Mean Inbreeding Coefficient Research Articles

An evaluation of potential inbreeding depression in wild Mexican wolves

AbstractEstimates of the influence of inbreeding on the fitness of wild animals can guide genetic conservation in rare species. Conservation genetics is important in Mexican wolves (Canis lupus baileyi) because the current population descended from 7 founders and mean inbreeding is relatively high. As an endangered subspecies, Mexican wolves are actively managed using select conflict avoidance measures and by placing captive‐born foster pups into wild litters. We obtained data on inbreeding coefficients of wolf pups and adults based on a pedigree dating to 1957 and data on reproduction for wild wolf packs during 1998–2022. We estimated trends in inbreeding coefficients and the associations between dam, sire, and pup inbreeding coefficients and pup recruitment to age 9 months, and assessed 3 components of recruitment: probability of producing a litter, number of pups produced, and recruitment conditional on successful reproduction. We generated estimates using generalized linear mixed models and bootstrapped estimates of confidence intervals. Mean inbreeding coefficients were high (0.227, SD = 0.047) in the wild population, but we detected no significant evidence of an increase during 2010–2022. Overall, the net associations of dam, sire, and pup inbreeding coefficients with our primary fitness metric, pup recruitment to age 9 months, did not differ from zero. While high inbreeding coefficients are a concern for the long‐term recovery of the subspecies, the stable level of inbreeding, lack of evidence for inbreeding depression, high pup production (5.1 pups/litter, SD = 1.64), and rapid population growth (384% increase from 2010–2022) indicate that inbreeding has not prevented rapid progress towards recovery goals under current management practices.

Pedigree analysis of Korean native chickens: unraveling inbreeding and genetic diversity

This study assessed the trends in inbreeding, effective population size, and genetic diversity across six Korean native chicken lines using pedigree records from 54,383 chickens. Understanding these genetic parameters is significantly important for maintaining healthy and viable chicken populations. The primary objective was to analyze the pedigree data to assess the levels of inbreeding and genetic diversity and to evaluate the effective population size across the different lines. Pedigree analysis revealed that pedigree completeness peaked in the first generation and declined in subsequent generations for all lines. Line A exhibited a mean inbreeding coefficient of 0.0201, whereas the other lines displayed lower mean values ranging from 0.0009 to 0.0098, indicating that inbreeding levels were within an acceptable range and considered safe from extinction. Average relatedness consistently increased with time. Individual increases in inbreeding were the highest in Line A (0.62%), with smaller increases in the other lines ranging from 0.02 to 0.23%. Effective population sizes varied from 81 to 2500, with average coancestry within parental populations ranging from 0.0032 to 0.0290. The fe/fa ratio between 1.00 and 1.69 in the 6 lines suggested a moderate impact during bottleneck events, with subsequent populations recovering well. The genetic diversity loss due to genetic drift and unequal founder contributions ranged from 0.66-3.15%, indicating that considerable genetic variability remains within the populations. The results of this study have practical applications in the management and conservation of genetic resources in poultry breeding programs. By highlighting the importance of monitoring inbreeding and maintaining genetic diversity, the findings can help develop strategies to ensure the long-term sustainability of these chicken lines. This study provides valuable insights into the genetic management of Korean native chicken lines, emphasizing the need for strategic breeding practices to preserve genetic health and diversity.

Evaluation of Inbreeding in the Slovak Simmental Breed and Its Effect on Length of Productive Life.

This study aimed to estimate the average inbreeding coefficient in Slovak Simmental dairy cattle and evaluate the effect of inbreeding on the length of productive life. All pedigrees included 463,282 animals dating back to 1914. The inbreeding coefficients for each animal in the pedigree were computed using the software CFC 1.0. Length of productive life (LPL) was defined as the time (days) from the first calving to culling, death, or censoring. The influence of inbreeding on the length of productive life was calculated and tested using the Weibull proportional hazards model. The average inbreeding coefficient, the average number of discrete generation equivalents, and the average longest ancestral path for inbred animals were 0.01, 6.59, and 13.08, respectively. While the largest decrease in the mean coefficient of inbreeding was observed from the year of birth 1995 (F = 1.50%) to 2001 (F = 0.59%), an increasing trend of inbreeding in the population was found from 2003 onwards. A weak but significant effect of inbreeding on the length of productive life of Simmental cows was confirmed using survival analysis.

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology.

The Hetian Qing donkey is an excellent local donkey breed in Xinjiang. It is of great significance to accelerate breeding and the speed of breeding and rejuvenation, as well as to understand the genetic basis of the strategies and population. This study collected a total of 4 male donkeys and 28 female donkeys. It then obtained genotype data through Simplified Genomic Sequencing (GBS) technology for data analysis. The results detected a total of 55,399 SNP loci, and the genotype detection rate of individuals was ≥90%. A total of 45,557 SNP loci were identified through quality control, of which 95.5% were polymorphic. The average minimum allele frequency was 0.250. The average observed heterozygosity was 0.347. The average expected heterozygosity was 0.340. The average IBS (state homologous) genetic distance was 0.268. ROH: 49 (homozygous fragments), with 73.47% of the length between 1 and 5 Mb. The average per-strip ROH length was 1.75 Mb. The mean inbreeding coefficient was 0.003. The 32 Hetian green donkeys could be divided into six families. The number of individuals in each family is significant. To sum up, the Hetian Qing donkey population has low heterozygosity, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the subsequent process of seed protection, seed selection should be conducted according to the divided pedigree to ensure the long-term protection of the genetic resources of Hetian green donkeys.

The genetic status and rescue measure for a geographically isolated population of Amur tigers

The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population’s genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.

Impact of inbreeding on production, fertility, and health traits in German Holstein dairy cattle utilizing various inbreeding estimators

In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the impact of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (Fped) together with 6 genomic-based methods, including 3 GCTA estimators (Fhat1, Fhat2, Fhat3), VanRaden's first method (FVR1, with observed allele frequencies and FVR0.5 when allele frequencies are set to 0.5), and one based on runs of homozygosity (Froh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from -0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (Fhat1) to 40.62 kg (Fhat3), 1.18 kg (Fhat2) to 1.70 kg (Fhat3), 0.90 kg (Fhat2) to 1.45 kg (Froh and Fhat3), 0.19 (Fped) to 0.34 d (Fhat3) for 305 d milk yield, fat, protein, and calving interval respectively. The health traits showed slight changes when inbreeding was gradually increased by 5% with digital dermatitis showing rather a contrasting trend to that of mastitis which reduced the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.

Genetic Variability of Tabebuia rosea (Bignoniaceae) from Plantations and Remnant Populations in the Mayan Forest

In Neotropical regions, plantations and remnant forest populations of native trees coexist in a highly fragmented matrix and may be affected by isolation and reduction in population size, leading to genetic structure, inbreeding, and genetic bottlenecks that reduce the population’s genetic diversity. Tabebuia rosea variability in the Mayan Forest was studied by genotyping 30 trees from three plantations and three remnant natural populations using simple sequence repeats (SSRs) and inter-simple sequence repeats (ISSRs). Ho-SSR estimates were lower than He; the mean inbreeding coefficient was 0.07 and did not differ among populations, but was eight times higher in plantations than in remnant populations. Using ISSR data, the individuals were assigned to k = 5 and k = 4 clusters under admixture without and with geographic information used as priors in Bayesian analysis assignments. Genetic differentiation estimated with the Bayesian estimator II (0.0275 ± 0.0052) was significantly different from 0, but FST was not (0.0985 ± 0.1826), while paired FST among populations ranged from 0.05 up to 0.16. Only one remnant population displayed evidence of a genetic bottleneck. T. rosea displays a genetic structure in which the isolated remnant forest populations show moderate inbreeding levels.

Pedigree-based analysis of genetic variability in the Chinese Crested dog population in Poland

The aim of the study was to analyse the level of genetic diversity within the small-sized population of Chinese Crested dogs bred in Poland, considering the common occurrence of hereditary diseases, probably related to the high level of inbreeding. The pedigree data provided by Polish Kennel Club were used to estimate different genealogical parameters in the ancestral (n=1,860) and active population (n=1,313). The mean equivalent number of complete generations known per animal reached 5.97 and 6.75 generations in the ancestral and active populations, respectively. The mean inbreeding coefficient values were 0.083 and 0.049 in the ancestral and in the active population, respectively. The effective number of founders (fe) and ancestors (fa) and the ratio fa/fe were 38, 20, 0.54 and 79, 34, 0.43 in the ancestral and active population, respectively. It should be concluded that the genetic variability of the Chinese Crested dogs in Poland is currently at a satisfactory level. However, high proportion of related male-female pairs may cause future mating problems. The population should be monitored for inbreeding and genetic variation. The breeders should choose reproducers in such a way as not to create large groups of paternal half-siblings in the offspring.

Identification of homozygosity-rich regions in the Holstein genome.

In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1-2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data.

Scavenging patterns of an inbred wolf population in a landscape with a pulse of human‐provided carrion

AbstractScavenging is an important part of food acquisition for many carnivore species that switch between scavenging and predation. In landscapes with anthropogenic impact, humans provide food that scavenging species can utilize. We quantified the magnitude of killing versus scavenging by gray wolves (Canis lupus) in Scandinavia where humans impact the ecosystem through hunter harvest, land use practices, and infrastructure. We investigated the cause of death of different animals utilized by wolves, and examined how the proportion of their consumption time spent scavenging was influenced by season, wolf social affiliation, level of inbreeding, density of moose (Alces alces) as their main prey, density of brown bear (Ursus arctos) as an intraguild competitor, and human density. We used data from 39 GPS‐collared wolves covering 3198 study days (2001–2019), including 14,205 feeding locations within space–time clusters, and 1362 carcasses utilized by wolves. Most carcasses were wolf‐killed (80.5%) while a small part had died from other natural causes (1.9%). The remaining had either anthropogenic mortality causes (4.7%), or the cause of death was unknown (12.9%). Time spent scavenging was higher during winter than during summer and autumn. Solitary wolves spent more time scavenging than pack‐living individuals, likely because individual hunting success is lower than pack success. Scavenging time increased with the mean inbreeding coefficient of the adult wolves, possibly indicating that more inbred individuals resort to scavenging, which requires less body strength. There was weak evidence for competition between wolves and brown bears as well as a positive relationship between human density and time spent scavenging. This study shows how both intrinsic and extrinsic factors drive wolf scavenging behavior, and that despite a high level of inbreeding and access to carrion of anthropogenic origin, wolves mainly utilized their own kills.

Increased genetic diversity and immigration after West Nile virus emergence in American crows: No evidence for a genetic bottleneck.

Infectious diseases can cause steep declines in wildlife populations, leading to changes in genetic diversity that may affect the susceptibility of individuals to infection and the overall resilience of populations to pathogen outbreaks. Here, we examine evidence for a genetic bottleneck in a population of American crows (Corvus brachyrhynchos) before and after the emergence of West Nile virus (WNV). More than 50% of marked birds in this population were lost over the 2-year period of the epizootic, representing a 10-fold increase in adult mortality. Using analyses of single-nucleotide polymorphisms (SNPs) and microsatellite markers, we tested for evidence of a genetic bottleneck and compared levels of inbreeding and immigration in the pre- and post-WNV populations. Counter to expectations, genetic diversity (allelic diversity and the number of new alleles) increased after WNV emergence. This was likely due to increases in immigration, as the estimated membership coefficients were lower in the post-WNV population. Simultaneously, however, the frequency of inbreeding appeared to increase: Mean inbreeding coefficients were higher among SNP markers, and heterozygosity-heterozygosity correlations were stronger among microsatellite markers, in the post-WNV population. These results indicate that loss of genetic diversity at the population level is not an inevitable consequence of a population decline, particularly in the presence of gene flow. The changes observed in post-WNV crows could have very different implications for their response to future pathogen risks, potentially making the population as a whole more resilient to a changing pathogen community, while increasing the frequency of inbred individuals with elevated susceptibility to disease.

Inbreeding depression and durability in the North American Thoroughbred horse.

The proportion of the genome containing runs of homozygosity (ROH) affects production traits in livestock populations. In European and Australasian Thoroughbreds inbreeding, quantified using ROH (FROH ), is associated with the probability of ever racing. Here, we measured FROH using 333 K SNP genotypes from 768 Thoroughbred horses born in North America to evaluate the effect of inbreeding on racing traits in that region. Among North American horses, FROH was not associated (p=0.518) with the probability of ever racing but was significantly associated with the number of race starts (p=0.002). Among raced horses, those with a 10% higher FROH than the mean inbreeding coefficient were predicted to have 3.5 fewer race starts compared to horses with a mean inbreeding coefficient. Considering the trend of increasing inbreeding and a decline in the average number of race starts per runner in North America, mitigating inbreeding in the population could positively influence racing durability.

Genetic Diversity and Trends of Ancestral and New Inbreeding in German Sheep Breeds by Pedigree Data.

In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of rams may risk losing genetic diversity and increasing rates of inbreeding. On the other hand, breeds with a low number of founder animals and only regional popularity may not leave their endangered status, as the number of breeders interested in the breed is limited. The objective of the present study was to determine demographic measures of genetic diversity and recent as well as ancestral trends of inbreeding in all autochthonous German sheep breeds and sheep of all breeding directions, including wool, meat, and milk. We used pedigree data from 1,435,562 sheep of 35 different breeds and a reference population of 981,093 sheep, born from 2010 to 2020. The mean number of equivalent generations, founders, effective founders, effective ancestors, and effective founder genomes were 5.77, 1669, 123.2, 63.5, and 33.0, respectively. Genetic drift accounted for 69% of the loss of genetic diversity, while loss due to unequal founder contributions was 31%. The mean inbreeding coefficient, individual rate of inbreeding (∆Fi), and realized effective population size across breeds were 0.031, 0.0074, and 91.4, respectively, with a significantly decreasing trend in ∆Fi in 11/35 breeds. New inbreeding, according to Kalinowski, contributed to 71.8% of individual inbreeding, but ancestral inbreeding coefficients showed an increasing trend in all breeds. In conclusion, in our study, all but one of the mountain-stone sheep breeds and the country sheep breed Wald were the most vulnerable populations, with Ne < 50. The next most endangered breeds are exotic, country, and heath breeds, with average Ne of 66, 83, and 89, respectively. The wool, meat, and milk breeds showed the highest genetic diversity, with average Ne of 158, 120, and 111, respectively. The results of our study should help strengthen conservation program efforts for the most endangered sheep breeds and maintain a high genetic diversity in all sheep breeds.

Changes in genomic inbreeding and diversity over half a century in Swedish Red and Swedish Holstein dairy cattle.

Swedish Red (SR) and Swedish Holstein (SH) are the dominating commercial dairy cattle breeds in Sweden. Both breeds have undergone substantial changes during the last half century due to intensive selection for breeding goal traits, but also resulting from increased international exchange of breeding animals and genetic drift. The aim of this study was to learn more about changes in genomic diversity and inbreeding in these two breeds over time. Therefore, semen samples from old bulls were genotyped using the 150K Genomic Profiler SNP array and combined with 50K SNP array genotype data, obtained for more recent bulls from the Nordic Cattle Genetic Evaluation. Different measures of level of homozygosity, genomic inbreeding, relatedness and changes in allele frequency were estimated for bulls born during different time periods from the 1950s until 2020. In total, more than 33,000 SNPs for 9737 SR and 5041 SH bulls were included in the analysis using PLINK v1.9. The results showed higher average homozygosity for SR than for SH bulls up to around 2000, but the difference was very small after that. The average inbreeding coefficients based on deviation from expected homozygosity as well as on runs of homozygosity decreased until the early 1980s in both breeds, whereafter they started to increase again for SH, but stayed more stable for SR. From the 1990s onwards, SH displayed higher average inbreeding coefficients than SR. In the last studied birth year group (2015-2020), the mean inbreeding coefficient based on runs of homozygosity was 5.9% for SH and 3.7% for SR. A principal component analysis showed a pattern of genetic relationships related to the birth year period of the bulls, illustrating the gradual change of the genetic material within each breed. The change in allele frequency over time was generally larger for SH than for SR. The results show that the inbreeding level was higher half a century ago than at present, and the inbreeding levels were lower than in some other studied populations. Still, the increase seen for inbreeding coefficients and homozygosity, especially in SH during recent years, should be considered in future breeding strategies.

Inbreeding and pedigree analysis of the European red dairy cattle

BackgroundRed dairy cattle breeds have an important role in the European dairy sector because of their functional characteristics and good health. Extensive pedigree information is available for these breeds and provides a unique opportunity to examine their population structure, such as effective population size, depth of the pedigree, and effective number of founders and ancestors, and inbreeding levels. Animals with the highest genetic contributions were identified. Pedigree data included 9,073,403 animals that were born between 1900 and 2019 from Denmark, Finland, Germany, Latvia, Lithuania, the Netherlands, Norway, Poland, and Sweden, and covered 32 breeds. The numerically largest breeds were Red Dairy Cattle and Meuse-Rhine-Yssel.ResultsThe deepest average complete generation equivalent (9.39) was found for Red Dairy Cattle in 2017. Mean pedigree completeness ranged from 0.6 for Finncattle to 7.51 for Red Dairy Cattle. An effective population size of 166 animals was estimated for the total pedigree and ranged from 35 (Rotes Höhenvieh) to 226 (Red Dairy Cattle). Average generation intervals were between 5 and 7 years. The mean inbreeding coefficient for animals born between 1960 and 2018 was 1.5%, with the highest inbreeding coefficients observed for Traditional Angler (4.2%) and Rotes Höhenvieh (4.1%). The most influential animal was a Dutch Meuse-Rhine-Yssel bull born in 1960. The mean inbreeding level for animals born between 2016 and 2018 was 2% and highest for the Meuse-Rhine-Yssel (4.64%) and Rotes Hohenvieh breeds (3.80%).ConclusionsWe provide the first detailed analysis of the genetic diversity and inbreeding levels of the European red dairy cattle breeds. Rotes Höhenvieh and Traditional Angler have high inbreeding levels and are either close to or below the minimal recommended effective population size, thus it is necessary to implement tools to monitor the selection process in order to control inbreeding in these breeds. Red Dairy Cattle, Vorderwälder, Swedish Polled and Hinterwälder hold more genetic diversity. Regarding the Meuse-Rhine-Yssel breed, given its decreased population size, increased inbreeding and low effective population size, we recommend implementation of a breeding program to prevent further loss in its genetic diversity.

Consanguinity in the Chaouia population (Morocco): prevalence, trends, determinants, fertility, and spontaneous abortions

BackgroundOne of the aspects that helps to understand the genetic structure of a population throughout its biological history is the description of its matrimonial practices. Thus, the objective of this study is to explore consanguinity, one of these practices, to its full extent by identifying the prevalence, determinants, and trends of a consanguineous marriage, as well as its impact on fertility and spontaneous abortions in the Chaouia population, a region located in the western center of Morocco. Therefore, a survey-based cross-sectional study was conducted between January 2019 and January 2020. The sample was collected by province using a stratified random sampling approach, yielding a sample of 788 people. The association between consanguinity and socioeconomic and demographic characteristics, as well as reproductive health and pregnancy outcomes, was described using chi-square and ANOVA analysis. Multivariate logistic regression analysis was used to determine the predictors of a consanguineous marriage.ResultsOur findings revealed a consanguinity rate of 25.38%. The mean inbreeding coefficient was 0.012214. The most common type of union was between first cousins. This practice was strongly associated with an early age at marriage for both genders and with endogamy and immobility of couples, according to their place of birth. Consanguinity was significantly associated with fertility (p < 0.001) and spontaneous abortions (p = 0.029). The average number of pregnancies and spontaneous abortions was higher in consanguineous unions (5.18 ± 0.20/0.47 ± 0.08) compared to non-consanguineous unions (4.33 ± 0.10/0.31 ± 0.03).ConclusionsConsanguinity is a deeply rooted social and cultural tradition in this population, providing individuals with a sense of social-economic stability while assuring their attachment to the group. Despite being highly associated with fertility, this practice has a significant influence on pregnancy outcomes, namely spontaneous abortions. Therefore, further studies are needed to examine the impact of consanguinity on various aspects of reproductive health and its association with numerous genetic abnormalities and diseases.

Effects of Selection on Breed Contribution in the Caballo de Deporte Español.

The equine breeding industry for sport's performance has evolved into a fairly profitable economic activity. In particular, the Caballo de Deporte Español (CDE) is bred for different disciplines with a special focus on Show Jumping. The main aim of this study was to determine the effects of 15 years of selection and to find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole pedigree of 19,045 horses registered as CDE was used, comprising 47,884 animals (18,799 males and 29,085 females). An analysis performed to check for the pedigree completeness level yielded a number of equivalent complete generations (t) equal to 1.95, an average generation interval (GI) of 10.87 years, mean inbreeding coefficient (F) of 0.32%, an average relatedness coefficient (AR) of 0.09% and an effective population size (Ne) of 204. For the analyses, animals were divided into fourteen breed groups. Additionally, in order to study the evolution of these breeds over time and their influence on CDE pedigree, five different periods were considered according to the year of birth of the animals. Performance data used in the analyses were the estimated breeding values (EBV) of the Show Jumping sport discipline of 12,197 horses in the CDE pedigree, available from the 2020 routine genetic evaluations of the CDE breeding program (starting in 2004). Dressage and Eventing EBV values were also assessed. Results showed values of F higher than expected under random mating; this pointed to some degree of inbred matings. With regard to the evolution of breeding values, we found that, in general, EBVs of offspring were higher than the EBVs of parents. Notwithstanding, there is still a need for improvement in population management and the coordination of the breeders to get higher responses but controlling the loss of genetic diversity in the CDE breed.

Genetic and non-genetic parameter estimates for growth traits and Kleiber ratios in Dorper × indigenous sheep

Genetic improvement programme will only be successful when accompanied by a good understanding of the influence of different environmental factors, knowledge of the genetic parameters and the genetic relationships between the traits of interest. This study aimed to evaluate the influence of non-genetic factors on growth traits and Kleiber ratios and to estimate genetic parameters for early growth traits in Dorper × indigenous crossbred sheep. The effects of fixed factors were analysed by the general linear model procedure of statistical analysis system, while the genetic parameters were estimated using a WOMBAT computer program fitted animal model. The overall least-square mean for birth weight (BRW), weaning weight (3MW), six-month weight, nine-month weight, and yearling weight were 3.03 ± 0.02, 14.5 ± 0.18, 20.4 ± 0.26, 24.8 ± 0.31, and 28.3 ± 0.40 kg, respectively. The overall least-square mean for Kleiber ratio from birth to weaning (KR1), weaning to six months, six to nine months and nine months to yearling age were 16.8 ± 0.10, 6.41 ± 0.17, 4.55 ± 0.21 and 3.38 ± 0.20 g/kg of metabolic weight, respectively. The inclusion of maternal genetic effect had a significant influence on BRW, and it explains 20% of the phenotypic variation. The total heritability estimates for BRW, 3MW, birth to weaning average daily weight gain and KR1 were 0.10, 0.14, 0.16 and 0.12, respectively. The phenotypic correlation varied from −0.11 ± 0.05 to 0.98 ± 0.02, whereas the direct genetic correlation ranged from −0.32 ± 0.40 to 0.98 ± 0.17. The mean inbreeding coefficient was 0.105% with an annual rate of 0.02%. The heritability estimates for growth traits and Kleiber ratio suggest that slow genetic progress would be expected from the selection. However, the integration of selection with crossbreeding programme can enhance genetic gain. Therefore, selection should be conducted based on breeding values estimated from multiple information sources to increase the selection response.

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

Simple SummaryDeutsch Drahthaar (DD) is the most popular hunting dog in Germany, fulfilling all aspects of hunting including searching for trails. This breed was newly created at the beginning of the 20th century from a large number existing versatile hunting dog breeds. The aim of the breed was, and still is, to achieve the best performance in all aspects of hunting. We analyzed pedigrees of DD using demographic measures to quantify genetic diversity such as probabilities of gene origin and degrees of ancestral and individual inbreeding. A large number of genetically diverse founder dogs should open up the opportunity of creating a breed with a high genetic diversity and a low increase of inbreeding per generation. On the other hand, intense use of top sires and dams from a limited number of breeding lines may accelerate breeding progress in hunting abilities but reduce genetic diversity. Monitoring genetic diversity should help to maintain a high diversity of breeding populations. Our analysis of pedigree data from 101,887 DD dogs revealed inbreeding measures (coefficient of inbreeding F = 0.042, individual rate of inbreeding ΔFi = 0.00551) and effective population size (Ne = 92) in the mean range compared to a wide range of other dog breeds. Ancestral inbreeding had a strong increasing trend, whereas trends in individual inbreeding and rate of individual inbreeding were slightly negative.Loss of genetic diversity and high inbreeding rates confer an increased risk of congenital anomalies and diseases and thus impacting dog breeding. In this study, we analyzed recent and ancestral inbreeding as well as other measures of genetic variability in the Deutsch Drahthaar (DD) dog population. Analyses included pedigree data from 101,887 animals and a reference population with 65,927 dogs born between 2000 and 2020. The mean equivalent complete generations was 8.6 with 69% known ancestors in generation 8. The mean realized effective population size was 92 with an increasing trend from 83 to 108 over birth years. The numbers of founders, effective founders and effective ancestors, as well as founder genomes, were 814, 66, 38 and 16.15, respectively. Thirteen ancestors explained 50% of the genetic diversity. The mean coefficient of inbreeding and individual rate of inbreeding (ΔFi) were 0.042 and 0.00551, respectively, with a slightly decreasing trend in ΔFi. Exposure of ancestors to identical-by-descent alleles explored through ancestral coefficients of inbreeding showed a strong increasing trend. Comparisons between new and ancestral inbreeding coefficients according to Kalinowski et al. showed an average relative contribution of 62% of new inbreeding to individual inbreeding. Comparisons among average coancestry within the parental population and average inbreeding in the reference population were not indicative of genetic substructures. In conclusion, the creation of the DD dog breed about 120 years ago resulted in a popular breed with considerable genetic diversity without substructuring into lines or subpopulations. The trend of new inbreeding was declining, while ancestral inbreeding through ancestors who were autozygous at least once in previous generations was increasing.

Effect of consanguinity on birth weight and birth defects in the Agadir region of Morocco

The material of this study consists of 3701 newborns in the neonatology section, Maternity Hassan II Hospital, Agadir, Morocco from April 2016 to April 2018. For each newborn, several variables were recorded (birth weight, sex, consanguinity, gestational age, economic and social situation of parents, etc.). They types of birth defects have been classified according to the International Classification of Diseases (ICD-10). Of the 3701 newborns, 171 are carriers of congenital anomalies. This represents a prevalence of 4.6% (95% CI: 3.9% - 5.3%). The prevalence of LBW was 8.7% (95% CI: 7.7% - 9.6%). Of all newborns, 715 (19,64 %) were from consanguineous marriages and the mean inbreeding coefficient for the present study was 0.012. The prevalence of congenital malformations were more frequently observed in consanguineous (7.69%) compared to non-consanguineous (3.76%). A significant association with consanguinity was observed for the congenital anomaly (p-value = 0.00052) and for LBW (p-value = 0.0008). Consanguinity was identified as significant risk factors associated with LBW and CA in this study.