Increase In Inbreeding Coefficient Research Articles

Genetic characterization of F0 outbred and F1 inbred Swiss albino mice using microsatellite markers and their performance evaluation

Swiss albino mice have been widely utilized in various biological researches worldwide. Phenotypic and fitness related traits of F0 and F1 inbred mice were estimated on 918 and 707 individual offsprings, respectively. The influence of fixed effects (litter size and sex) on birth weight (BW), weaning weight (WW) and adult body weight (ABW) in both the generations were found to be statistically significant. Genetic characterization of F0 outbred and the F1 inbred strain of Swiss albino mice were evaluated by using 10 microsatellites markers. The results indicated that total number of alleles per locus ranged from 3 (D2Mit61, D3Mit55, D8Mit14, D9Mit27, D10Mit180, D11Mit167) to 4 (D1Mit15, D2Mit51, D5Mit18, D7Mit323) in F0 and F1 inbred population, with a mean value of 3.4 indicating polymorphism in all 10 loci. The mean of effective number of alleles was 2.935 and 2.733 in F0 and F1 population, respectively. Estimates of the FIS ranged from 0.139 (D10Mit180) to 0.999 (D9Mit27); and from 0.109 (D3Mit55) to 0.679 (D2Mit51) in F0 and F1 inbred population, respectively. The estimated mean markerbased FIS was 0.294 and 0.372 in F0 and F1 populations, respectively. The mean values of observed heterozygosity (Ho) and expected heterozygosity (He) were 0.460 and 0.654, respectively for F0 and 0.390 and 0.627, respectively for F1 inbred mice population. Slight reduction in heterozygosity and 7.8% increase in inbreeding coefficient were observed in F1 inbred in comparison to F0 population. The results suggested that genome wide microsatellite genotyping might be more useful for accurate measuring and reliable estimation of population genetic parameters and inbreeding coefficient.

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

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

Analysis of Genetic Diversity in the Czech Spotted Dog.

Simple SummaryLosses of genetic diversity have a particular impact on breed populations in countries with a small breeding base or national breeds with a small registry. Among them, it is possible to include the breed of the Czech Spotted Dog (CSD), whose variability has been low since the beginning of breeding due to the small number of founders and mating of close relatives. Through study of its pedigree records, we recorded a severe loss of genetic variability and high relatedness between animals. Moreover, the population is not free of genetic diseases; therefore, future existence of the breed is in danger.Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed—the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity—which was calculated based on the reference population and pedigree completeness—were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence.

Quantifying the effect of inbreeding on average daily gain and Kleiber ratio in Mazandaran native chickens.

The aims of this study was to evaluate inbreeding effects for growth rate (average daily gain from hatch to 8weeks of age (ADG1-8), average daily gain from hatch to 12weeks of age (ADG1-12), average daily gain from 8weeks of age to 12weeks (ADG8-12), average daily gain from hatch to sex maturity (ADG1-SM), average daily gain from 8weeks of age to sex maturity (ADG8-SM), average daily gain from 12weeks to sex maturity (ADG12-SM), and Kleiber ratios (KR1-8, KR1-12, KR8-12) in Mazandaran native chickens. The data set of 82,446 pedigreed individuals over 21 generations was analyzed. All individuals were grouped into three classes based on the inbreeding coefficient: First class contained non-inbred birds (F = 0) and second and third classes contained inbred individuals (0 < F ≤ 5% and F > 5%, respectively). The effects of inbreeding coefficient on the studied traits were estimated by the restricted maximum likelihood method (REML) applying the WOMBAT software and fitting individual increase in inbreeding coefficient (ΔFi) of birds as linear covariates under 6 different animal models. ADG8-SM and ADG12-SM increased non-significantly by 0.003 and 0.005g, respectively, due to 1% increase in ΔFi, while ADG1-8, ADG1-12, ADG8-12, ADG1-SM, KR1-8, and KR1-12 decreased (P < 0.001), respectively, by 0.012g, 0.011g, 0.010g, 0.014g, 0.003g, and 0.002g. Also, KR8-12 non-significantly decreased by 0.001g. Estimates of direct heritability of traits based on the most appropriate models ranged from 0.05 (KR8-12) to 0.26 (ADG12-SM). Results showed that it is important to regularly analyze inbreeding level in the herd in an attempt to prevent the reduction of performance.

Impact of inbreeding on milk fatty acids of a Brazilian Holstein cattle

Context Reproductive technologies may either contribute to the increase of genetic gains or inbreeding levels in dairy cattle breeding programs and herds. In general, studies have evaluated the impacts of inbreeding on traditional traits, such as production and reproduction. However, studies on novel traits, such as milk fatty acids profile, are scarce in the literature. Aim We aimed to evaluate the impact of inbreeding levels on milk fatty acids profile measured in a Brazilian Holstein cattle population. Methods Monthly records of the percentages (%) of palmitic, stearic, oleic, total saturated, unsaturated, monounsaturated and polyunsaturated fatty acids in milk were collected from 2047 Holstein cows between May and December 2012. The pedigree file contained 7963 animals over seven generations. The inbreeding trend was evaluated by linear regression of inbreeding coefficients on generations. The inbreeding impacts on breeding and phenotypic values were evaluated by linear regression of breeding values and phenotypic values on generations respectively. Breeding values were obtained by a Bayesian approach based on an animal model that included the systematic effect of contemporary group, cubic effect of days in milk as a covariate, and the random direct additive genetic and animal permanent environmental effects. Key results The average inbreeding coefficient was 0.28% for all animals, and 1.39% for inbred animals. Inbreeding tended to increase 0.24% per generation (P-value &amp;lt;0.0001). The regression coefficients of phenotypic values on inbreeding were not significant for saturated, unsaturated, monounsaturated, palmitic, stearic and oleic fatty acids (P-values &amp;gt;0.18, 0.10, 0.16, 0.26, 0.51 and 0.09 respectively); whereas for polyunsaturated fatty acids, they were significant (P-value &amp;lt;0.04), with an increase of –0.000978% on phenotypic values for each 1% increase in inbreeding. The regression coefficients of breeding values on inbreeding were not significant for unsaturated, monounsaturated, polyunsaturated, stearic and oleic fatty acids (P-values &amp;gt;0.33, 0.78, 0.48, 0.32 and 0.07 respectively). However, they were significant for saturated and palmitic fatty acids (P-values &amp;lt;0.03 and 0.0001 respectively), presenting an increase of 0.000689% and 0.000283% respectively on breeding values for each 1% increase in inbreeding. Conclusions There was a significant increase in inbreeding coefficients over the studied generations; however, the impacts on both breeding and phenotypic values were small, when significant. Implications Our study may contribute to the understanding of how inbreeding levels may affect the fatty acids profile in a Brazilian Holstein cattle population, as well as encourage future research on this subject.

Genetic variability in a Holstein population using SNP markers and their use for monitoring mating strategies

As genotyping costs continue to decrease, the demand for genotyping has increased among farmers. In most livestock herds, an important issue is controlling the increase in inbreeding coefficient. While this remains a large motive to genotype, producers are often unaware of the other benefits that genotyping could bring. The aim of this study was to demonstrate that SNP chips could be used as an effective herd management tool by utilizing a population of Italian Holstein-Friesian cattle. After filtering, the total number of animals and SNPs retained for analyses were 44 and 27,365, respectively. The principal component analyses (PCA) were able to identify a sire and origin-of-sire effect within the herd, while determining that sires do not influence individual genomic selection index values. The inbreeding coefficients calculated from genotypes (FIS) provided a glimpse into the herd’s heterozygosity and determined that the genetic variability is being well maintained. On the other hand, inbreeding coefficients on the genomic level were deduced from runs of homozygosity (FROH) and were compared to the inbreeding coefficients based on pedigree (FPED). Furthermore, 1,950 runs of homozygosity (ROH) were identified with the average length of ROH being 4.66 Mb. Genes and QTL within the genomic regions most commonly associated (top 1% and top 5% of SNP) with ROH were characterized. These results indicate that genotyping small herds, albeit at low-density, provides insights to the genetic variability within the herd and thus allows producers the ability to manage their stock from a genetic standpoint.

Estimation of inbreeding effect on conception in Czech Holstein

The influence of calculated inbreeding coefficients on the conception of heifers and cows was analysed by a two-trait binary model for conceived/not conceived after each insemination on 677 234 Czech Holstein cows and heifers with 3 248 299 insemination records as the covariable in a statistical model. The data between 1996 and 2014 were analysed. Various effects and their statistical influence on traits were tested by a generalized linear model. Consequently, genetic parameters were estimated by the Gibbs sampling method and used in predicting breeding values using the best linear unbiased prediction by animal model (BLUP-AM). The mean for the conception rate of cows averaged over lactations was 33.7% and for heifers it reached 53.8%. Average inbreeding coefficient increased from 1% in 1996 to almost 5% by 2013 and was in the range of 0–45%. The rate of inbreeding per generation was 0.20%. Although the effect of inbreeding was statistically significant (P = 0.05) for both traits, the proportion of variability explained by the models was relatively low. Estimated genetic parameters were low for both traits. Coefficient of heritability was 2.00% and 1.30% for cows and heifers, respectively, whereas coefficients of repeatability reached 6.09% and 7.08% for cows and heifers, respectively. The random effect of the permanent environment (PE) reached higher values than the additive genetic variance (G) and explained 5.67% and 4.09% of variability for cows and heifers, respectively. A negative impact of inbreeding on heifer and cow conception was observed, whereby every 10% increase in inbreeding coefficient resulted in a conception decline by 2.23%. Calculated Spearman’s rank correlation coefficient between estimated breeding values considering and not considering the effect of inbreeding was close to one. Presented results indicate that inbreeding has a negligible influence on the breeding values of conception. The results also indicate that it is not necessary to include inbreeding coefficient in the routine breeding value evaluation of conception rate of heifers and cows. On the other hand, monitoring of inbreeding is necessary to avoid an increase of its rate.

Methods and applications of animal genomic mating

Genomic selection (GS) is a powerful tool which can be used to estimate the breeding value of individual animals by using the molecular markers of the animal's entire genome. GS improves the accuracy and intensity of selection, reduces the interval of generation, and realizes the effects of early accuracy selection contributing to a significant evolution in animal breeding. In the past decade, GS was successfully applied in the genetic improvement of dairy animals with improved selection accuracy and genetic gain of breeding animals. However, GS focuses on the genetic gain of target traits while it ignores the genetic relationship between mating pairs such that it ignores long term genetic merits such as an increase in inbreeding coefficient of offspring population, a decrease of genetic diversity and the homozygous presentation of harmful genes. In 2016, genomic mating (GM) was proposed as a sustainable genetic selection method using genomic information of the breeding candidate individuals to optimize selection and mating with resultant control of the growth rate of population inbreeding coefficient and achieving long-term and sustainable genetic progress. Therefore, GM is more suitable for modern animal breeding than GS, especially for the genetic improvement of indigenous species. In this review, we summarize the basic concepts, methods, and applications of GM, and then present examples comparing the effects of six simulated mating schemes. This review serves as a valuable reference for the applications of animal breeding methods.

Genetic parameters and inbreeding effects for production traits of Thai native chickens

ObjectiveEstimate genetic parameters, the rate of inbreeding, and the effect of inbreeding on growth and egg production traits of a Thai native chicken breed Lueng Hang Kao Kabinburi housed under intensive management under a tropical climate.MethodsGenetic parameters were estimated for weight measured at four weekly intervals from body weight at day 1 (BW1D) to body weight at 24 weeks (BW24) of age, as well as weight at first egg, age at first egg (AFE), egg weight at first egg, and total number of eggs (EN) produced during the first 17 weeks of lay using restricted maximum likelihood. Inbreeding depression was estimated using a linear regression of individual phenotype on inbreeding coefficient.ResultsDirect additive genetic effect was significant for all traits. Maternal genetic effect and permanent environmental hen effects were significant for all early growth traits, expect for BW24. For BW24, maternal genetic effect was also significant. Permanent environmental hen effect was significant for AFE. Direct heritabilities ranged from 0.10 to 0.47 for growth traits and ranged from 0.15 to 0.16 for egg production traits. Early growth traits had high genetic correlations between them. The EN was lowly negatively correlated with other traits. The average rate of inbreeding for the population was 0.09% per year. Overall, the inbreeding had no effect on body weight traits, except for BW1D. An increase in inbreeding coefficient by 1% reduced BWID by 0.09 g (0.29% of the mean).ConclusionImprovement in body weight gain can be achieved by selecting for early growth traits. Selection for higher body weight traits is expected to increase the weight of first egg. Due to low but unfavorable correlations with body weight traits, selection on EN needs to be combined with other traits via multi-trait index selection to improve body weight and EN simultaneously.

EFFECT OF INBREEDING ON SOME BODY WEIGHTS IN EGYPTIAN BARKI SHEEP

SUMMARYThe present study utilized the pedigree records of 3191 Barki lamb progenies of 186 sires and 1640 dams reared at two research stations; Ras-Elhekma (from 1963 to 1972) and Maryout (from 1973 to 2004). The current study investigated the effect of inbreeding on body weights at birth, BW, weaning, W120, yearling, W360 and at first mating, W480 in Egyptian Barki sheep flock of the Desert Research Centre. The non-genetic factors affecting the studied traits were investigated. It was found that 4.92% of the present dataset were inbred animals. Average inbreeding coefficient of inbred animals was estimated as 3.57% and appeared to be ranged from 0.05% to 25.20%. Estimate of inbreeding regression coefficient on year of birth for inbred animals were significantly negative in Ras-Elhekma (-0.015) and was not significant in Maryout research station (0.003). Results of pooled data from both stations showed that each one percent increase in inbreeding coefficient resulted in a reduction in BW (-0.0156 kg), W120 (-0.0364 kg) and W360 (-0.0079 kg) together with an increase in W480 (0.0559 kg). The effect of inbreeding seemed to be negligible for the studied body weights with no consistent trend in both research stations.

Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites.

BackgroundPopulations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes. Furthermore, the occurrence of L. rubellus lineages across the UK allows for inferences of mechanisms associated with drivers of speciation and local adaptation.ResultsUsing RADseq, we were able to define population structure between the two lineages through the use of draft genomes for each, demonstrating an absence of admixture between lineages and that populations over extensive geographic distances form discrete populations. Between the two British lineages, we were able to provide evidence for selection near to genes associated with epigenetic and morphological functions, as well as near a gene encoding a pheromone. Earthworms inhabiting highly contaminated soils bare close genomic resemblance to those from proximal control soils. We were able to define a number of SNPs that largely segregate populations and are indicative of genes that are likely under selection for managing metal toxicity. This includes calcium and phosphate-handling mechanisms linked to lead and arsenic contaminants, respectively, while we also observed evidence for glutathione-related mechanisms, including metallothionein, across multiple populations. Population genomic end points demonstrate no consistent reduction in nucleotide diversity, or increase in inbreeding coefficient, relative to history of exposure.ConclusionsThough we can clearly define lineage membership using genomic markers, as well as population structure between geographic localities, it is difficult to resolve markers that segregate entirely between populations in response to soil metal concentrations. This may represent a highly variable series of traits in response to the heterogenous nature of the soil environment, but ultimately demonstrates the maintenance of lineage-specific genetic variation among local populations. L. rubellus appears to provide an exemplary system for exploring drivers for speciation, with a continuum of lineages coexisting across continental Europe, while distinct lineages exist in isolation throughout the UK.

Comparison of growth and survival among selected population, inbreeding population, and wild population in Fenneropenaeus chinensis

In this study, inbreeding population was constructed by full-sib mating of “Huang Hai No. 2” core population in Fenneropenaeus chinensis. Growth and survival of three different stages were studied in three populations, including selected population, inbreeding population, and wild population. The growth experimental results show that body weight of selected population in all the three growth stages was significantly higher than those of inbreeding population and wild population (P < 0.05). At day 90, body weight of the selected population increased by 13.1 and 19.4%, compared with those of inbreeding population and wild population and the specific growth rate (SGR) for body weight of three populations were 2.24, 2.16, and 2.11. Coefficient of variation of body weight among the three populations were different; the highest was 23.75% in the selected population and the lowest was 16.76% in the wild population, which showed that there is potentiality for further selection. The survival results indicated that the difference of survival of the three populations were significant (P < 0.05), that of the selected population increased by 10.78 and 14.20%, compared with those of inbreeding population and wild population, and the average survival rate of the three populations were 74, 66.8, and 64.8%, respectively. Full-sib matings revealed that the amount of inbreeding depression of body weight varied from −7.68 to −11.53%, and the estimated average inbreeding depression coefficient was −4.61 per 10% increase of inbreeding coefficient of F. For survival trait, the estimated average inbreeding depression coefficient ranged from −2.62–3.81%, and the inbreeding depression was −1.05 per 10% increase of inbreeding coefficient of F, lower than the estimate obtained for growth. These results suggest that selection works well in the breeding program of F. chinensis, and inbreeding especially full-sib matings should be avoided in the following breeding programs.

Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation.

Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to the reduction of genetic diversity. Estimates of marginal contributions of ancestors suggest that the bottlenecks arose mainly because related stallions had been used for breeding. A tendency for an increase in inbreeding coefficients was observed. F-statistics revealed that a small effective population size majorly contributed to this increase, although non-random mating in particular regions also contributed. Because the bottlenecks are thought to have reduced the effective population size, our results imply that mitigation of bottlenecks is important for conservation. To this end, breeding should involve genetically diverse stallions. In addition, to prevent non-random mating observed in particular regions, efforts should be made to plan mating with consideration of kinships.

Inbreeding depression in growth traits of Baluchi sheep

The objective of this study was to evaluate inbreeding and inbreeding depression in Baluchi sheep. Data and pedigree information were retrieved from the Baluchi sheep Breeding Station, Khorasan Razavi, Iran. Traits included were birth weight (BW), weaning weight (WW), 6-month weight (W6), 9-month weight (W9), yearling weight (W12), average daily gain from birth to weaning (ADGa), average daily gain from weaning to 6 months of age (ADGb) and average daily gain from weaning to 12 months of age (ADGc). Animals were grouped in three classes: first class included non-inbred animals (F=0) and second and third classes included inbred animals (0<F≤5% and F>5%, respectively). Inbreeding depression was studied for all traits by fitting individual increase in inbreeding coefficient (ΔFi) of the lambs as linear covariates under univariate animal models. The mean inbreeding in the whole population was 1.60%. It increased with some fluctuations from 1981 to 2005 and decreased thereafter. The average equivalent complete generation, as a measure of pedigree completeness, in the studied population was 2.49 and the value of effective population size (Ne) estimated from the ΔFi was 166. Of 10863 pedigreed lambs, 5931, 3943 and 989 animals belonged to first, second and third inbreeding class, respectively, with significant differences in their body weights and average daily gains. In some cases, growth traits of male and female lambs as well as single and twin lambs grouped in three inbreeding classes differed significantly. Among traits studied, W6, W9, W12, ADGb and ADGc were significantly affected by inbreeding (P<0.01) in such a way that one percent increase in ΔFi of the lambs significantly reduced W6, W9, W12, ADGb and ADGc by 18, 10, 131, 1.810 and 1.345g, respectively. Selection of rams with the lowest relationship with ewes in the flock was recommended to decrease the rate of inbreeding in the population.

Effect of inbreeding and individual increase in inbreeding on growth in Nilagiri and Sandyno breeds of sheep

SummaryIndividual increase in inbreeding coefficients (ΔFi) has been recommended as an alternate measure of inbreeding. It can account for the differences in pedigree knowledge of individual animals and avoids overestimation due to increased number of known generations. The effect of inbreeding (F) and equivalent inbreeding (EF) calculated fromΔFi, on growth traits were studied in Nilagiri and Sandyno flocks of sheep. The study was based on data maintained at the Sheep Breeding Research Station, Sandynallah. The pedigree information and equivalent number of generations were less in Sandyno compared with Nilagiri sheep. The average F and EF for the Nilagiri population were 2.17 and 2.44, respectively and the corresponding values for Sandyno sheep were 0.83 and 0.84, respectively. The trend of inbreeding over years in both the populations indicated that EF was higher during earlier generations when pedigree information was shallow. Among the significant effects of inbreeding, the depression in growth per 1 percent increase in inbreeding ranged from 0.04 kg in weaning weight to 0.10 kg in yearling weight. In general, more traits were affected by inbreeding in Nilagiri sheep, in which greater regression of growth traits was noticed with F compared with EF. Higher values of EF than F in earlier generations in both the populations indicate that EF avoided the potential overestimation of inbreeding coefficient during recent generations. In the Sandyno population, the magnitude of depression noticed among growth traits with significant effects of inbreeding was higher. The differences in response to F and EF noticed in the two populations and possible causes for the trait wise differences in response to F and EF are appropriately discussed.

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient (F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH (FROH) in three local dairy cattle breeds. FROH values were compared with F estimated from the genomic relationship matrix (FGRM), based on the difference between observed v. expected number of homozygous genotypes (FHOM) and the genomic homozygosity of individual i (FMOL i). The molecular coancestry coefficient (fMOL ij) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of FROH, whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between FHOM and FROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among FROH and other estimated F coefficients were generally lower ranged from 0.45 (FMOL i−FROH) in Cinisara to 0.17 (FGRM−FROH) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.

Better Fitness in Captive Cuvier's Gazelle despite Inbreeding Increase: Evidence of Purging?

Captive breeding of endangered species often aims at preserving genetic diversity and to avoid the harmful effects of inbreeding. However, deleterious alleles causing inbreeding depression can be purged when inbreeding persists over several generations. Despite its great importance both for evolutionary biology and for captive breeding programmes, few studies have addressed whether and to which extent purging may occur. Here we undertake a longitudinal study with the largest captive population of Cuvier's gazelle managed under a European Endangered Species Programme since 1975. Previous results in this population have shown that highly inbred mothers tend to produce more daughters, and this fact was used in 2006 to reach a more appropriate sex-ratio in this polygynous species by changing the pairing strategy (i.e., pairing some inbred females instead of keeping them as surplus individuals in the population). Here, by using studbook data we explore whether purging has occurred in the population by investigating whether after the change in pairing strategy a) inbreeding and homozygosity increased at the population level, b) fitness (survival) increased, and c) the relationship between inbreeding and juvenile survival, was positive. Consistent with the existence of purging, we found an increase in inbreeding coefficients, homozygosity and juvenile survival. In addition, we showed that in the course of the breeding programme the relationship between inbreeding and juvenile survival was not uniform but rather changed over time: it was negative in the early years, flat in the middle years and positive after the change in pairing strategy. We highlight that by allowing inbred individuals to mate in captive stocks we may favour sex-ratio bias towards females, a desirable managing strategy to reduce the surplus of males that force most zoos to use ethical culling and euthanizing management tools. We discuss these possibilities but also acknowledge that many other effects should be considered before implementing inbreeding and purging as elements in management decisions.

Inbreeding on productive and reproductive traits of dairy Gyr cattle

The objective of this study was to estimate genetic parameters and to evaluate the effects of inbreeding on productive and reproductive traits of dairy Gyr cattle. Single-trait animal models were used to estimate genetic parameters and solutions for inbreeding coefficients for milk (milk 305-d), fat (fat 305-d), protein (protein 305-d), lactose (lactose 305-d), and total solids (TS 305-d) yield up to 305 days of lactation, days in milk (DIM), age at first calving (AFC) and calving intervals (CI). The mean inbreeding coefficient was 2.82%. The models with linear and quadratic effects of inbreeding coefficients fitted the data better than the models without or with only linear effect of inbreeding coefficient for all traits. The increase in inbreeding coefficient caused several losses in productive and reproductive traits of dairy Gyr cattle. Estimates of heritability for milk 305-d, fat 305-d, protein 305-d, lactose 305-d, TS 305-d, DIM, AFC, and CI were 0.28, 0.27, 0.22, 0.21, 0.22, 0.17, 0.20, and 0.10, respectively. It is possible to achieve genetic progress in productive traits (especially in milk 305-d and fat 305-d) and age at first calving in dairy Gyr cattle through selection.

Inbreeding and Offspring Sex Ratio in the Pygmy Hippopotamus (Cheoropsis liberiensis) Population Kept in Zoological Gardens.

The aim of this study was to estimate the inbreeding level and its impact on offspring sex ratio in the pygmy hippopotamus population kept in zoological gardens. Records of pygmy hippopotamus born between 1873-2013 were extracted from the international studbook. Totally, 1357 individuals originating from 148 breeding units were included (individuals with unknown sex were omitted). The offspring sex ratio is defined as the number of sons to the total number of progeny of each dam and sire. Spearman's rank correlation was employed to examine the relationships between the inbreeding level and offspring sex ratio. Inbreeding coefficients and individual increase in inbreeding coefficients (included as a linear co-variable) were examined as well as the geographic region and birth period using general linear models. The average inbreeding coefficient was 5.39%. The following sex proportion was observed for the inbred population: 57% and 43% for females and males, respectively. A significant relationship between inbreeding level of parents and their offspring sex ratio were estimated for European zoological gardens, whereas in others geographic regions the dependencies were insignificant.

Estimating the inbreeding depression on cognitive behavior: a population based study of child cohort.

BackgroundCognitive ability tests are widely assumed to measure maximal intellectual performance and predictive associations between intelligence quotient (IQ) scores and later mental health problems. Very few epidemiologic studies have been done to demonstrate the relationship between familial inbreeding and modest cognitive impairments in children.ObjectiveWe aimed to estimate the effect of inbreeding on children’s cognitive behavior in comparison with non-inbred children.MethodologyA cohort of 408 children (6 to 15 years of age) was selected from inbred and non-inbred families of five Muslim populations of Jammu region. The Wechsler Intelligence Scales for Children (WISC) was used to measure the verbal IQ (VIQ), performance IQ (PIQ) and full scale IQ (FSIQ). Family pedigrees were drawn to access the family history and children’s inbred status in terms of coefficient of inbreeding (F).ResultsWe found significant decline in child cognitive abilities due to inbreeding and high frequency of mental retardation among offspring from inbred families. The mean differences (95% C.I.) were reported for the VIQ, being −22.00 (−24.82, −19.17), PIQ −26.92 (−29.96, −23.87) and FSIQ −24.47 (−27.35, −21.59) for inbred as compared to non-inbred children (p>0.001). The higher risk of being mentally retarded was found to be more obvious among inbred categories corresponding to the degree of inbreeding and the same accounts least for non-inbred children (p<0.0001). We observed an increase in the difference in mean values for VIQ, PIQ and FSIQ with the increase of inbreeding coefficient and these were found to be statistically significant (p<0.05). The regression analysis showed a fitness decline (depression) for VIQ (R2 = 0.436), PIQ (R2 = 0.468) and FSIQ (R2 = 0.464) with increasing inbreeding coefficients (p<0.01).ConclusionsOur comprehensive assessment provides the evidence for inbreeding depression on cognitive abilities among children.