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At least 19 recordsLinked to original sources
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↗
PubMed1987

Inbreeding and prereproductive mortality in the Old Order Amish. III. Direct and indirect effects of inbreeding.

Direct and indirect (mediated by biologic factors) effects of inbreeding on prereproductive mortality (death before age 20 years) were investigated in a case-control study conducted in the Lancaster County, Pennsylvania, Old Order Amish. A total of 211 cases of prereproductive death between 1969 and 1980 and 213 live controls were compared for differences in inbreeding coefficients, congenital malformations, birth weight, gestational age, birth complications, and other demographic factors, obtained by linking cases and controls to vital records and the Amish genealogic registry dating back to the 1700s. Inbreeding coefficients (F) for cases and controls were computed using the path method of tracing common ancestors in the multigenerational pedigrees. Close inbreeding (F greater than or equal to 1/64) was a significant risk factor for prereproductive mortality; odds ratio = 1.55. Using the log-linear model, the effect of close inbreeding on mortality was found to be mediated by three indirect casual mechanisms: Regardless of case-control status, inbreeding was significantly related to congenital malformations (recorded at birth), intrauterine growth retardation (birth weight less than 10th percentile for gestational age), and the occurrence of other deaths in the sibship. In turn, each of these factors was independently related to mortality regardless of inbreeding. No significant direct effect of inbreeding remained after adjustment for these factors. There were no effects of inbreeding on prematurity (less than 37 weeks), or birth complications. This study suggests that inbreeding increases the risk of prereproductive mortality by increasing the risk of intrauterine growth retardation and congenital malformations but not prematurity. The log-linear model provides a useful approach to the analysis of direct and indirect risk factors using biologic mechanisms.

Congenital Abnormalities↗
PubMed1986

Average inbreeding or equilibrium inbreeding?

The equilibrium inbreeding is always higher than the average inbreeding. For human populations with high inbreeding levels, the inbreeding equilibrium is more than 25% higher than the average inbreeding. Assuming no initial inbreeding in the population, the equilibrium inbreeding value is closely approached in 10 generations or less. A secondary effect of this higher inbreeding level is that the equilibrium frequency of recessive detrimental alleles is somewhat lower than expected using average inbreeding.

Consanguinity↗
PubMed1987

Inbreeding and prereproductive mortality in the Old Order Amish. I. Genealogic epidemiology of inbreeding.

Epidemiologic patterns of inbreeding in the Old Order Amish were investigated using a unique genealogic registry of Lancaster County, Pennsylvania, Amish that contains information on 8,163 marriages, dating back to the time of the pioneer migrants in the 1700s and spanning more than 10 generations. The kinship coefficient for each marriage was computed using the path method of tracing common ancestors in the multigenerational pedigrees. Because of extensive genealogic connections, mean kinship coefficients and the proportion of related marriages have increased significantly over time, from 0.004 and 37%, respectively, for marriages before 1850 to 0.012 and 98%, respectively, for marriages after 1950. Demographic factors related to higher kinship levels include young age at marriage, large sibship size for both husband and wife, husband being a farmer, and marriages occurring in the marriage season (November or December). The rise in inbreeding levels in the Amish over time can be uniquely contrasted with the decline in inbreeding in most areas of the world. Furthermore, because some of the demographic factors related to high inbreeding levels may be associated with levels of mortality, such factors have to be taken into account when studying the effects of inbreeding on mortality in the Amish. This study uses an epidemiologic approach to the evaluation of inbreeding patterns in a population over time.

Consanguinity↗
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↗
PubMed1988

Inbreeding and genetic disease in Sottunga, Finland.

The contribution of inbreeding to the prevalence of recessive genetic diseases in the Aland Island parish of Sottunga is investigated. Genealogical data for 3,030 individuals spanning up to 15 generations were used to estimate inbreeding. This small island community shows a low average inbreeding value of .0031 for the period 1725-1975. A cohort analysis shows that inbreeding increased from 1750 to 1900, when maximum inbreeding for those born in Sottunga reached .0057. A sharp decline in inbreeding occurred thereafter. Individuals with island-born parents made the largest contributions to inbreeding in all time periods compared to those with one or two migrant parents. These trends are consistent with changing migration patterns and isolate breakdown in Aland since 1900. An analysis of pedigree development demonstrates that remote consanguinity contributed more to inbreeding through time than close consanguinity. Both the number of common ancestors and the number of paths of relationship between spouses increased dramatically through time, the latter at a much faster rate. The contribution to average inbreeding per path, however, diminished rapidly through time. This analysis indicates that inbreeding does not account for the high incidence of autosomal recessive disorders, such as tapetoretinal disease, found in the parish.

Consanguinity↗
PubMed1991

Effects of a change in the level of inbreeding on the genetic load.

"The effects of inbreeding may not be as noticeable in the first generation as the invigoration immediately apparent after crossing". This statement, published in 1919, has received little attention, and has apparently never been tested empirically, although the reduction of the genetic load of populations by inbreeding is well known in theoretical terms. Because inbreeding increases homozygosity, and hence the effectiveness of selection against recessive or partially recessive detrimental alleles, changes in levels of inbreeding can lead to a reduction in the frequencies of such mutant alleles. This results in equilibration at higher population mean fitness and is referred to as 'purging' populations of their genetic load. Severe inbreeding can also reduce genetic load due to overdominant alleles, provided selection coefficients are not symmetrical at all loci, because alleles giving lower fitness will be reduced in frequency at equilibrium. With either fitness model, however, reduction in genetic load takes time, and the initial effect of an increase in inbreeding is reduced fitness due to homozygosity. There are few data relating to the extent to which fitness is reduced during inbreeding in a set of lines and to how long the reduction lasts before increasing again to the initial level, or higher. Inbreeding experiments involving sib mating in mice and Drosophila subobscura, and successive bottlenecks in house flies have yielded some evidence consistent with the purging hypothesis. Here, we report results of an experiment demonstrating a prolonged time-course of recovery of mean fitness under self-fertilization of a naturally outcrossing plant, and also compare our results with expectations derived by computer calculations. Our results show that the genetic load present in an outcrossing population can be explained only with a high mutation rate to partially recessive deleterious alleles, and that inbreeding purges the population of mutant alleles.

Animals↗
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↗
PubMed1987

Inbreeding and prereproductive mortality in the Old Order Amish. II. Genealogic epidemiology of prereproductive mortality.

The effects of offspring and parental inbreeding on prereproductive mortality (death before age 20 years) in the historical population of the Lancaster County, Pennsylvania, Old Order Amish were investigated using the Amish genealogic registry, which contains information on 42,465 births dating to the time of the pioneer migrants in the 1700s. Inbreeding coefficients for offspring and parents were computed using the path method of tracing common ancestors in the multigenerational pedigrees. In this population, prereproductive mortality declined from about 15% in the late 1800s to about 5% after 1930. Offspring inbreeding was found to be an independent predictor of prereproductive mortality after multivariate adjustment for demographic risk factors for mortality. Moreover, the higher the coefficient, the higher the relative risk of prereproductive death, and the higher the risk of multiple deaths in the same sibship. There was no evidence of declining inbreeding effects over 10 generations of continuous inbreeding, nor of any significant parental inbreeding effects. Because of the high levels of inbreeding, it could be shown that inbreeding accounts for about 40% of all prereproductive deaths in the present population. Genetic load analysis showed an average of about 1.7 lethal equivalents and a mostly mutational load.

Adult↗
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↗