapidly advance into congestive heart failure. Heightened prevalence in certain breeds, such as the Cavalier King Charles Spaniel, has indicated that MMVD is under a genetic influence. The genetic characterisation of the factors that underlie the difference in progression of disease is of strong interest to those concerned with dog longevity and welfare. Advanced genomic technologies have the potential to provide information that may impact treatment, prevalence, or severity of MMVD through the elucidation of pathogenic mechanisms and the detection of predisposing genetic loci of major effect. Here we describe briefly the clinical nature of the disorder and consider the physiological mechanisms that might impact its occurrence in the domestic dog. Using results from comparative genomics we suggest possible genetic approaches for identifying genetic risk factors within breeds. The Cavalier King Charles Spaniel breed represents a robust resource for uncovering the genetic basis of MMVD.

Evaluation of genetic diversity and management of disease in Border Collie dogs

Maintaining genetic diversity in dog breeds is an important consideration for the management of inherited diseases. We evaluated genetic diversity in Border Collies using molecular and genealogical methods, and examined changes to genetic diversity when carriers for Trapped Neutrophil Syndrome (TNS) and Neuronal Ceroid Lipofuscinosis (NCL) are removed from the genotyped population. Genotype data for 255 Border Collies and a pedigree database of 83,996 Border Collies were used for analysis. Molecular estimates revealed a mean multi-locus heterozygosity (MLH) of 0.311 (SD 0.027), 20.79% of the genome consisted of runs of homozygosity (ROH ) > 1 Mb, effective population size (N_e) was 84.7, and mean inbreeding (F) was 0.052 (SD 0.083). For 227 genotyped Border Collies that had available pedigree information (GenoPed), molecular and pedigree estimates of diversity were compared. A reference population (dogs born between 2005 and 2015, inclusive; N = 13,523; RefPop) and their ancestors (N = 12,478) were used to evaluate the diversity of the population that are contributing to the current generation. The reference population had a N_e of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (f), 205.5 effective founders (f_e), 28 effective ancestors (f_a) and 10.65 (SD 2.82) founder genomes (N_g). Removing TNS and NCL carriers from the genotyped population had a small impact on diversity measures (ROH > 1 Mb, MLH, heterozygosity), however, there was a loss of > 10% minor allele frequency for 89 SNPs around the TNS mutation (maximum loss of 12.7%), and a loss of > 5% for 5 SNPs around the NCL mutation (maximum 5.18%). A common ancestor was identified for 38 TNS-affected dogs and 64 TNS carriers, and a different common ancestor was identified for 33 NCL-affected dogs and 28 carriers, with some overlap of prominent individuals between both pedigrees. Overall, Border Collies have a high level of genetic diversity compared to other breeds.

Inbreeding levels in an open-registry pedigreed dog breed: The Australian working kelpie

The depletion in genetic diversity of closed-pedigree dog breeds can be a contentious topic and can lead to calls for open-registry. However, strong evidence in support of proposed open-registry solutions is lacking, with the reproductive isolation of these breeds unlikely to be the sole cause of elevated inbreeding levels. Human-induced limitations, such as popular sire effects, are unlikely to be confined to closed-registry breeds and conceivably play an important role in maintaining genetic diversity within all breeds. Consequently, the aim of the current study was to explore inbreeding levels in an open-registry breed and determine the impact open-registry has on genetic diversity. Complete pedigree records on all Australian working kelpies (AWKs) were provided by the Working Kelpie Council with the cleaned pedigree consisting of 86,671 individuals with a median pedigree depth of 6.6 generations. The average inbreeding coefficient in the AWK population was 0.049 with an increase in inbreeding coefficient of 0.0016/year. This demonstrates that opening a breed registry can have a beneficial impact on the level of inbreeding within a population over the longer-term. However, allowing for a generation length of 5.1 years yielded an effective population size of 61 for AWKs and demonstrated a pattern consistent with closed-registry dog populations of comparable size.

Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data

Simple Summary

Dogs are an important part of society. The Polish Lowland Sheepdog (PON) is one of 353 of the world’s largest cynological organization listed dog breeds. Breeds with small population sizes, like the PONs, are often characterized by high inbreeding rates and thus an increased risk of congenital diseases. To examine the endangerment of the PONs, measures for genetic diversity and inbreeding were calculated for the German PON population. The study showed that the PONs had to be classified as a minimally endangered population according to threshold values specified by the European Association for Animal Production. However, the very recent trend showed a slight improvement.

Abstract

Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients F_Ped based on pedigree data and F_ROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r^² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.

Analysis of Genetic Diversity in the Czech Spotted Dog

Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed-the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity-which was calculated based on the reference population and pedigree completeness-were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence.

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C

BACKGROUND

The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties.

FINDINGS

Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy.

CONCLUSIONS

GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.

The dog 2.0: Lessons learned from the past

In recent years, concerns have been raised on the diversity, health and welfare of our (pedigree) dog population. Somewhat justified, the popular sire effect, population bottlenecks, the founder effect and inbreeding have left their marks on the dog as we know it. In order to improve the health and welfare of the canine population in general, individual breeding programs should adhere to the concept of ethical breeding (i.e. "the use of healthy animals true to their species in behaviour and looks, and when applicable, showing a sustainable performance") when population-specific breeding goals are defined. Even though every population has its own problems, the approach to get to possible solution(s) is similar. The starting point will always be the identification of which (un)desirable pheno- and genotypes are segregating and what their prevalence is, followed by an evaluation of the genetic diversity. Based on that information and, when applicable, additional criteria like breed standards, breeding goals can be defined. It is of critical importance that these goals are put forward with a long term vision in mind and with consensus from the stakeholders to ensure collaboration. Upon prioritization of the most important goals, when necessary with the help of specifically developed tools, the final step is choosing the most optimal combination of breeding strategies. This paper aims to provide a stepwise approach to identify and tackle population-specific problems encountered in breeding programs.

Tracing genetic resurrection of pointing dog breeds: Cesky Fousek as both survivor and rescuer

Cesky Fousek is considered to be one of the oldest pointing dog breeds in Europe and has been appreciated for its versatile working skills. Because it faced extinction in the past, the Cesky Fousek was restored from German Wirehaired and Shorthaired Pointers. Additionally, the breed was recently used in the USA with the initial intent of improvement of the Wirehaired Pointing Griffon (synonymous with Korthals Griffon) by the Bohemian Wirehaired Pointing Griffon Club of America. This study evaluates genetic diversity parameters of Cesky Fousek and compares them to the other continental pointing dogs that played a role in the formation of its gene pool. DNA from buccal swab and blood samples (n = 405) were analyzed using 18 microsatellite markers. Parameters of genetic polymorphism show that the Cesky Fousek breed has a comparable rate of variation as other hunting breeds despite the low population size and severe historical bottlenecks. Clustering analyses reveal a unique genetic status as a distinct pointing dog breed and the relatedness of the breeds is in good concordance with historical data. The present study demonstrates that despite historical admixture among lineages, separate pointing breeds constitute genetically differentiated units, mirroring unique breeding stocks and pedigree isolation among specific breed clubs, reflecting differences in breeding programs under each association.

Heterozygosity testing and multiplex DNA panel screening as a potential tool to monitor health and inbreeding in a small, closed dog population

Background

Selective breeding in populations with a limited effective population size may result in a loss of genetic diversity, which can cause an increased concentration of specific disease liability genes. The Dutch Shepherd Dog (DSD) in the Netherlands is an example of such a breed with a small effective population.

Objective

To evaluate the measurement of genetic diversity and multiplex DNA panel screening for implementation in a breeding strategy for the Dutch Shepherd Dog (DSD) and to investigate the clinical relevance of potentially identified mutations in the multiplex DNA panel screening.

Results

Genome-wide SNP testing showed genetic isolation and reduced genetic diversity within coat variety subgroups of the DSD. Panel screening identified a Von Willebrand's Disease type I mutation. Although decreased Von Willebrand's Factor proteins were significantly lower in DSDs carrying the VWD-I allele compared to the wildtype, clinical follow-up did not show a significant association between the clinical phenotype and VWD-I genotype.

Conclusions

Genetic relationship measurement within a breed population may be a useful tool to enable breeding strategies to conserve genetic diversity. Results from a disease panel screening need to be evaluated for clinical relevance before breed selection restrictions can be considered.

Battle of the Sexes in Best of Breed: Sex Influences Dogs' Success in the Show Ring

Simple Summary

When breeding dogs, the dam and the sire contribute equally to the genetics of each of their puppies, and so each parent should be equally important to show-ring success. The current study collated samples of dog show results to explore relationships between sex and the likelihood of success in the show ring. It focused on toy and giant breeds to explore any differences in equity, if it existed, at either end of the size spectrum. It revealed that the rate at which male and female dogs were exhibited were similar but that male dogs were a significant advantage of winning Best of Breed titles.

Abstract

Much of the research on pedigree dog breeding has been directed towards understanding the implications of reduced genetic diversity and the prevalence of inherited disorders. An example is the potential role of the popular sire effect in perpetuating genetic defects. If male dogs are more likely than bitches to be identified as examples of members of a breed that align with breed standard, they may be selected for breeding earlier. This may contribute to the influence of individual males and contribute to popular sire effect. Conversely, if breed standards are written in a sex-neutral fashion, and if dogs are entered, exhibited, and judged in a sex-neutral fashion, then we would expect the success of female dogs in the show ring to be equal to that of their male counterparts. With a focus on toy and giant breeds, the current pilot study collated samples of dog show results to explore relationships between sex and the likelihood of success in the show ring. It focused on toy and giant breeds to explore any differences in equity, if it existed, at either end of the size and concomitant age-at-maturation spectrum. For the purpose of this study, toy breeds were those that weigh < 10 kg at maturity while giant breed dogs were those that exceed 45 kg. Within these two clusters, the least (n = 3) and most popular (n = 3) breeds were then selected to explore any potential role of sex on success in the show ring. The popularity of breeds was determined using the numbers of dogs registered with the Australian National Kennel Council. Using results from dog shows (n = 18) from 2015 to 2016, data on 1,080 dogs were obtained. Within these 12 breeds for the 18 shows, there were 137 Best of Breed (BOB) titles awarded: Pug (n = 18), Toy Poodle (n = 18), Bullmastiff (n = 14), Rottweiler (n = 17), Fox Terrier (Smooth) (n = 18), Bloodhound (n = 3), Schnauzer (miniature) (n = 15), Great Dane (n = 17), Norfolk Terrier (n = 10), Norwich Terrier (n = 5), Central Asian Shepherd Dog (n = 2). Despite the near parity of male and female dogs being exhibited, of these 137 titles, 86 (62.8%) were awarded to male dogs (at least 41 individuals) and 51 (37.2%) to female dogs (at least 32 individuals) showing that male dogs are more likely to win BOB titles (χ² = 9.4455, df = 1, p-value = 0.002117). Among the toy subset of breeds, this effect was higher (χ² = 6.798, df = 1, p-value = 0.009126) than among the giant breed subset, for whom the advantage to male dogs did not reach statistical significance versus χ² = 3.0967, df = 1, p-value = 0.07845). This suggests that judges find the male dogs more appealing, presumably because they are more aligned with breed standards.

Genomic characterization of the Braque Français type Pyrénées dog and relationship with other breeds

The evaluation of genetic variability is a useful research tool for the correct management of selection and conservation strategies in dog breeds. In addition to pedigree genealogies, genomic data allow a deeper knowledge of the variability and genetic structure of populations. To date, many dog breeds, such as small regional breeds, still remain uncharacterized. Braque Français type Pyrénées (BRA) is a dog breed originating from a very old type of gun-dog used for pointing the location of game birds to hunters. Despite the ancient background, the knowledge about levels of genetic diversity, degree of inbreeding and population structure is scarce. This may raise concerns on the possibility that few inbred bloodlines may dominate the breed, and on its future health. The aim of this work was therefore to provide a high-resolution representation of the genome-wide diversity and population structure of BRA dogs, using the 170K genome-wide SNP array. Genome-wide polymorphisms in BRA were compared with those of other worldwide dog breeds. Between-dog relationships estimated from genomic data were very similar to pedigree relationships (Pearson correlation r_g,a = 0.92). Results showed that BRA generally presents moderate levels of genetic diversity when compared with the major canine breeds. The estimated effective population size (recent N_e = 51) shows a similar declining pattern over generations as all other dog breeds, pointing at a common demographic history of modern canine breeds, clearly different from the demography of feral wolves. Multidimensional scaling (MDS), Bayesian clustering and Neighbor Joining tree were used to visualize and explore the genetic relationships among breeds, and revealed that BRA was highly differentiated and presented only low levels of admixture with other breeds. Brittany Spaniel, English Setter, Gordon Setter and Weimaraner dogs are the closest breeds to BRA. The exact reason for BRA being so divergent from other dog breeds, based on these results, is not yet clear. Further studies including additional ≪braccoid≫ breeds will be needed to refine the results presented here and to investigate the origin of the BRA breed. Nonetheless, the genome-wide characterization reported here provides a comprehensive insight into the genome diversity and population structure of the Braque Français, type Pyrénées breed.

Assessing the relative importance of health and conformation traits in the cavalier king Charles spaniel

Background

The selection of a future breeding dog is a complicated task, in which disease characteristics and different traits have to be combined and weighed against one another. Truncation selection, that is the exclusion of affected animals, may be very inefficient when selecting on a large number of traits, and may result in a reduction of the genetic diversity in a population or breed. Selection could be facilitated by the use of a selection index that combines multiple traits or breeding values into one score. This however requires a consideration of their relative value according to their economic weight, which is difficult to express in monetary units for health traits. The use of a choice experiment to derive non-market values might be a solution to this problem. This is a pilot study to assess the potential use of choice experiments to ascertain the public preference and relative importance attached to health- and conformation traits in the selection of a Cavalier King Charles spaniel. The focus was on two prevalent disorders, mitral valve disease and syringomyelia, and on several important conformation traits such as muzzle length and eye shape. Based on available prior information, a Bayesian D-optimal design approach was used to develop a choice experiment and the resulting choice sets.

Results

Every participant (breeder or owner) in the choice experiment was presented with a total of 17 choice sets, in which at most four traits could vary to reduce the cognitive burden. A total of 114 respondents participated in the choice experiment and results showed that respondents (breeders/owners) current attitudes were directed towards health (syringomyelia and mitral valve disease), followed by eye shape and level of inbreeding.

Conclusions

This approach identifies the value breeders and owners attach to certain traits in the breeding objective. The resulting relative weights, represented as the logworths obtained from the choice experiment, could be an alternative to economic weights. They could be implemented as a weight when breeding values are available, but more study on this topic will be necessary. A challenge in this approach is to scale up the experiment with additional traits. Moreover, for other traits, the genetic parameters and correlations should be known first, in order to include them in the health selection index as well.

Genetic correlations of hip dysplasia scores for Golden retrievers and Labrador retrievers in France, Sweden and the UK

In order to reduce the prevalence of inherited diseases in pedigree dogs, the feasibility of implementation of an international breeding program was investigated. One prerequisite is a strong genetic correlation between countries and our objective was to estimate this correlation for canine hip dysplasia (HD) across three countries to evaluate the feasibility of an international genetic evaluation. Data were provided by the Société Centrale Canine (SCC, France), Svenska Kennelklubben (SKK, Sweden) and The Kennel Club (KC, UK) on Golden retriever and Labrador retriever dogs. Trivariate analysis on the three different modes of scoring HD in France, Sweden and the UK was performed using a mixed linear animal model. Heritability, genetic correlation, number of common sires, genetic similarity, selection differentials and accuracy of selection were calculated. The estimated heritabilities of Golden retrievers (Labrador retrievers) for HD scores were 0.28 (0.15), 0.28 (0.29) and 0.41 (0.34) in France, Sweden and the UK, respectively. The feasibility of performing a genetic evaluation of HD across countries was indicated by the favourable genetic correlations estimated between score modes (ranged from 0.48 to 0.99). The accuracy of selection for the most recent birth year cohorts of male dogs was not improved by international evaluation compared to national evaluation. Improvement in genetic progress can however be achieved by selection across populations in different countries, particularly for small populations, which were indicated by the large difference between selection differentials based on the national and international evaluations.

Canine atopic dermatitis: breed risk in Australia and evidence for a susceptible clade

BACKGROUND

Genetic studies on canine atopic dermatitis (CAD) indicate that large populations from one geographical location are preferred for the identification of relevant susceptibility genes. Australian dogs are relatively isolated; studies on CAD in this population are limited.

HYPOTHESIS/OBJECTIVES

To identify breeds at risk in the Australian dog population and to compare with worldwide breed predisposition.

ANIMALS

Case records (n = 23,000) from University Veterinary Teaching Hospital (UVTH) dogs, including 722 with CAD.

METHODS

The breed proportion of CAD and odds risk (OR) were calculated. A systematic review of 13 previous studies (1971-2010) was performed and compared to the study results by implementing an atopic dermatitis (AD)-to-reference population ratio (ADRPR).

RESULTS

Eleven dog breeds with significant increased OR (≥1.0) were identified; all with breed CAD cases proportionally higher than their base hospital population. Gender risk in males from the pug dog breed (P = 0.007) was detected and the bichon frise breed had a similar trend (P = 0.05). Sixteen predisposed dog breeds were identified by systematic review. All breeds with significant increased OR in UVTH had ADRPR > 1.4; five (boxer, bulldog, Labrador retriever, pug, West Highland white terrier) were recognized as predisposed worldwide. One clade of breeds with common ancestry was highly represented in CAD cases worldwide and in Australia (81% of the significant OR cases).

CONCLUSION AND CLINICAL IMPORTANCE

The use of a large population from one geographical location and ADRPR provided an objective comparison between worldwide AD studies; it identified one common clade of susceptible breeds. Breed genetics and related clinical presentation may help CAD diagnosis and treatment.

Selection of Breeding Stock among Australian Purebred Dog Breeders, with Particular Emphasis on the Dam

Every year, thousands of purebred domestic dogs are bred by registered dog breeders. Yet, little is known about the rearing environment of these dogs, or the attitudes and priorities surrounding breeding practices of these dog breeders. The objective of this study was to explore some of the factors that dog breeders consider important for stock selection, with a particular emphasis on issues relating to the dam. Two-hundred and seventy-four Australian purebred dog breeders, covering 91 breeds across all Australian National Kennel Club breed groups, completed an online survey relating to breeding practices. Most breeders surveyed (76%) reported specialising in one breed of dog, the median number of dogs and bitches per breeder was two and three respectively, and most breeders bred two litters or less a year. We identified four components, relating to the dam, that were considered important to breeders. These were defined as Maternal Care, Offspring Potential, Dam Temperament, and Dam Genetics and Health. Overall, differences were observed in attitudes and beliefs across these components, showing that there is variation according to breed/breed groups. In particular, the importance of Maternal Care varied according to dog breed group. Breeders of brachycephalic breeds tended to differ the most in relation to Offspring Potential and Dam Genetics and Health. The number of breeding dogs/bitches influenced breeding priority, especially in relation to Dam Temperament, however no effect was found relating to the number of puppies bred each year. Only 24% of breeders used their own sire for breeding. The finding that some breeders did not test for diseases relevant to their breed, such as hip dysplasia in Labrador Retrievers and German Shepherds, provides important information on the need to educate some breeders, and also buyers of purebred puppies, that screening for significant diseases should occur. Further research into the selection of breeding dams and sires will inform future strategies to improve the health and behaviour of our best friend.

Merging pedigree databases to describe and compare mating practices and gene flow between pedigree dogs in France, Sweden and the UK

Merging pedigree databases across countries may improve the ability of kennel organizations to monitor genetic variability and health-related issues of pedigree dogs. We used data provided by the Société Centrale Canine (France), Svenska Kennelklubben (Sweden) and the Kennel Club (UK) to study the feasibility of merging pedigree databases across countries and describe breeding practices and international gene flow within the following four breeds: Bullmastiff (BMA), English setter (ESE), Bernese mountain dog (BMD) and Labrador retriever (LBR). After merging the databases, genealogical parameters and founder contributions were calculated according to the birth period, breed and registration country of the dogs. Throughout the investigated period, mating between close relatives, measured as the proportion of inbred individuals (considering only two generations of pedigree), decreased or remained stable, with the exception of LBR in France. Gene flow between countries became more frequent, and the origins of populations within countries became more diverse over time. In conclusion, the potential to reduce inbreeding within purebred dog populations through exchanging breeding animals across countries was confirmed by an improved effective population size when merging populations from different countries.

Epidemiology, presentation and population genetics of patent ductus arteriosus (PDA) in the Dutch Stabyhoun dog

Background

Patent ductus arteriosus (PDA) is one of the most common congenital heart defects in dogs and is considered to be a complex, polygenic threshold trait for which a female sex predisposition has been described. Histological studies in dogs suggest that smooth muscle hypoplasia and asymmetry of the ductus tissue is the major cause of PDA. The Stabyhoun population is small and a predisposition for PDA has been suggested. The aims of this study were to describe the incidence, presentation from a clinical and histopathological perspective, and the population genetics of PDA in the Dutch Stabyhoun population.

Results

Forty-six cases were identified between 2000 and 2013. Between 2009 and 2012 the birth incidence of PDA in the Stabyhoun breed was 1.05 %. We estimated this to be 7–13 times higher than expected in the general dog population. Twelve of the 46 cases were part of a litter in which more than one sibling was affected. There was no sex predilection in our case cohort. Dogs diagnosed in adulthood showed severe cardiomegaly. The mean inbreeding coefficient of the reference population of Stabyhoun dogs was 31.4 % and the actual and effective numbers of founders were 14 and 6.5, respectively. The heritability of PDA was 0.51 (±0.09) for the reference population and 0.41 (±0.10) for the phenotyped population. Histopathology of sections of the PDA from two dogs showed findings similar to those described in other breeds although the smooth muscle of the ductus adjacent to the pulmonary artery appeared more hypoplastic than that in the ductus adjacent to the aorta.

Conclusions

The Stabyhoun breed shows a strong predisposition for PDA. Apart from the absence of a higher incidence in females, no other significant features distinguish PDA in Stabyhouns from the condition in other dog breeds. Heritability and the mean inbreeding coefficient are both very high making the Dutch Stabyhoun breed particularly suited to the study of inherited risk factors for PDA.

Visualization of Genome Diversity in German Shepherd Dogs

A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. This provides a potential tool for advising dog breeders and developing breeding programs within a breed. A challenge in doing this is to present complex relationship data in a form that can be readily utilized. Here, we demonstrate the use of a pipeline, known as NetView, to visualize the network of relationships in a subpopulation of German Shepherd Dogs.

Comparative Analysis of Genome Diversity in Bullmastiff Dogs

Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (fe) of 79; an effective number of ancestors (fa) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial.

Genetic management of Dutch golden retriever dogs with a simulation tool

Excessive inbreeding rates and small effective population sizes are an important problem in many populations of dogs. Proper genetic management of these populations can decrease the problem, and several measures are available. However, the effectiveness of these measures is not clear beforehand. Therefore, a simulation model was developed to test measures that aim to decrease the rate of inbreeding. The simulation program was used to evaluate inbreeding restriction measures in the Dutch golden retriever dog population. This population consisted of approximately 600 dams and 150 sires that produce 300 litters each year. The five most popular sires sire approximately 25% of the litters in a year. Simulations show that the small number of popular sires and their high contribution to the next generation are the main determinants of the inbreeding rates. Restricting breeding to animals with a low average relatedness to all other animals in the population was the most effective measure and decreased the rate of inbreeding per generation from 0.41 to 0.12%. Minimizing co-ancestry of parents was not effective in the long run, but decreased variation in inbreeding rates. Restricting the number of litters per sire generally decreased the generation interval because sires were replaced more quickly, once they met their restriction. In some instances, this lead to an increase in inbreeding rates because the next generations were more related. The simulation tool proved to be a powerful and educational tool for deciding which breeding restrictions to apply, and can be effective in different breeds and species as well.

Recent breeding history of dog breeds in Sweden: modest rates of inbreeding, extensive loss of genetic diversity and lack of correlation between inbreeding and health

One problem in modern dogs is a high occurrence of physical diseases, defects and disorders. Many breeds exhibit physical problems that affect individual dogs throughout life. A potential cause of these problems is inbreeding that is known to reduce the viability of individuals. We investigated the possible correlation between recent inbreeding and health problems in dogs and used studbook data from 26 breeds provided by the Swedish Kennel Club for this purpose. The pedigrees date back to the mid-20th century and comprise 5-10 generations and 1 000-50 000 individuals per pedigree over our study period of 1980-2010. We compared levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals during this period in the investigated dog breeds that we classified as 'healthy' (11 breeds) or 'unhealthy' (15) based on statistics on the extent of veterinary care obtained from Sweden's four largest insurance companies for pets. We found extensive loss of genetic variation and moderate levels of recent inbreeding in all breeds examined, but no strong indication of a difference in these parameters between healthy versus unhealthy breeds over this period. Thus, recent breeding history with respect to rate of inbreeding does not appear to be a main cause of poor health in the investigated dog breeds in Sweden. We identified both strengths and weaknesses of the dog pedigree data important to consider in future work of monitoring and conserving genetic diversity of dog breeds.

An insight into population structure and gene flow within pure-bred cats

Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree-based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, FIS ranged between 0.96 and 1.83%, with this result being related to mating practices such as close inbreeding (on average 5% of individuals being inbred within two generations). Within the three groups of varieties studied, FIT ranged from 1.59 to 3%, while FST¯ values were estimated between 0.04 and 0.91%, which was linked to various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high individual inbreeding level caused by close inbreeding practices.

Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

Background

Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.

Results

Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusions

When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.

Inbreeding and genetic diversity in dogs: results from DNA analysis

This review assesses evidence from DNA analysis to determine whether there is sufficient genetic diversity within breeds to ensure that populations are sustainable in the absence of cross breeding and to determine whether genetic diversity is declining. On average, dog breeds currently retain approximately 87% of the available domestic canine genetic diversity. Requirements that breeding stock must be 'clear' for all genetic disorders may firstly place undue genetic pressure on animals tested as being 'clear' of known genetic disorders, secondly may contribute to loss of diversity and thirdly may result in the dissemination of new recessive disorders for which no genetic tests are available. Global exchange of genetic material may hasten the loss of alleles and this practice should be discussed in relation to the current effective population size of a breed and its expected future popularity. Genomic data do not always support the results from pedigree analysis and possible reasons for this are discussed.