Genetic diversity, inbreeding and breeding practices in dogs: results from pedigree analyses

Pedigree analysis constitutes a classical approach for the study of the evolution of genetic diversity, genetic structure, history and breeding practices within a given breed. As a consequence of selection pressure, management in closed populations and historical bottlenecks, many dog breeds have experienced considerable inbreeding and show (on the basis of a pedigree approach) comparable diversity loss compared to other domestic species. This evolution is linked to breeding practices such as the overuse of popular sires or mating between related animals. The popular sire phenomenon is the most problematic breeding practice, since it has also led to the dissemination of a large number of inherited defects. The practice should be limited by taking measures such as restricting the number of litters (or offspring) per breeding animal.     

Population genetic analysis of the new dog breed Elo

The breeding of the dog breed Elo was started in 1987. This dog breed was established by using 16 dogs of nine different breeds. All pedigree information of the dogs from 1987 to 2002 was included for the analysis of the proportion of genes of the different founder breeds, of the inbreeding coefficient, and relationship coefficients. Additionally, the number of died puppies per litter were investigated. The Eurasian dog breed contributed about 48% of the genes in the whole Elo dog population. Old English sheepdog and Chow Chow contributed about 23% and 10% of the genes. The other dog breeds were of minor importance. The mean inbreeding and relationship coefficients of the whole Elo dog population were 12.04% and 19.22%, respectively. With the exception of 3.5% of animals, all Elo dogs were related to each other. The mean litter size was 6.39 puppies. The percentage of stillborn puppies per litter averaged at 9.47%. The inbreeding coefficients of the puppies and of their dams, the age of the sire and the dam at the time of birth of the puppies, the litter size, the puppies' year of birth and the proportion of genes of the Chow Chow showed a significant effect on the number of stillborn puppies per litter. The heritability for the frequency of stillborn puppies was estimated using a linear animal model. After transformation of the linear estimates to the underlying liability scale, the heritability amounted to h2 = 0.15.     

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.     

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.     

Resolution of parentage in dogs by examination of microsatellites after death of putative sire: case report.

A case of disputed paternity in dogs is reported. DNA examinations were carried out from hair samples of the individuals several months after the death of the putative sire. Ten short tandem repeat (STR) loci were analysed by fluorescence-labelled multiplex PCR using ABI PRISM 310 Genetic Analyser. Based on the results the candidate sire was included in the pedigree records as the biological sire. In spite of the genetic homogeneity of pedigree dogs due to inbreeding, canine microsatellites can provide an adequate basis for assigning paternity in pure breeds.     

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.     

Inbreeding trends and pedigree analysis of Bavarian mountain hounds, Hanoverian hounds and Tyrolean hounds

The objective of this study was to analyse genetic diversity for the three scent-hound breeds Bavarian mountain hound (BMH), Hanoverian hound (HH) and Tyrolean hound (TH) using all available pedigree information from scent-hound kennel clubs for these three breeds throughout Europe. The pedigree data of the BMH and the HH date back to 1912 and 1894, respectively. Pedigree data of the TH were available from the 1960s onwards. The reference populations included all BMH (n = 3231), HH (n = 1371) and TH (n = 1167) dogs registered between 1992 and 2004. Average generation intervals were 5.3 years for the BMH and 5.0 years for the HH and TH. Average inbreeding coefficients for the reference populations were 4.5%, 6.8% and 9.5% for the BMH, HH and TH. The effective numbers of founders, ancestors and founder genomes were lowest for the TH and highest for the BMH. The effective numbers of founder genomes were 10.9, 5.6 and 4.3 for the BMH, HH and TH. Effective population size was largest for the BMH with 72.7 effective breeding animals, followed by the HH with 50.9 and TH with 26.5. The most important ten ancestors had genetic contributions to the reference populations of 54.4%, 65.2% and 77.9% in the BMH, HH and TH. The results of our study indicate the need for careful breed management in these highly specialized hound breeds to maintain genetic diversity. European stud books should be established for these dog breeds in order to avoid inbreeding due to missing pedigree records.     

Identification and characterization of hierarchical structures in dog breeding schemes, a novel method applied to the Norfolk Terrier

Popular sires, a limited population size, and the founder event are widely considered the main reasons for the low genetic diversity observed in many dog breeds. However, these factors have had only a small role in the historic decrease in diversity observed in the Norfolk Terrier breed. We show that the decrease in this breed has been mainly due to large, popular kennels. Dogs from these kennels have, on average, larger genetic contributions to subsequent generations than others. A test for the presence of a popular kennel effect is proposed and applied (P < 0.001). These kennels were found to be the same as nuclei of selection existing in other livestock species. This result revealed a hierarchical structure of dog breeding schemes, with an asymmetric gene flow predominantly from the nuclei toward the main population. Possible reasons for this structure and implications for future population management are discussed. The main reason is probably that the breed type was established by large, popular kennels and that small kennel breeders used their stud dogs to benefit from the achievements of the popular kennels. Many kennels, however, were unable to make their own substantial genetic contributions to the breed.     

Estimation of inbreeding and effective population size of full‐blood wagyu cattle registered with the American Wagyu Cattle Association

The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (F_IT and F_ST) and the effective population size (N_e) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (F_ROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (F_ROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.     

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, F_IS 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, F_IT ranged from 1.59 to 3%, while 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.     

Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans

Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on F_ST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour‐joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed relatedness, but in small populations even more importantly by stochastic effects.     

Serum alpha-tocopherol concentrations in German shepherd dogs with chronic degenerative radiculomyelopathy

The concentration of serum alpha-tocopherol was measured in German shepherd dogs with chronic degenerative radiculomyopathy, and in German shepherd dogs and dogs of other breeds unaffected by the condition. The mean concentration was significantly higher in German shepherd dogs with the condition than in other breeds of dog unaffected by it, but it was not significantly higher than in unaffected German shepherd dogs. Estimates of components of variance indicated that the concentration varied more widely in individual affected dogs than in unaffected dogs, irrespective of breed. These results suggest that chronic degenerative radiculomyopathy in German shepherd dogs is unlikely to be due to uncomplicated vitamin E deficiency.     

Development of the population size, contribution of foreign breeds, inbreeding and degree of relationships of the entire Hanoverian scenthound population registered in the stud book of the kennel club Hirschmann e.V

The entire dog population of Hanoveranian Scenthounds registered since the foundation of the kennel club Hirschmann in the year 1894 was analysed for the development of the inbreeding and relationship coefficient and the contribution of Hanoveranian Scenthound population of foreign countries. The analyses were performed using all available pedigree information. In the history, the breeding of the Hanoveranian Scenthound was difficult because of the low number of breeding dogs which was additionally reduced during World War I and II. The mean coefficient of inbreeding of the entire German population was 6.35%. From 1950 to 1990, the mean coefficient of inbreeding increased from 8.3% to 9.7%. In the birth years from 1990 to 2002, the mean coefficient of inbreeding decreased slightly to 9.2%. The rates of inbreeding decreased since 1950. For the last 8 generations the increase of the coefficients of inbreeding per generation was 0.71%. The mean degree of relationship of the entire population was 7.17%, whereby values higher than 75% were found. Gene contributions of 8 other European stud books for the Hanoveranian Scenthound could be found in the German population. Hereby, the Austrian Hanoveranian Scenthounds had the largest impact on the German population with 24.4%. The proportion of genes from the German stud book amounted to 67%.     

Long-term study of aerobic bacteria of the genital tract in stud dogs.

The aerobic bacterial flora of the genital tract was characterized in 15 stud dogs in an 18-month study. The dogs represented 4 breeds and were from 3 kennels. Bacterial samples from the prepuce and semen were collected every month, except in connection with matings, when they were collected weekly (464 samples). The dogs that were included all mated at least once during the study. The mean pregnancy rate, litter size, and pup mortality for the bitches with which they had mated were all within normal limits. The most frequent bacteria isolated from the prepuce and semen were Pasteurella multocida, beta-hemolytic streptococci, and Escherichia coli. There was a tendency for breeds to differ in frequency of the most common bacterial species. Bacterial culture yielded no aerobic growth in 14.2% of the preputial samples and 69.8% of the semen samples. Bacteria were transferred between dog and bitch at mating. In this study of healthy breeding dogs, neither the fertility of the dog nor that of the bitch was affected by the bacteria transferred.     

Half of 23 Belgian dog breeds has a compromised genetic diversity,as revealed by genealogical and molecular data analysis

The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity.     

Characteristics of 234 dog bite incidents in Ireland during 2004 and 2005

Information was obtained by telephone interview from 100 dog owners whose dog had bitten a person, and from 134 victims of bites by a dog not owned by the victim. Three-quarters of the victims were female and aged from 21 to 60 years. The majority of the dogs were owned, male, two to six years old, over 10 kg in bodyweight and belonged to the popular breeds: collies, cocker/springer spaniels, terrier breeds, Jack Russell terriers, German shepherd dogs, golden retrievers and crossbreeds. The numbers of bites by the different breeds indicated that those that inflicted the most bites were the popular breeds rather than the breeds with any greater propensity to bite. Most attacks were rapid single bites and in 50 per cent of the cases, neither the owner nor the victim was able to identify any signal of the dog's intention to bite. Overall, 21 per cent of the incidents were rated as 'serious' and 2 per cent as 'life threatening'. One fifth of the dogs were euthanased as a result of the incident. Half the incidents required professional medical assistance for the victim. Almost half the incidents took place while the victim was walking or passing close to the dog's territory, or while the victim was interacting with the dog at home.     

Collie eye anomaly in Hokkaido dogs: case study

Objective To describe a Hokkaido dog, one of the traditional Japanese breeds that was affected by Collie eye anomaly (CEA), and to report the genotype of this dog and the Hokkaido dog allelic frequency of the CEA‐associated mutation. Case A nine‐month‐old intact female Hokkaido dog without any obvious visual disturbance was diagnosed ophthalmoscopically with CEA. Severe choroidal hypoplasia was observed in the bilateral temporal area adjacent to the optic nerve head, appearing as whitish areas. Therefore, the dog was suspected of possessing the CEA‐associated mutation that was previously reported as an intronic 7.8‐kilo base deletion in the canine NHEJ1 gene. Procedures SYBR Green‐based real‐time PCR with a melting curve analysis, conventional PCR with agarose gel electrophoresis, and direct DNA sequencing were carried out to determine the genotype of the dog. Furthermore, a preliminary genotyping survey was carried out in 17 Hokkaido dogs from three kennels using the real‐time PCR method, and the pedigree relationships were analyzed using their pedigree papers. Results The Hokkaido dog affected by CEA was proven to possess the CEA‐associated mutation. Of these 17 Hokkaido dogs, 12 dogs were heterozygous carriers and five dogs were affected by this mutation. The preliminary genotyping survey and pedigree analysis demonstrated that the allelic frequency of the CEA‐associated mutation is very high in Hokkaido dogs. Conclusion These data suggest that the Hokkaido breed is highly susceptible to CEA because of the known CEA‐associated mutation much like the Collie‐related breeds.     

Population parameters to compare dog breeds: differences between five Dutch purebred populations

Differences in five purebred dog populations born in 1994 in the Netherlands were evaluated using different parameters. Numerically, the Golden Retriever was the largest breed (840 litters of 234 sires) and the Kooiker Dog (101 litters of 41 sires) the smallest. The litter per sire ratio was largest in the Bernese Mountain Dog (4.59) and lowest in the Kooiker Dog (2.46). The mean relatedness and the actual mean level of inbreeding in the studied generations were 0.102 and 0.056 respectively for the Bernese Mountain Dog, 0.041 and 0.046 for the Bouvier des Flandres, 0.087 and 0.061 for the Boxer, 0.020 and 0.018 for the Golden Retriever, and 0.146 and 0.070 for the Kooiker Dog. Quantification and visualization of population parameters for purebred dogs will facilitate the comparison of breeds and the comparison of breeds in different periods or countries. It appears unlikely that the increase in inbreeding is a major determinant of the possible increase in the frequency of genetic diseases.     

Prevalence of canine cataract: preliminary results of a cross-sectional study

Objective In this study 2000 dogs were examined ophthalmoscopically to determine presence of cataract. Materials and methods The dogs examined were predominantly from veterinary hospital populations but also from the Waltham Center For Pet Nutrition, rehoming charities and breeding kennels. Prevalence of cataract was thus determined for different age groups (year cohorts). The age at which prevalence of cataract was 50% (C₅₀) was determined indirectly from a fitted prevalence curve. Results The mean ± standard deviation of C₅₀ for all dogs in the study was 9.4 ± 3.3 years. All dogs over 13.5 years were affected by some degree of lens opacity. C₅₀ was determined for animals of different genders and different breeds. For dogs of six breeds sufficient data were available for calculation of breed‐specific C₅₀. In these dogs C₅₀ was positively correlated with longevity with a least squares correlation coefficient of 0.74. Conclusion The study yields novel findings regarding the prevalence and incidence of cataract in the dog and forms the basis for considerable further work on the epidemiology and pathophysiology of age‐related cataract in the dog.     

Inherited defects in pedigree dogs. Part 2: Disorders that are not related to breed standards

Recent debate concerning health problems in pedigree animals has highlighted gaps in current knowledge of the prevalence, severity and welfare implications of deleterious inherited traits within the pedigree-dog population. In this second part of a two-part review, inherited disorders in the top 50 UK Kennel Club registered breeds were researched using systematic searches of existing databases. A set of inclusion and exclusion criteria, including an evidence strength scale (SEHB), were applied to search results. A total of 312 non-conformation linked inherited disorders was identified, with German shepherd dogs and Golden retrievers associated with the greatest number of disorders. The most commonly reported mode of inheritance was autosomal recessive (71%; 57 breed-disorder combinations), and the most common primarily affected body system was the nervous sensory system. To provide a true assessment of the scale of inherited disorders in the pedigree dogs studied more effort is required to collect accurate prevalence data.