Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations

Using genome‐wide SNP data, we calculated genomic inbreeding coefficients (F_ROH > _1 Mb, F_{ROH > 2 Mb}, F_{ROH > 8 Mb} and F_{ROH > 16 Mb}) derived from runs of homozygosity (ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity (F_HOM). We compared these values of inbreeding coefficients with those calculated from pedigrees (F_PED) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients F_{ROH > 8 Mb} and F_{ROH > 16 Mb} were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh (F_PED = 0.014, F_{ROH > 8 Mb} = 0.019 and F_{ROH > 16 Mb} = 0.008); the highest, for Brown Swiss (F_PED = 0.048, F_{ROH > 8 Mb} = 0.074 and F_{ROH > 16 Mb} = 0.037). In contrast, inbreeding estimates based on the genomic coefficients F_{ROH > 1 Mb} and F_{ROH > 2 Mb} were considerably higher than pedigree‐derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3–1.7‐fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors.     

Genetic diversity and genomic inbreeding in Japanese Black cows in the islands of Okinawa Prefecture evaluated using single-nucleotide polymorphism array

Maintaining genetic diversity and inbreeding control are important in Japanese Black cattle production, especially in remote areas such as the islands of Okinawa Prefecture. Using a single-nucleotide polymorphism (SNP) array, we evaluated the genetic diversity and genomic inbreeding in Japanese Black cows from the islands of Okinawa Prefecture and compared them to those from other locations across Japan. Linkage disequilibrium decay was slower in cows in the islands of Okinawa Prefecture. The estimated effective population size declined over time in both populations. The genomic inbreeding coefficient (F_ROH) was estimated using long stretches of consecutive homozygous SNPs (runs of homozygosity; ROH). F_ROH was higher in the cows on the islands of Okinawa Prefecture than on other locations. In total, 818 ROH fragments, including those containing NCAPG and PLAG1, which are major quantitative trait loci for carcass weight in Japanese Black cattle, were present at significantly higher frequencies in cows in the islands of Okinawa Prefecture. This suggests that the ROH fragments are under strong selection and that cows in the islands of Okinawa Prefecture have low genetic diversity and high genomic inbreeding relative to those at other locations. SNP arrays are useful tools for evaluating genetic diversity and genomic inbreeding in cattle.     

Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population

Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low‐density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (F_PH), runs of homozygosity (F_ROH) and pedigree (F_PED). Phenotypic records were available for 13,712 animals including non‐return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average F_PED was 0.02, F_ROH 0.06 and F_PH 0.63. A correlation of 0.71 was found between F_PED and F_ROH, 0.66 between F_PED and F_PH and 0.94 between F_ROH and F_PH. Pedigree‐based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when F_ROH or F_PH was used as a covariate, significant inbreeding depression was observed; a 10% increase in F_ROH was associated with 5 days longer IFL0 and IFL1, 2 weeks longer IFL3 and 3 days longer ICF2 compared to non‐inbred cows.     

Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds

The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (F_PED), or runs of homozygosity (ROH; F_ROH) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each breed. VdB showed higher inbreeding coefficients compared to SAR, with both breeds showing lower estimates as the minimum ROH length increased. Significant inbreeding depression was found only for milk yield, with a loss of around 7 g/day (for SAR) and 9 g/day (VdB) for a 1% increase of F_ROH. The present study confirms how the use of genomic information can be used to manage intra-breed diversity and to calculate the effects of inbreeding on phenotypic traits.     

Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (N_ge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N_ge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.     

Genome‐wide analysis of homozygosity regions in european simmental bulls

The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH‐based coefficient of inbreeding (F_ROH) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) F_ROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome‐wide ROH‐traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.     

Variance of actual inbreeding derived from the number and variance of chromosome segment

The inbreeding coefficient (F) is used as a central parameter inferring a proportion of alleles identical by descent within an individual and by genetic variability within a population. The actual inbreeding coefficient varies around a central value, the inbreeding coefficient. C ockerham and W eir (1983) derived the method for computing the variance of inbreeding while reviewing several other methods. The variance of inbreeding in their report was considered to be of two components: one within population and the other between population of varied pedigrees. If pedigree is fixed, F is easily computed for an individual by the standard method (F alconer 1989). For domestic animals, pedigree information is usually available because it is requisite for a programme of genetic improvement. In this study, the variance of inbreeding coefficient was derived for an individual with a pedigree having a single path to a foundation animal.     

Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP‐derived metrics

Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi‐generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP‐derived metrics of homozygosity (r = 0.814–0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality‐checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.     

Population genetic structure of Santa Inês sheep in Brazil

This study aimed to describe the population genetic structure and evaluate the state of conservation of the genetic variability of Santa Inês sheep in Brazil. We used pedigree data of the Santa Inês breed available in electronic processing of the Brazilian Association of Sheep Breeders. A file with 20,206 records, which enabled the calculation of the genetic conservation index (GCI), individual inbreeding coefficient (F), change in inbreeding (ΔF), effective population size (Ne), effective number of founders (?_e), effective number of ancestors (?_ɑ), generation interval (L), average relatedness coefficient of each individual (AR), and Wright’s F-statistics (F _IT, F _IS, and F _ST). For pedigree analysis and calculation of population parameters, the program ENDOG was used. The average inbreeding coefficient (\( \overline{F} \)) was 0.97% and the mean average relatedness (\( \overline{\mathrm{AR}} \)) 0.49%. The effective numbers of founders and ancestors were, respectively, 199 and 161. The average values of F and AR increased significantly over the years. The effective population size fluctuated over the years concurrently to oscillations in inbreeding rates, wherein N _e reached just 68 in the year 2012. The mean average generation interval was 5.3 years. The Santa Inês breed in Brazil is under genetic drift process, with loss of genetic variation. It requires the implementation of a genetic management plan in the herd, for conservation and improvement of the breed.     

Implementation of genetic evaluation and mating designs for the endangered local pig breed ‘Bunte Bentheimer’

A pedigree including 1538 individuals of the endangered pig breed ‘Bunte Bentheimer’ and 3008 records of the fertility traits ‘number of piglets born alive’ (NBA) and ‘number of piglets weaned’ (NW) were used to i) characterize the population structure, ii) to estimate genetic (co)variance components and estimated breeding values (EBVs) and iii) to use EBVs for the application of the concept of optimal genetic contributions. The average coefficient of inbreeding increased from F = 0.103 to F = 0.121 within the two recent cohorts. Average rate of inbreeding amounted to 1.66%, which resulted in an effective population size of N_e = 30 animals in the recent cohort. Average generation interval was 3.07 years considering the whole pedigree, and in total, only 612 sows and boars generated offspring. Estimated heritabilities for both traits NBA and NW were 0.12, and the estimated genetic correlation between both traits was 0.96. The variance component due to the service sire was higher than in commercial pig breeds, presumably due to the widespread use of natural service boars. The EBVs for NBA from 333 selection candidates (63 boars and 270 sows) were used to determine optimal genetic contributions. Based on selected animals and their optimal genetic contributions, specific mating designs were evaluated to minimize inbreeding in the next generation. Best results were achieved when using a simulated annealing algorithm and allowing artificial insemination.     

Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed

The Catalonian donkey is one of the most endangered donkey breeds in the world. At present, five main subpopulations exist: AFRAC, which consists of many genetically connected Catalonian localities; Berga, which consists of a single herd located also in Catalunya but under private management; and three minor non‐Catalonian subpopulations (Huesca, Sevilla and Toledo). In this study, we analysed the pedigree information of the Catalonian donkey herdbook to assess the genetic diversity and population structure of the breed. We found that the Catalonian donkey has suffered an important loss of genetic diversity and moderate to high increases of inbreeding because of the abuse of a few individuals in matings. This scenario is mainly characterized by the fact that both the effective number of founders and ancestors for the whole population was 70.6 and 27, respectively, while the equivalent number of founders was 146.5 and the number of ancestors explaining overall genetic variability was 93. In addition, only 14% of animals born between the 1960s and 1970s were significantly represented in the pedigree. Our results also show that subpopulations where breeders exchanged reproductive individuals had low levels of inbreeding and average relatedness. One subpopulation, Berga, was reproductively isolated and showed high levels of inbreeding (F = 7.22%), with average relatedness (AR = 6.61%) playing an important role in increasing the values of these coefficients in the whole pedigree. Using genealogical F‐statistics we have found little evidence of population structuring (F_ST = 0.0083) with major genetic differences among non‐Catalonian subpopulations.     

500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data

The Carthusian horse is a Pura Raza Español (PRE) strain (CS), bred as a closed population since its creation more than 500 years ago. The aim of this study was to analyse for the first time its population structure and situation of variability combining both genealogical (GEL) and genomic (GEN) data. The GEL data comprised 348,429 pedigree records (56,105 CS horses), while the GEN analysis included the high-density genotypes (670,804 SNPs) of 287 horses. Pedigree completeness demonstrated its accuracy, showing a good correlation of GEL (F) and GEN (F_ROH) inbreeding coefficient in the case of PRE subpopulations partially related and non-related to Carthusian strain (0.68) but a lower value in the 100% Carthusian horses (0.42), due to the high weight of founders not detected by GEL analysis. GEN (PCA, AMOVA, and Admixture) and GEL analysis showed a good differentiation of subpopulations, but also a high level of introgression of the CS in the breed during past decades. A recent change in this trend was noteworthy, with a considerable reduction in CS variability and a genetic bottleneck (effective population sizes of 31.57 and 30.20 in GEL and GEN analysis, respectively, in last generation). The PRE has maintained its variability, and a considerable difference in estimated N_e by GEL (60.77) and GEN (188.0) data was observed. Using two sources of complementary information, it was found the existence of an ancient PRE strain with a unique genetic landmark, practically free from the influence of other equine populations.     

Population structure of Mazandaran native fowls using pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability of the Mazandaran native fowls in Iran by quantifying the pedigree completeness index, effective population size, genetic diversity, inbreeding level, and individual increase in inbreeding. The pedigree completeness analysis showed 3.31 full, 10.19 maximum, and 6.30 equivalent generations. The effective number of founders (f _e) was 131, representing 5% of the potential number of founders. The effective number of ancestors (f _a) was 81, and the genetic contribution of the 37 most influent ancestors explained 50% of the genetic variability in the population. The ratio f _e/f _a (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.62. The inbreeding coefficient increased over generations and the average was 1.93%. The average relatedness coefficient between individuals of the population was estimated to be 2.59%. The effective population size, based on the number of full generations, was 56. Family size analysis showed that fewer males than females were used, resulting in the observed levels of inbreeding. Average inbreeding coefficient in the Mazandaran native fowls can be regarded to be below critical levels. However, considering the relationship coefficients of individuals is recommended to aid maintaining genetic diversity of Mazandaran native fowls.     

Assessing effective population size,coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed

The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X‐linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, f_X = 0.46 and 0.22 and F_X = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non‐founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole‐genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis: ?0.20 born piglets per litter by a 10% of new inbreeding, and ?0.03 and ?0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in ?0.91 and ?0.17 piglets by a 10% of old and X‐linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals.     

Relationship between genealogical and microsatellite information characterizing losses of genetic variability: Empirical evidence from the rare Xalda sheep breed

Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (H_o) and expected (H_e) heterozygosity, individual coancestry coefficients (f and f_m), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (f_a), effective population size (N_e and N_e(m)) and founder genome equivalents (N_g and N_g(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (f_m, Mk and N_g(m)). However, H_o and H_e showed the highest values for C1 and the molecular heterozygote deficiency within population (F_IS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f_(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.     

Assessment of inbreeding depression for body measurements in Spanish Purebred (Andalusian) horses

Our aim was to ascertain inbreeding depression in the Spanish Purebred horses for eight body measurements. A total of 16,472 individuals were measured for height at withers, height at chest, leg length, body length, width of chest, heart girth circumference, knee perimeter and cannon bone circumference. Three different multivariate animal models including, respectively, no measure of inbreeding, individual inbreeding coefficients (F_i) or individual increase in inbreeding coefficients (ΔF_i) as linear covariates were used. Significant inbreeding depression was assessed. Even though the models including measures of inbreeding fitted better with data, no effect on estimates of genetic parameters was assessed. However, the inclusion of inbreeding measures affected the ranking order according to the Expected Breeding Values (EBV). Due to the better fit with data and nice properties (the adjustment of individual inbreeding coefficients with the pedigree depth and linear behaviour) the use of ΔF_i in the evaluation models can be recommended for morphological traits in horses.     

A genealogical survey of Australian registered dog breeds

Breeding practices were analysed for 32 registered dog breeds representing very small registries (120 Central Asian shepherd dogs) through to very large registries (252,521 German shepherd dogs) in Australia. The vast majority (91%) of registered kennels in Australia that were sampled did not regularly employ either close breeding or popular sire usage in their kennels and the weighted mean inbreeding coefficient of Australian pedigree dogs was <5%. Australian breed mean inbreeding coefficients ranged from 0% (Central Asian shepherd dog) to 10.1% (Bichon Frise). Breed effective population sizes ranged from 26 (Ibizan hound) to 1090 (Golden retriever), comparable with other species of domesticated animals. The relatively low levels of inbreeding suggest that pedigree dog disorders are unlikely to arise frequently from the use of popular sires or close breeding in Australian registered dog breeds. It is possible that deleterious allele fixation might be driven by founder effects, genetic drift or adverse selection practices, which were not assessed in this analysis. European popular sire definitions should be revisited for rare breeds.     

Rates of inbreeding and genetic diversity in Iranian Holstein Cattle

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1 048 572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non‐founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non‐founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co‐ancestry and inbreeding, which would lead to better handling of the effective population size.     

利用满二叉树遍历算法搜索个体奶牛的祖先谱系

在项目搭建的“奶牛精细养殖综合技术平台”上，将对动物个体祖先谱系的跟踪问题转化为满二叉树的数据结构后，选用前序遍历搜索算法，编写了追溯奶牛个体面向4代祖先的自定义“找祖先”函数，利用平台系统设定参数产生的模拟数据，实现了4代以内祖先的谱系跟踪，同时还提供雌性祖先的生产性能数据；以跟踪的谱系数据为基础，将“找祖先”函数和计算近交系数的原理相结合，实现了某个体与指定公牛（或母牛）交配后裔的近交系数监测，以控制近亲繁殖。研究还进一步指出，只要改变寻找祖先的起点，就能实现超过4代的祖先谱系分析。但是，个体谱系高世代（中亲或远亲）追踪必须以超越时空的、完整的奶牛繁殖档案数据库为基础，因此建议尽快建立我国奶牛繁殖科学数据库。     

The relationship between homozygosity and the occurrence of specific diseases in Bouvier Belge des Flandres dogs in the Netherlands

Summary

Since purebred dog populations represent closed gene pools, a relatively high level of consanguinity between individuals, and hence of inbreeding, is common. This case control study was conducted to establish the possible connection between the actual level of homozygosity due to inbreeding and specific diseases (flea allergy, osteochondrosis, laryngeal paralysis, neoplasm, autoimmune disease, hypoplastic trachea, and food allergy) occurring in the Bouvier Belge des Flandres breed.

One hundred and sixty‐eight animals referred to the Utrecht University Clinic formed the patient group. Each of the seven diseases was chosen because of the demonstrability of the diagnosis. Each animal was chosen because one of the selected diseases was established in that individual, and because its pedigree was complete. All dogs of the patient group were born between 1 January 1980 and 31 December 1985. A control group (n=123) was randomly chosen from the total population of registered Bouviers born in the Netherlands in the same period Pedigree data were obtained from the Dutch Kennel Club. The extent of inbreeding was determined for all animals using Wright's inbreeding coefficient. The distribution of inbreeding coefficients in each patient group was compared with the distribution in controls.

Inbreeding coefficients in the control group ranged from 0.0 to 0.406. Animals in which osteochondrosis, food allergy, autoimmune disease, neoplasm, or hypoplastic trachea was diagnosed had higher inbreeding coefficients than controls. It was concluded that in the Bouvier Belge des Flandres dog population examined, the level of homozygosity was positively correlated with occurrence of these diseases.