Inbreeding trends and pedigree analysis of Irish dairy and beef cattle populations

The objective of this study was to determine the inbreeding levels and to analyze the pedigree of Irish purebred populations of Charolais, Limousin, Hereford, Angus, and Simmental beef cattle, as well as the Holstein-Friesian dairy breed. Pedigree analyses included quantifying the depth of known pedigree, average generation intervals, effective population size, the effective number of founders, ancestors, and founder genomes, as well as identifying the most influential animals within the current population of each breed. The annual rate of increase in inbreeding over the past decade was 0.13% (P < 0.001) in the Hereford, 0.06% (P < 0.001) in the Simmental, and 0.10% (P < 0.001) in the Holstein-Friesian breeds. Inbreeding in the other breeds remained relatively constant over the past decade. Herefords had the greatest mean inbreeding in 2004, at 2.19%, whereas Charolais had the lowest, at 0.54%. Over half of each purebred population in 2004 was inbred to some degree; the population with the greatest proportion of animals inbred was the Hereford breed (85%). All 6 breeds displayed a generation interval of approximately 6 yr in recent years. In the pure-bred females born in 2004, the 3 most influential animals contributed between 11% (Limousin) and 24% (Hereford) of the genes. Effective population size was estimated for the Hereford, Simmental, and Holstein-Friesian only, and was 64, 127, and 75, respectively. The effective number of founders varied from 55 (Simmental) to 357 (Charolais), whereas the effective number of ancestors varied from 35 (Simmental and Hereford) to 82 (Limousin). Thus, despite the majority of animals being inbred, the inbreeding level across breeds is low but rising at a slow rate in the Hereford, Simmental, and Holstein-Friesian.     

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.     

Inbreeding in populations with incomplete pedigrees

Inbreeding has detrimental effects on a number of economically important traits. W iggans et al. (1995) estimated inbreeding depression of ?29 kg, ?1.08 kg and ?0.97 kg for each 1% increase of inbreeding for the traits milk, fat and protein yield, respectively, across several dairy cattle breeds. For post-weaning gain in Hereford cattle, the depression was ?0.24 kg (G engler et al. 1998). For the number of piglets born alive, 21-day litter weight, and days to 104.5 kg, it was ?0.023, ?0.052 and 0.21, respectively (C ulbertson et al. 1998). Inbreeding also adversely impacts reproductive traits, such as delayed puberty, reduced conception rates, higher likelihood of losing established pregnancies, increased mortality of calves and lowered bull fertility (Y oung et al. 1969). National genetic evaluations involve animals with incomplete pedigrees. Regular inbreeding algorithms (RA) based on the definition of W right (1922), such as those by Q uaas (1976), calculate the inbreeding of animals with at least one parent missing as zero. Even if an animal has both parents known, its inbreeding will be underestimated if some of its ancestors are unidentified. If the proportion of missing parents is large, the inbreeding trend in a population could be seriously underestimated. Subsequently, losses from inbreeding would be underestimated, and steps to slow the increase of inbreeding, such as using sires that are less related to the general population or mating less-related animals (T oro and P erez -E nciso , 1990; G rundy et al. 1994; M euwissen and S onneson 1998; V an R aden and S mith 1999), may be delayed. In particular, use of a mating system can result in matings adjusted for both inbreeding and dominance (M isztal et al. 1999). In populations that use AI substantially, unidentified parents may not differ genetically from identified parents, on average. Therefore the real average inbreeding in animals with unidentified parent(s) may be similar to their contemporaries with both parents known. V an R aden (1992) proposed an algorithm (VRA), where the inbreeding of animals whose parent(s) are unknown is equal to the mean inbreeding of their contemporaries with known parents. Contemporaries are stratified along unknown parent groups (UPG). VRA has been applied to a few US dairy breeds (V an R aden 1992; W iggans et al. 1995). The calculated inbreeding for the youngest Holstein animals was 3.7% with RA and increased to 4.2% with VRA (V an R aden 1992). The increase was small because the number of unidentified animals was small. However, the performance of VRA in recovering inbreeding lost for a range of incomplete pedigrees has not been evaluated. The objectives of this study were (i) to determine average inbreeding coefficients when pedigrees are increasingly more incomplete; (ii) to assess the efficacy of VRA in recovering these inbreeding coefficients; and (iii) to determine the mean inbreeding using the two inbreeding algorithms in a large beef population.     

Indicators of genetic erosion in an endangered population: the Alentejana cattle breed in Portugal

A study was conducted to characterize genetic diversity in the Alentejana breed of cattle based on its demographic trends and to investigate the major factors affecting genetic erosion in this breed. Herdbook information collected between 1940 and 2004, including pedigree records on 100,562 animals in 155 herds, was used to estimate demographic parameters. The mean generation intervals were 6.0 +/- 2.4 yr and 6.8 +/- 3.2 yr for sires and dams of calves, respectively. Average inbreeding increased steadily over the period analyzed, with an annual rate of inbreeding of 0.33 +/- 0.004% (P < 0.01) and an effective population size of 23.3. In the reference population (28,531 calves born between 2000 and 2003) the average inbreeding was 8.35 +/- 9.02% and nearly 80% of the calves were inbred, whereas the average relationship among all animals was 0.026 +/- 0.040. Nevertheless, the mean relationship was 0.328 +/- 0.264 and 0.022 +/- 0.026 for animals born in the same and in different herds, respectively. The computed genetic contributions to the reference population resulted in estimates for the effective number of founders, ancestors, founding herds, and herds supplying sires of 121.6, 55.0, 17.1, and 26.9, respectively, the 2 most influential herds and ancestors contributing 24.2 and 15.1%, respectively, of the current genetic pool. Of the 671 founding sires, only 24 Y-chromosomes are currently represented, but 1 sire alone contributes nearly 60% of this representation, such that the effective number of Y-chromosomes is only 2.73. The observed inbreeding per herd was, on average, 0.053 +/- 0.071 lower than expected from the relationship among the generation of parents of calves in the reference population, indicating that producers have followed breeding strategies that have kept inbreeding at lower levels than anticipated with random selection and mating. When compared with other cattle breeds, Alentejana has some of the highest levels of mean inbreeding and annual rate of inbreeding, and an effective population size that is nearly half of the minimum recommended for maintenance of genetic variability. These critical indicators demonstrate the need to adopt strategies aimed at minimizing inbreeding to avoid further losses of genetic diversity.     

Pedigree analysis of four decades of Quarter Horse breeding

Pedigrees of randomly selected Quarter Horses born in each of the years 1946, 1956, 1966 and 1976 and of winning halter, cutting and race horses born in the same years were evaluated and compared. Average inbreeding and inter se relationship levels and relationships of influential ancestors to the sample were calculated for each sample. The amount of Thoroughbred influence and the average generation interval were also determined for each random sample. The levels of inbreeding found in the random samples were low, ranging from 1.3% in 1956 to 2.6% in 1966; however, these levels were higher than would be expected if mating were random. Show and race winners born in 1976 appeared to be less inbred than random horses of the breed. The estimated average inter se relationship within the random samples increased from 0% in 1946 to 3% in 1966, decreasing again to 0% in 1976. Horses in the elite samples appeared to be more closely related to each other than those in the random samples. Fifteen ancestors of horses in the random samples were identified as influential to the Quarter Horse breed. Many of these same ancestors were influential in the halter and cutting samples, but only one was influential in the race samples. The percentage of pedigree lines in the random samples that contained a Thoroughbred ancestor were as follows; 1946, 27.5%; 1956, 19.2%; 1966, 23.2% and 1976, 31.4%. The average generation interval fluctuated from approximately 8 yr to approximately 10 yr for the random samples.     

Pedigree analysis of the Hungarian Thoroughbred population

The aim of the study was to analyse the pedigree information of Thoroughbred horses which were participating in gallop races between 1998 and 2010 in Hungary. Among the 3043 individuals of the reference population there were imported animals from foreign countries (e.g. Germany, England or Ireland) and horses that were born in Hungary. The number of complete generations was 15.64 (varied between 0 for the founders and 25.20), the mean number of full generations was 6.69, and the mean maximum generations were 28.96. The number of founders was 1062, and the effective number of founders was 42. Two hundred and thirty-two founders were born before 1793 (when the stud book of the Thoroughbred breed was closed), therefore these founders are considered as true founders of the breed. These 232 founders were responsible for 88.58% of the gene pool in the reference genome. The significant difference between the number of founders and effective number of founders indicate that the genetic diversity decreased greatly from the founders to the reference population. The number of ancestors was 908 and only 6 of them were responsible for 50% of the genetic diversity in the examined population. The effective number of ancestors was 15.32. From the ratio of the effective number of founders and effective number of ancestors we concluded to a bottleneck effect that characterizes the pedigree under study. Generation interval was more than a year longer for stallions (12.17) than it was for mares (10.64). More than 94% of the individuals in the pedigree were inbred, and the average inbreeding of the population was 9.58%. Considering the changes of the inbreeding status of the examined population 4 large time periods were appointed. The first lasted until 1780, the second period was from 1780 until 1952, the third period was between 1946 and 1998 and the last one was from 1998 until 2008. Rate of inbreeding in the last generation was 0.3%, which forecasts further increase in inbreeding. The effective population size was above 100 in the last 30 generations, proving the genetic diversity did not decrease by a level that would make long-term selection impossible.     

Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information

The study investigates the genetic diversity present as well as its development in the Brown Cattle population of Switzerland from pedigree information. The population consisted of three subpopulations, the Braunvieh (BV), the original Braunvieh (OB) and the US‐Brown Swiss (BS). The BV is a cross of OB with BS where crossing still continues. The OB is without any genetic influence of BS. The diversity measures effective population size, effective number of ancestors (explaining 99% of reference genome) and founder genome equivalents were calculated for 11 reference populations of animals born in a single year from 1992 onwards. The BS‐subpopulation consisted of animals and their known ancestors which were used in the crossing scheme and was, therefore, quite small. The youngest animals were born in 2002, the oldest ones in the 1920s. Average inbreeding was by far the highest in BS, in spite of the lowest quality of pedigrees, and lowest in OB. Effective population size obtained from the difference between average inbreeding of offspring and their parents was, mostly due to the heavy use of few highly inbred BS‐sires, strongly overestimated in some BV‐reference populations. If this parameter was calculated from the yearly rate of inbreeding and a generation interval of 5 years, no bias was observed and ranking of populations from high to low was OB – BV – BS, i.e. equal to the other diversity parameters. The high genetic diversity found in OB was a consequence of the use of many natural service sires. Rate of decrease of effective number of ancestors was steeper in BV than OB was, however, equal for founder genome equivalents. Founder genome equivalents were more stable than effective population sizes calculated from the difference between average inbreeding of offspring and parents. The five most important ancestors contributed one‐third of the 2002‐reference genomes of BV and OB, in BV all were BS‐sires. The relative amount of BS‐genes in the BV‐genome increased from 59.2% to 78.5% during the 11 years considered.     

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.     

Inbreeding effects on postweaning production traits, conformation, and calving performance in Irish beef cattle

The objective of this study was to quantify the effect of inbreeding on carcass quality, growth rate, live conformation measures, and calving performance in purebred populations of Charolais, Limousin, Simmental, Hereford, and Angus beef cattle using data from Irish commercial and pedigree herds. Variables analyzed are reflective of commercial farming practices. Inbreeding was included in a linear mixed model as either a class variable or a linear continuous variable. Nonlinear effects were nonsignificant across all traits. Inbred animals had decreased carcass weight and less carcass fat. The effects of inbreeding were more pronounced in the British beef breeds. Effects for carcass weight ranged from -0.87 kg (Charolais) to -1.90 kg (Hereford) per 1% increase in inbreeding. Inbred Charolais and Hereford animals were younger at slaughter by 3 and 5 d, respectively, per percentage of increase in inbreeding, whereas the effect of inbreeding on age at slaughter differed significantly with animal sex in the Limousin and Angus breeds. Inbred Limousin and Angus heifers were younger at slaughter by 5 and 7 d, respectively, per percentage of increase in inbreeding. Continental animals were more affected by inbreeding for live muscling and skeletal conformational measurements than the British breeds; inbred animals were smaller and narrower with poorer developed muscle. Calf inbreeding significantly affected perinatal mortality in Charolais, Simmental, and Hereford animals. The effects were dependent upon dam parity and calf sex; however, where significant, the association was always unfavorable. Dam inbreeding significantly affected perinatal mortality in Limousin and Hereford animals. Effects differed by parity in Limousins. Inbred first-parity Angus dams had a greater incidence of dystocia. Although the effects of inbreeding were some-times significant, they were small and are unlikely to make a large financial effect on commercial beef production in Ireland.     

Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32?% of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50?% of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8?% for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64?%. The average relatedness coefficient between individuals of the population was estimated to be 2.05?%??the highest individual coefficient was 10.31?%. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help breeders and farmers adopt better precautionary measures against inbreeding depression and other deleterious genetic effects.     

Genetic diversity in and conservation strategy considerations for Navajo Churro sheep

The objectives of this study were to 1) evaluate the genetic diversity of Navajo-Churro sheep using pedigree information; 2) examine the distribution of the Navajo-Churro population; and 3) evaluate the effect of breeder dynamics on genetic conservation of the breed. Pedigree data and breeder information (city and state) were obtained from the Navajo-Churro Sheep Breed Association. Inbreeding coefficients were calculated for each individual animal using pedigree information. A geographic information system program was used to divide the United States into four regions and overlay breeder locations, flock size, and flock inbreeding level. The small correlation between level of inbreeding and flock size (r = -0.07, P = 0.07) indicated that inbreeding levels are not different across flock sizes. The mean flock inbreeding levels ranged from 0 to 11% across regions. The level of inbreeding did not differ among regions (P = 0.15), except for Region 4 (Kansas and Missouri; P = 0.001). The number of breeders registering sheep averaged 34 per year. Most of the breeders were transient, with only eight breeders maintaining ownership for more than 7 yr. Average inbreeding level for 2000 was found to be 1.2%, with a linear increase in inbreeding of 0.1%/yr over the period studied, suggesting a minimal loss of genetic diversity for the Navajo-Churro. However, given the relatively small effective population size (92) and the transient nature of the breeders, development of an ex situ cryo-preserved germplasm bank may be the best long-term strategy for maintaining this breed's genetic diversity.     

Growth patterns of Angus, Hereford and shorthorn cattle. II. Relationship of growth patterns of dams with progeny performance

Relationships between estimated growth curve parameters of dams and performance traits of their progeny were studied in Angus, Hereford and Shorthorn herds, each divided into four inbred and two noninbred lines. Growth curve parameters were calculated from the growth function Yt=A(1-Be-Kt), where Yt was weight at age t, A was estimated mature weight, B was an estimate related to early life weight changes and provided for a Y-intercept term and K was estimated general rate of maturing. Least-squares analyses of progeny variables were calculated separately for each breed and sex. Line differences did not influence any of the progeny variables except weaning type score of Shorthorn males (P less than .01). Birth year exerted a curvilinear effect on birth weights of Angus female progeny (P less than .01), a linear influence on 205-d weights of Shorthorn male progeny (P less than .05) and a curvilinear effect on weaning type scores of Angus and Shorthorn male progeny (P less than .01). Regression coefficients on weaning age indicated that calves born earlier in the calving season had lighter birth weights and that older calves at weaning received higher type scores. Inbreeding of the progeny negatively influenced (P less than .05) birth weights of Angus male and Hereford female progeny. Hereford male and Shorthorn female 205-d weights were negatively affected (P less than .05) by inbreeding, while weaning type scores of Shorthorn female progeny were negatively influenced (P less than .001) by inbreeding. Regression coefficients of all progeny variables on inbreeding in all analyses indicated negative trends.(ABSTRACT TRUNCATED AT 250 WORDS)     

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

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.     

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.     

Gene Dropping Analysis of Ancestral Contributions and Allele Survival in Japanese Thoroughbred Population

Genetic contributions of nine historically important ancestors and allelic diversity in the Japanese Thoroughbred population were examined by applying the gene dropping simulation to the foals produced from 1978 to 2005. Full pedigree records traced to ancestors (base animals) born around 1890 were used for the simulation. Alleles originated from some of the historically important ancestors were found to be at risk of future extinction, although their genetic contributions to the foal population have increased during the last three decades. The proportion of surviving alleles to the total alleles assigned to the base animals was 8.0% in the foal population in 2005, suggesting that a large part of genetic variability contained in the base animals is extinct in the current population.     

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.     

The effect of inbreeding on the manifestations of some physiological traits in the Kladrub Black Horse strain

Inbreeding was used in the regeneration process in the breeding of the Kladrub Black Horse. Inbreeding rate is realized in practice, as related to the manifestation of the selected characteristics of this unique horse population. The evaluation of the effect of inbreeding on conception rate and fertility did not demonstrate any differences between the group of inbred mares and non-inbred mares. The study was conducted in mares used for breeding for 10 years. The results provide evidence that inbreeding causes no depression in this characteristics in the Kladrub Black Horse which would otherwise be the first physiological function in the reproduction process to be altered as a result of inbreeding. The evaluation of the effect of inbreeding on growth rate by comparing it with the standard growth curves which were characterized by the exponential function y = A (1 -- e-k(t-to)) did not indicate any statistically significant differences in growth dynamics between foals with a zero Fx value and inbred foals. This study was based on the evaluation of growth rate in the basic body traits and weight. It is inferred that inbreeding does not reduce growth dynamics of different body measurements and weight. Similarly, the evaluation of the body dimensions and weight of inbred and non-inbred adults showed no significant differences. Similar results were obtained from the evaluation of the relation between inbreeding and body constitution, character, and temperament. All the correlation coefficients are very low, almost equal to zero.     

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.     

Analysis of pedigree and conformation data to explain genetic variability of the horse breed Franches-Montagnes

Franches‐Montagnes is the only native horse breed in Switzerland, therefore special efforts should be made for ensuring its survival. The objectives of this study were to characterize the structure of this population as well as genetic variability with pedigree data, conformation traits and molecular markers. Studies were focused to clarify if this population is composed of a heavy‐ and a light‐type subpopulation. Extended pedigree records of 3‐year‐old stallions (n = 68) and mares (n = 108) were available. Evaluations of body conformation traits as well as pedigree data and molecular markers did not support the two‐subpopulation hypothesis. The generation interval ranged from 7.8 to 9.3 years. The complete generation equivalent was high (>12). The number of effective ancestors varied between 18.9 and 20.1, whereof 50% of the genetic variability was attributed to seven of them. Genetic contribution of Warmblood horses ranged from 36% to 42% and that of Coldblood horses from 4% to 6%. The average inbreeding coefficient reached 6%. Inbreeding effective population size was 114.5 when the average increase of the inbreeding coefficient per year since 1910 was taken. Our results suggest that bottleneck situations occurred because of selection of a small number of sire lines. Promotion of planned matings between parents that are less related is recommended in order to avoid a reduction of the genetic diversity.     

Inbreeding and effective population size of Japanese Black cattle

The objective of this research was to estimate the amount of inbreeding and effective population size of the Japanese Black breed using pedigree records from bulls and heifers registered between 1985 and 1997. Inbreeding was quantified by three F-statistics: actual inbreeding, inbreeding expected under random mating, and inbreeding due to population subdivision. During the period of 1985 to 1997, the inbreeding expected under random mating increased from 2.3% to 5.0%, whereas the increase of actual inbreeding was more gradual (from 4.7% to 5.4%). The inbreeding due to population subdivision decreased almost linearly and reached 0.5% in 1997, indicating that genetic subdivision of the Japanese Black cattle population has essentially disappeared. The effective size of the breed was estimated from the increasing rate of inbreeding expected under random mating. In the earlier half of this period (1986 to 1990), the breed maintained an effective size of approximately 30. However, after 1991 the effective size sharply decreased and the harmonic mean between 1993 and 1997 was only 17.2. The main cause of this reduction of the effective size was considered to be the intensive use of a few prominent sires. To increase the effective size, an upper limit in the use of AI semen per sire should be imposed.