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PubMed2026

Genomic inbreeding coefficients and inbreeding depression of semen production traits at genome-wide and chromosomal levels in Japanese Holstein bulls.

We aimed to estimate inbreeding coefficients and the effects of inbreeding depression on semen production traits at both the genome-wide and chromosomal levels. We utilized pedigree data for 19,921 animals, single nucleotide polymorphism (SNP) data on 5700 Japanese Holstein bulls, and 52,193 semen collection records from 775 bulls. We estimated 4 different inbreeding coefficients, namely a pedigree-based coefficient (FPED) and 3 genomic coefficients derived from SNP data. The genomic coefficients consisted of one based on the genomic relationship matrix (FGRM), one based on runs of homozygosity (ROH), and one based on homozygous-by-descent (HBD) segments (FHBD). These genomic coefficients were estimated at both the genome-wide and chromosomal levels. Furthermore, we investigated the effects of these coefficients on semen production traits: semen volume (VOL), sperm concentration (CON), sperm number (NUM), and sperm motility (MOT). In the genome-wide-level analysis, inbreeding coefficients increased markedly in bulls born after 2009, coinciding with the introduction of genomic selection. Significant inbreeding depression of VOL was found. At the chromosomal level, the inbreeding coefficients for most chromosomes showed a similar trend to the genome-wide metrics, although some (e.g., chr10 and chr20) exhibited a more pronounced trend. Suggestive inbreeding effects were detected on specific chromosomes for all traits (chr1 and chr22 for VOL, chr24 and chr29 for CON, chr1, chr12, and chr27 for NUM, chr10 and chr18 for MOT), including the traits that were not significant at the genome-wide level. Our results highlight that chromosomal-level analysis provides information complementary to whole-genome metrics, offering a more detailed perspective for managing inbreeding effects. To mitigate the adverse effects of inbreeding on semen production traits, future breeding programs would benefit from the control of inbreeding effects on high-risk chromosomal regions.

Genomic inbreeding coefficient↗

PubMed1992

Analysis of levels of inbreeding and inbreeding depression in Jersey cattle.

A pedigree file of 157,015 male and female Jersey cattle (born after 1955) from the Canadian herdbooks was investigated for the occurrence of inbreeding. A large proportion of Jersey bulls and cows were inbred (32.4 and 36.3% for bulls and cows, respectively). However, average inbreeding coefficients of these inbred cows and of all cows were low. First lactation milk, fat, and fat percentage records for 53,592 Jersey cows were analyzed. Inbreeding was included in the animal model as a linear covariate. The regression coefficients of milk, fat, and fat percentage on inbreeding were -9.84 kg, -.55 kg, and -.0011% per 1% increase of inbreeding. Inbreeding depression was not enough to cause large reductions of milk and fat yield of a cow with average inbreeding. However, when the inbreeding coefficient was greater than 12.5%, the inbreeding depression was significantly higher than expected and such that intentional inbreeding is not justified unless the mating is to an animal with exceptionally high breeding value.

Algorithms↗

PubMed1991

Effects of inbreeding on reproduction and wool production of Rambouillet, Targhee, and Columbia ewes.

Because of a traditional interest in inbreeding as a tool for breed improvement, it was desirable to evaluate the effects of inbreeding on the most important products of the sheep industry, lamb and wool production. The data for this study were based on 13,807 ewe and 16,470 lamb records from Rambouillet (R), Targhee (T), and Columbia (C) sheep collected over 9 or 10 yr from 54 inbred lines. Average inbreeding of the lambs and ewes involved was near 25 and 20%, respectively. The combined effects of lamb's and dam's inbreeding reduced litter weight weaned at 120 d approximately .5 kg for each percentage of increase in inbreeding in every breed. For ewes and lambs of average inbreeding, the reductions relative to noninbred ewes amounted to 12.4, 10.3, and 11.3 kg for R, T, and C, respectively. The reductions constituted declines in weight weaned per ewe of 34, 25, and 28%. Similarly, net reproduction rate (lambs weaned per ewes put into breeding) was reduced more than one percentage point for each percentage of increase in inbreeding, with net declines at average inbreeding of 31.7, 23.5, and 25.7 percentage points for each breed, respectively. These reductions were equivalent to reductions in net rate of 29, 20, and 23%. The combined effect of lamb and dam inbreeding reduced weaning weight by 3.5, 2.6, and 2.2 kg, which constituted reductions of 10, 7, and 6%, respectively. Reduced weaning weight was approximately 30% as important as reduced net reproduction rate in contributing to the decline in litter weight weaned. Effects on fleece weight were curvilinear and amounted to reductions of .35, .18, and .00 kg, respectively, at levels of average inbreeding; however, Columbia fleece weights declined rapidly at levels exceeding 20% for ewes. Potential selection differentials were reduced 16% at inbreeding levels of 25 and 20% for lambs and dams, respectively, and 62% at levels of 55 and 50%. The average economic loss per ewe in value of production was estimated at $17 for average inbreeding and as high as $36 for inbreeding approaching 50%. It seems that the use of inbreeding as a tool for improving productive merit in sheep is much more certain to be a detriment, economically and genetically, than an advantage.

Animals↗

PubMed1991

"Runaway" social evolution: reinforcing selection for inbreeding and altruism.

Kin selection theory predicts that altruistic behaviors, those that decrease the fitness of the individual performing the behavior but increase the fitness of the recipient, can increase in frequency if the individuals interacting are closely related. Several studies have shown that inbreeding therefore generally increases the effectiveness of kin selection when fitnesses are linear, additive functions of the number of altruists in the family, although with extreme forms of altruism, inbreeding can actually retard the evolution of altruism. These models assume that a constant proportion of the population mates at random and a constant proportion practices some form of inbreeding. In order to investigate the effect of inbreeding on the evolution of altruistic behavior when the mating structure is allowed to evolve, we examined a two-locus model by computer simulation of a diploid case and illustrated the important qualitative features by mathematical analysis of a haploid case. One locus determines an individual's propensity to perform altruistic social behavior and the second locus determines the probability that an individual will mate within its sibship. We assumed positive selection for altruism and no direct selection at the inbreeding locus. We observed that the altruistic allele and the inbreeding allele become positively associated, even when the initial conditions of the model assume independence between these loci. This linkage disequilibrium becomes established, because the altruistic allele increases more rapidly in the inbreeding segment of the population. This association subsequently results in indirect selection on the inbreeding locus. However, the dynamics of this model go beyond a simple "hitch-hiking" effect, because high levels of altruism lead to increased inbreeding, and high degrees of inbreeding accelerate the rate of change of the altruistic allele in the entire population. Thus, the dynamics of this model are similar to those of "runaway" sexual selection, with gene frequency change at the two loci interactively causing rapid evolutionary change.

Alleles↗

PubMed2025

Inbreeding load in finite populations from dominant and overdominant mutations.

Inbreeding depression is a widespread phenomenon that reflects the burden of deleterious effects hidden in heterozygosis in non-inbred populations but exposed in homozygosis in inbred individuals, known as inbreeding load (B). This load can be due to partially or fully recessive deleterious mutations (dominance model) or to heterozygote advantage (overdominance model, where both homozygotes are deleterious relative to the heterozygote). There are many studies addressing the changes in inbreeding load in finite populations assuming the dominance model. However, the contribution of overdominance to inbreeding depression has been focused on infinite-size populations. We carried out computer simulations to investigate the joint impact of dominant and pure overdominant mutations on inbreeding load, both for self-fertilizing populations and for panmictic populations suffering from a drastic bottleneck. We found that the overdominant inbreeding load can be substantially reduced by drift even for symmetrical overdominance, at least when considering mutations of small effect. For panmictic bottlenecked populations, the reduction in inbreeding load under dominance and overdominance loci cannot be easily distinguished. However, while purging depletes inbreeding load from dominant loci, slowing inbreeding depression and leading to partial fitness recovery, for overdominant loci fitness declines monotonically.

Inbreeding↗

PubMed1992

Inbreeding in Swiss Braunvieh and its influence on breeding values predicted from a repeatability animal model.

Inbreeding coefficients were computed for 910,444 animals of the Swiss Braunvieh population. Of the animals born in 1984, 71.5% were inbred with 67.9, 3.4, and .2% having inbreeding coefficients between greater than 0 and 5%, greater than 5 to 10%, and greater than 10%, respectively. The average inbreeding coefficient was 1.14% but, for animals with both parents and at least one grandparent known, it was 1.67%. Breeding values for total milk, fat, and protein yields and for fat and protein percentages were predicted using a repeatability animal model including a regression on the inbreeding coefficient. Phenotypic performance was sizeably depressed for milk yield only (-26 kg/% of inbreeding or 2.4% of the phenotypic standard deviation). Adjusting for inbreeding increased the estimated genetic trend slightly. Inbreeding is only partially accounted for when it is ignored in the construction of the inverse of the numerator relationship matrix. This effect was investigated by comparing predicted breeding values from a model including the complete matrix with predicted breeding values from a model including a matrix constructed with inbreeding ignored. Only .8% of all predicted breeding values were affected by more than +/- 5.5 kg. The maximum difference observed was 55.3 kg. The observed average absolute differences between the breeding values of offspring predicted with the two models increased with inbreeding of parents.

Animals↗

PubMed1992

Comparison of selection methods at the same level of inbreeding.

Animal geneticists predict higher genetic responses to selection by increasing the accuracy of selection using BLUP with information on relatives. Comparison of different selection methods is usually made with the same total number tested and with the same number of parents and mating structure so as to give some acceptable (low) level of inbreeding. Use of family information by BLUP results in the individuals selected being more closely related, and the levels of inbreeding are increased, thereby breaking the original restriction on inbreeding. An alternative is to compare methods at the same level of inbreeding. This would allow more intense selection (fewer males selected) with the less accurate methods. Stochastic simulation shows that, at the same level of inbreeding, differences between the methods are much smaller than if inbreeding is unrestricted. If low to moderate inbreeding levels are targeted, as in a closed line of limited size, then selection on phenotype can yield higher genetic responses than selection on BLUP. Extra responses by BLUP are at the expense of extra inbreeding. The results derived here show that selection on BLUP of breeding values may not be optimal in all cases. Thus, current theory and teaching on selection methods are queried. Revision of the methodology and a reappraisal of the optimization results of selection theory are required.

Animals↗

PubMed1978

Inbreeding as measured by isonymy, pedigrees, and population size in Törbel, Switzerland.

Törbel provides an interesting test case for the study of the relationship between inbreeding measured by pedigrees and inbreeding measured by isonymy. At the start of this investigation, we were aware that isonymy could introduce biases into the calculation of the inbreeding coefficient in either direction. However, it was expected that in Switzerland, inbreeding from isonymy would be an overestimate due to patrilocal residence and polyphyletic names. One way of dealing with this problem [13] was not to be concerned with the absolute value of inbreeding but only in the difference between estimates. Any bias introduced in the estimate itself disappears in such comparisons, so that a trend of inbreeding can be ascertained correctly. However, it was considered equally important to subject several populations to both a complete pedigree analysis and an isonymic analysis to determine the relationship between estimates of inbreeding. Despite the fact that several authors (Swedlund [18], for example) warned users of isonymy to exercise caution, the careless application of isonymy still persists. In the present study, estimates of inbreeding from isonymy were brought into line with other methods based on pedigree analysis and population size. However, it was possible to do this only in Törbel where pedigree depth was extensive and relatively complete. Similar corrections are possible only when the distribution of mono- and polyphyletic names is known and when migration data are reliable. If the trouble is taken to make these corrections, the same time and effort might as well be spent in pedigree analysis (when fairly complete ascertainment is possible) to achieve the same end result.

Consanguinity↗

PubMed2024

Detecting inbreeding depression in structured populations.

Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ([Formula: see text]) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different [Formula: see text] and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on [Formula: see text] based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.

Humans↗

PubMed2026

Runs of Homozygosity Predict Inbreeding Depression Across Taxa: A Systematic Review and Meta-Analysis.

Measuring inbreeding via runs of homozygosity (ROH) captures realized autozygosity and can infer inbreeding timing through ROH length. A growing body of literature links the proportion of the genome in ROH (FROH) to fitness outcomes across taxa, yet systematic synthesis has been lacking. Here, we conduct a systematic review and meta-analysis to quantify FROH-fitness associations, identify drivers of variation and derive conservation-relevant recommendations. Narrative synthesis of 44 studies revealed that inbreeding depression operates through multiple interconnected pathways (survival, maternal effects, disease susceptibility, reproduction). Critically, purging cannot be relied upon to eliminate inbreeding depression as substantial fitness costs persist even in historically small populations. Meta-analysis of 62 effect sizes revealed a significant negative association between genomic inbreeding and fitness across taxa (Fisher's z = -0.103, r = -0.10, p < 0.0001). Study group, whether wildlife, livestock or humans, explained 22.5% of variance, with wildlife showing strongest effects (6-fold stronger than humans). Survival traits showed the greatest sensitivity to the effects of ROH (r = -0.22). Additionally, ROH detection methodology significantly influenced effect sizes: comprehensive approaches (all ROH lengths) detected stronger depression (r = -0.18) than long-ROH-only analyses (r = -0.08, p = 0.008), indicating cumulative genetic load matters. Overall, results indicate significant but variable fitness associations with ROH, with effect magnitude depending on biological context and methodological approach. Comprehensive ROH-based approaches show promise as conservation monitoring tools, but limited wildlife studies, particularly for non-mammalian taxa, highlight an urgent need for standardized protocols and expanded empirical research.

Animals↗

PubMed1975

[Inbreeding in the Samarkand region].

Data on the frequency of inbreeding in some isolated populations of Samarkand region are given. Statistically significant differences were established in the frequency of inbreeding in separate groups and in the general population of the region. Inbreeding marriages were more observed between paralel cousins, occasionally they were made between secon cousins. Strict time dependence of inbreeding frequency was not found, but it was noticed that the level of inbreeding was reduced since 1930 to 1949.

Consanguinity↗

PubMed1975

[Inbreeding in the Samarkand region].

Data on the frequency of inbreeding in some isolated populations of Samarkand region are given. Statistically significant differences were established in the frequency of inbreeding in separate groups and in the general population of the region. Inbreeding marriages were more often observed between paralel cousins, occasionally they were made between second cousins. Strict time dependence of inbreeding frequency was not found, but it was noticed that the level of inbreeding was reduced since 1930 to 1949.

Consanguinity↗

PubMed1991

[Marital and migration structure and inbreeding in the Adyg population].

Endogamy and gametic indices for both Russian and Adyg populations living in the Adyg autonomous region of Krasnodar district were determined on different levels of territorial units: village, rural, community (a group of villagers) and rural region. Inbreeding coefficient was estimated for Adyg population and its structure analysed: a random component contributes mostly to the inbreeding coefficient (Fst = 0.00991), non-random component of the inbreeding coefficient being Fis = 0.010009, which testifies to negative marital assortativity among Adygs. Local inbreeding "a" and decline in the inbreeding "phi" coefficient at a distance from 0 to 500 km were calculated using the Malecot's formula: the coefficient "a" was found to be 0.00397, which is in good accordance with the Fst.

Consanguinity↗

PubMed2026

Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.

Duroc (DD), Landrace (LL), and Yorkshire (YY) are among the most widely used commercial pig breeds, having undergone intense long-term selection within closed breeding systems. This study presents a comprehensive genomic analysis of genetic diversity, inbreeding patterns, and selection signatures in DD, LL, and YY populations that have been subject to close breeding for over 15 years. Genomic and pedigree data were available for 1,088 animals (DD = 348, LL = 276, YY = 464), genotyped using the GenoBaits® Porcine 100 K SNP panel. Principal component analysis and genetic diversity metrics revealed distinct population structures among the three breeds. Pairwise genetic differentiation supported this pattern, with DD showing the greatest divergence from LL (0.34 ± 0.24) and YY (0.33 ± 0.24), while LL and YY were more closely related (FST = 0.22 ± 0.19). Linkage disequilibrium (LD) analysis further confirmed these differences, as DD exhibited the highest average r² (0.34), followed by LL (0.28) and YY (0.25). Within-breed genetic diversity metrics, including observed heterozygosity (HO: 0.37 in DD, 0.39 in LL, 0.38 in YY), expected heterozygosity (HE: 0.36 in DD, 0.37 in LL, 0.38 in YY), and minor allele frequency (MAF: 0.27 in DD, 0.28 in LL, 0.29 in YY), indicated greater genetic variability in LL and YY compared to DD. Runs of homozygosity (ROH) analyses revealed different patterns of autozygosity, with DD exhibiting more long ROH indicative of recent inbreeding, while YY harbored a higher number of short ROH, suggestive of more ancient demographic events. ROH-based inbreeding coefficients (FROH) consistently exceeded pedigree-based estimates (FPED) across all breeds, highlighting the presence of recent or unrecorded inbreeding that pedigree data may not fully capture. According to Generation Proxy Selection Mapping (GPSM), 17, 1, and 12 significant SNPs were detected in DD, LL, and YY, respectively. Functional annotation of ROH islands and GPSM-significant loci revealed both breed-specific and overlapping QTLs related to traits such as growth, reproduction, and carcass. In general, the findings of this study contribute to a deeper understanding of the genomic consequences of long-term closed breeding and provide reference information to support consideration of breeding strategies that balance continued selection for productivity with the maintenance of genetic diversity in modern commercial pig populations.

Animals↗

PubMedDate not supplied

Interactions between ageing and inbreeding effects on development of Drosophila melanogaster embryos.

Ageing and brother-sister inbreeding effects were studied simultaneously during the development of Drosophila melanogaster. Egg hatchability and adult emergence were investigated in relation to age of females laying the eggs and the age of the parents of these females. Each couple was followed individually. The effects of parental age varied according to the mating system used. Both hatchability and emergency of inbred eggs were affected by ageing. This indicates that parental constitution can influence early and later stages of development. Control of embryonic and larvo-pupal developments may involve processes perturbed by both ageing and inbreeding. Thus, information related to the genetic control system of development varies with the age of the flies and of their parents and consequently modulates the inbreeding effects. It is postulated that inbreeding and ageing may both involve cytoplasmic-genome interactions implicated in the control of embryogenesis.

Aging↗

PubMed1978

On the evolutionary stability of the female-biased sex ratio in the wood lemming (Myopus schisticolor): the effect of inbreeding.

The evolutionary stability of the female-biased sex ratio observed in the wood lemming (Myopus schisticolor) is discussed. The hypothesis analysed is that the skewed sex ratio is maintained as a result of partial and/or recurrent inbreeding. Fredga et al. (1976, 1977) have suggested that an X-linked mutant gene, X, affects the male-determining action of the Y chromosome, thus converting some XY individuals into females. By a mechanism of selective non-disjunction in the foetal ovary only X-carrying eggs are produced. In particular the stability of that genetic mechanism (or the X chromosome) is analysed by considering the introduction of a "suppressing" sex-linked mutant gene Y. Several deterministic simulation models assuming father-daughter and/or brother-sister matings have been developed and analysed. It is concluded that in the case of extremely strong inbreeding, the hypothesised genetic mechanism may, as a result, be evolutionarily stable. Interpreting field observations on microtine rodents in general it is concluded that only a few species are likely to experience such extreme cases of inbreeding. The wood lemming and the related collared lemming (Dicrostonyx troquatus), another case which seems to have XY-females, are likely to exhibit sufficiently strong inbreeding.

Animals↗

PubMed1976

Inbreeding components of body weight and growth rate in Japanese Quail.

1. The parental inbreeding component of body weight and daily gain was partitioned into paternal and maternal inbreeding components and the latter were found to be the mor important. 2. The contribution of the maternal inbreeding to the depression of characters was more pronounced on 1-d-old chicks, but declined as the chicks grew. 3. The body weight taken near sexual maturity showed a low and non-significant decline. 4. In spite of differences in the body weight of the two populations of Japanese quail the inbreeding components were similar.

Animals↗

PubMed1976

Effects of different rates of inbreeding on the body weight and rate of gain of Japanese quail.

1. The effect of regular full-sib and double first cousin mating on body weight and rate of gain over six generations of Japanese quail was determined. 2. The depression of characters was more pronounced in the full-sib than in the double first cousin mating system, the relative depression due to parental inbreeding and offspring inbreeding depending on the magnitude of parental effect and individual's own genotypic effect on the character. 3. The body weight and rate of gain taken at an early age showed greater depression due to parental inbreeding whereas that taken near sexual maturity was depressed mainly due to individual's own inbreeding.

Animals↗