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PubMed1995

Production traits of Holstein cattle: estimation of nonadditive genetic variance components and inbreeding depression.

Additive, dominance, and additive by additive components of genetic variance and inbreeding depression were estimated for production traits from a group of daughters of young sires from the Canadian Holstein population. First lactations of 92,838 cows were analyzed. Three sire and dam models (additive, additive plus dominance, additive plus dominance plus additive by additive genetic effects), all including regression of the trait on inbreeding coefficient of the cow, were used to estimate the effect of inbreeding on production traits. For all production traits, heritability in the narrow sense was overestimated with the simplest model, in which only the additive effect was fitted. Estimates of dominance variance were low for all traits, .9 to 3%. Additive by additive components were low for milk, 2.8%, and fat yield, 2.8%, but higher for protein yield, 6.8%, and for fat, 9%, and protein percentages, 8.9%. Estimates of inbreeding depression for the five traits were similar across all models (-25, -.9, and -.8 kg; .05% and .05% per 1% increase in inbreeding for milk, fat, and protein production and fat and protein percentages, respectively). More accurate estimates of additive effects might be obtained with the inclusion of nonadditive effects for genetic evaluation. If the estimation of inbreeding depression is the only objective, simple models and small random samples of the population may be adequate.

Animals↗

PubMed1988

Inbreeding effects on fertility and hatchability associated with the formation of sublines.

The deleterious effect of inbreeding on fertility and hatchability was studied in a population of Leghorns developed primarily for immunogenetics studies. The 1983 population averaged 42% inbreeding and traced back to only two sires and five dams of the 1965 base population. Up to 1975 (Period 1), the population was maintained as a single-unit closed flock, during which time inbreeding increased an average of 1.44% per year. After 1975 (Period 2), the population was split into five sublines. Inbreeding then increased at the average rate of 2.7% per year. The regression of fertility on inbreeding was -.31 +/- .04 in Period 1 and -.17 +/- .06 in Period 2. Corresponding values for hatchability of fertile eggs were +.08 +/- .05 in Period 1 and -.24 +/- .07 in Period 2. The regression of hatchability of total eggs set was -.15 +/- .04 in Period 1 and -.35 +/- .10 in Period 2. The evidence implies that both fertility and hatchability have a heritable basis. As expected, the deleterious effects of inbreeding on reproduction was more severe in Period 2, with sublining.

Animals↗

PubMedDate not supplied

[Development of the population size, contribution of foreign breeds, inbreeding and degree of relationships of the entire Hanoverian scenthound population registered in the stud book of the kennel club Hirschmann e.V].

The entire dog population of Hanoveranian Scenthounds registered since the foundation of the kennel club Hirschmann in the year 1894 was analysed for the development of the inbreeding and relationship coefficient and the contribution of Hanoveranian Scenthound population of foreign countries. The analyses were performed using all available pedigree information. In the history, the breeding of the Hanoveranian Scenthound was difficult because of the low number of breeding dogs which was additionally reduced during World War I and II. The mean coefficient of inbreeding of the entire German population was 6.35%. From 1950 to 1990, the mean coefficient of inbreeding increased from 8.3% to 9.7%. In the birth years from 1990 to 2002, the mean coefficient of inbreeding decreased slightly to 9.2%. The rates of inbreeding decreased since 1950. For the last 8 generations the increase of the coefficients of inbreeding per generation was 0.71%. The mean degree of relationship of the entire population was 7.17%, whereby values higher than 75% were found. Gene contributions of 8 other European stud books for the Hanoveranian Scenthound could be found in the German population. Hereby, the Austrian Hanoveranian Scenthounds had the largest impact on the German population with 24.4%. The proportion of genes from the German stud book amounted to 67%.

Animals↗

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↗

PubMed1999

The distribution of individual inbreeding coefficients and pairwise relatedness in a population of mimulus guttatus

In order to infer population structure at the individual level, we estimated individual inbreeding coefficients and examined the relationship between geographical distance and genetic relatedness from polymorphic microsatellite data for a population of Mimulus guttatus that has an intermediate selfing rate. Expected heterozygosities for five microsatellites ranged from 0.79 to 0.93. The population inbreeding coefficient was calculated to be 0.19 (SE=0.023). A method-of-moments estimator developed by Ritland (1996b) was used to estimate the distribution of inbreeding among and relatedness between individuals of a natural population. The mean individual inbreeding coefficient (F=0.16) did not differ significantly from the population-level estimate. Most of the individuals appeared to be outbred, and there were very few plants that had estimated inbreeding coefficients greater than one-half. Individuals sampled from one transect showed significantly more inbreeding than individuals sampled along the other (P=0.005). There was no apparent relationship between interplant distance (range: 0-14 m) and mean genetic relatedness between individuals. These results represent the first application of polymorphic microsatellites to estimate fine-scale genetic population structure.

Journal Article↗

PubMed2001

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield.

To understand the genetic basis of inbreeding depression and heterosis in rice, main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers, replicated phenotyping experiments, and the mixed model approach. The mapping populations included 254 F(10) recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers (Zhong 413 and IR64). For both BY and GY, there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations. The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements. The hybrid breakdown (part of inbreeding depression) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids, indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice. A large number of epistatic QTL pairs and a few main-effect QTL were identified, which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation. Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results. First, most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis. Second, most ( approximately 90%) QTL contributing to heterosis appeared to be overdominant. These observations tend to implicate epistasis and overdominance, rather than dominance, as the major genetic basis of heterosis in rice. The implications of our results in rice evolution and improvement are discussed.

Breeding↗

PubMed2003

Effect of inbreeding and endogamy on occlusal traits in human isolates.

OBJECTIVE: To discuss the genetic basis of occlusal traits through analysis of the effects of inbreeding in a subdivided isolated community. SUBJECTS AND METHODS: The sample comprised dental casts of 224 children, aged 7-14 years, from 15 villages of the Island of Hvar, Croatia. MAIN OUTCOME MEASURES: Studied traits were Angle class, overjet, vertical bite, overbite, and crowding/spacing. DESIGN: Children with complete grandparental endogamy (all four grandparents born in the village of residence of the examinee) were compared to children with incomplete grandparental endogamy. In addition, children resident in the group of villages with a high prevalence of inbreeding were compared to children resident in the groups of villages with moderate and low prevalence of inbreeding. RESULTS: In both designs, inbreeding seemed to increase the mean values of overjet, overbite, and vertical bite, while it had little or no effect on crowding/spacing. Angle classes were correlated to inbreeding at the individual level, but this was not supported at the population level. The effects were stronger in the subsample with bilaterally concordant Angle classes. CONCLUSION: The observed inbreeding effects imply that the genetic basis of some occlusal traits is polygenic and, in considerable part, influenced by rare and recessive genetic variants.

Adolescent↗

PubMed2000

Evaluation of major genetic loci contributing to inbreeding depression for survival and early growth in a selfed family of Pinus taeda.

The magnitude of fitness effects at genetic loci causing inbreeding depression at various life stages has been an important question in plant evolution. We used genetic mapping in a selfed family of loblolly pine (Pinus taeda L.) to gain insights on inbreeding depression for early growth and viability. Two quantitative trait loci (QTLs) were identified that explain much of the phenotypic variation in height growth through age 3 and may account for more than 13% inbreeding depression in this family. One of these QTLs maps to the location of cad-nl, a lignin biosynthesis mutation. Both QTLs show evidence of overdominance, although evidence for true versus pseudo-overdominance is inconclusive. Evidence of directional dominance for height growth was noted throughout the genome, suggesting that additional loci may contribute to inbreeding depression. A chlorophyll-deficiency mutation, spf did not appear to be associated with growth effects, but had significant effects on survival through age 3. Previously identified embryonic viability loci had little or no overall effect on germination, survival, or growth. Our results challenge, at least in part, the prevailing hypothesis that inbreeding depression for growth is due to alleles of small effect. However, our data support predictions that loci affecting inbreeding depression are largely stage specific.

Biological Evolution↗

PubMed2004

Inbreeding patterns in La Cabrera, Spain: dispensations, multiple consanguinity analysis, and isonymy.

Marital structure and inbreeding coefficients were analyzed in La Cabrera, an isolated mountain region in northwestern Spain. A total of 5,714 marriages were celebrated from 1880 to 1989 in the 37 parishes of the area. The total frequency of consanguineous marriages (up to the fourth degree) is 23.05%; multiple consanguineous marriages are remarkably common, reaching 5.43% of the total. The first cousin/second cousin ratio (referred to as kinship-type frequencies) is 0.43. The inbreeding values are the highest recorded in Spain and in Europe: alpha3 is 4.82 x 10(-3) for the whole period and alpha4 is 6.78 x 10(-3) for 1880--1919. The temporal trend of inbreeding shows high values (alpha3 > 4.5 x 10(-3)) for a particularly long period (1900--1959) and a rapid decline from 1960 onward. This historical inbreeding trend is clearly related to changes in population size. The frequencies of multiple consanguineous marriages and the analysis of isonymy show that the inbreeding structure is related to geographic and demographic factors. Comparing the results at two hierarchical levels (La Cabrera as a whole and the 37 parishes individually), we conclude that the inbreeding values are affected by internal geographic subdivision of the population (Wahlund effect). Social and cultural factors, such as avoidance of or preference for consanguineous marriages, are less important but depend on the kinship type involved.

Consanguinity↗

PubMed2005

Outbreeding depression, but no inbreeding depression in haplodiploid Ambrosia beetles with regular sibling mating.

In sexual reproduction the genetic similarity or dissimilarity between mates strongly affects offspring fitness. When mating partners are too closely related, increased homozygosity generally causes inbreeding depression, whereas crossing between too distantly related individuals may disrupt local adaptations or coadaptations within the genome and result in outbreeding depression. The optimal degree of inbreeding or outbreeding depends on population structure. A long history of inbreeding is expected to reduce inbreeding depression due to purging of deleterious alleles, and to promote outbreeding depression because of increased genetic variation between lineages. Ambrosia beetles (Xyleborini) are bark beetles with haplodiploid sex determination, strong local mate competition due to regular sibling mating within the natal chamber, and heavily biased sex ratios. We experimentally mated females of Xylosandrus germanus to brothers and unrelated males and measured offspring fitness. Inbred matings did not produce offspring with reduced fitness in any of the examined life-history traits. In contrast, outcrossed offspring suffered from reduced hatching rates. Reduction in inbreeding depression is usually attributed to purging of deleterious alleles, and the absence of inbreeding depression in X. germanus may represent the highest degree of purging of all examined species so far. Outbreeding depression within the same population has previously only been reported from plants. The causes and consequences of our findings are discussed with respect to mating strategies, sex ratios, and speciation in this unusual system.

Analysis of Variance↗

PubMed2004

Inbreeding influences herbivory in Cucurbita pepo ssp. texana (Cucurbitaceae).

In a series of field experiments Diabrotica beetle herbivory was found to influence the magnitude of inbreeding depression in Cucurbita pepo ssp. texana, an annual monoecious vine. Beetles damage flowers and fruits and chew dime-sized holes in leaf tissue between major veins. Inbred plants were found to be more likely to be damaged by beetles and to have more leaves damaged per plant than outcrossed plants. A positive linear association was found between the coefficient of inbreeding and the magnitude of leaf damage, whereas a negative association was found between coefficient of inbreeding and several male and female fitness traits. When pesticides were used to control beetle herbivory, the interaction between coefficient of inbreeding and pesticide treatment was significant for fruit production and marginally significant for pollen quantity per anther. Therefore, the magnitude of inbreeding depression in C. pepo ssp. texana varies depending on the severity of beetle herbivory.

Analysis of Variance↗

PubMed1983

The effect of inbreeding on the BB/W diabetic rat.

The Worcester colony of BB/W diabetic rats has been inbred by brother X sister matings for 12 generations. The litter size at both birth and weaning was dependent on whether the female was normal or diabetic. At the beginning of the inbreeding, the normal females produced 2.1 more young per litter than did the diabetic females, but the eleventh generation of inbreeding this difference had been reduced to 0.68 young. Diabetic males had little influence on litter size. At weaning, the normal mothers had raised litters that had 3.64 more young than the diabetics in the early generations, but this had dropped to 1.48 in later generations. After 11 generations of inbreeding, there was a 1.95 decrease in litter size from normal matings, but only a 0.86 decrease from diabetic matings. The average loss from birth to weaning was one pup for normal females and two pups for diabetic females. The time of onset (median 85 days) has not changed with inbreeding, nor is the onset pattern and severity different in any of the nine inbred lines. The penetrance in the D X D matings did change from 45% in the first five generations to 60% in the next six, but there has been no significant change in generations 6 through 11. Inbreeding changed the results obtained from outcrossing to nondiabetic lines. All crosses produced no diabetics in the F1, but noninbreds produced less than 2% in the F2 and 4% in the BC, whereas inbreds produced 18 to 32% in the BCs. These latter figures are consistent with the ratio of 7:3 expected with 60% penetrance.

Age Factors↗

PubMed1995

The inbreeding decline and average dominance of genes affecting male life-history characters in Drosophila melanogaster.

This paper describes the results of assays of male life-history characters in a large outbred laboratory population of D. melanogaster. Lines of flies homozygous for the entire third chromosome and lines of flies carrying two different third chromosomes were assayed for age-specific male mating ability (MMA), age-specific survivorship, male fertility, and body mass. The results of these assays were used to calculate the inbreeding decline associated with each of these traits, the average dominance of deleterious alleles that affect the traits, the genotypic and environmental components of variance for the homozygous lines, and phenotypic and genotypic correlations among the characters. Significant inbreeding decline was found for all characters except the Gompertz intercept and fertility. Early and late MMA show larger effects of inbreeding than any other trait. The inbreeding load for MMA is about the same magnitude as that for egg-to-adult viability, but is substantially less than that associated with total fitness. The estimated inbreeding decline and average dominance of male life-history characters are comparable to estimates for other Drosophila fitness components.

Alleles↗

PubMed2000

Inbreeding depression due to mildly deleterious mutations in finite populations: size does matter.

We studied the effects of population size on the inbreeding depression and genetic load caused by deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as population size becomes smaller and/or the rate of inbreeding increases. This pattern contrasts with that for the load, which increases as population size becomes smaller but decreases as inbreeding rate goes up. The depression and load both approach asymptotic limits when the population size becomes very large or very small. Numerical results show that the transition between the small and the large population regimes is quite rapid, and occurs largely over a range of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may bias some estimates of the genomic rate of deleterious mutation. These effects could also be important in the evolution of breeding systems in hermaphroditic organisms and in the conservation of endangered populations.

Genetics, Population↗

PubMed1999

The genetic basis of inbreeding depression.

Data on the effects of inbreeding on fitness components are reviewed in the light of population genetic models of the possible genetic causes of inbreeding depression. Deleterious mutations probably play a major role in causing inbreeding depression. Putting together the different kinds of quantitative genetic data, it is difficult to account for the very large effects of inbreeding on fitness in Drosophila and outcrossing plants without a significant contribution from variability maintained by selection. Overdominant effects of alleles on fitness components seem not to be important in most cases. Recessive or partially recessive deleterious effects of alleles, some maintained by mutation pressure and some by balancing selection, thus seem to be the most important source of inbreeding depression. Possible experimental approaches to resolving outstanding questions are discussed.

Animals↗

PubMed2003

Evolution of advantageous alleles affecting population ecological characteristics in partially inbreeding populations.

The fate of advantageous alleles affecting intrinsic growth rate, carrying capacity or intra-specific competitive ability was examined in a partially inbreeding population. Generally, inbreeding had an effect on the evolution of advantageous alleles affecting population ecological characteristics. For example, in a specific underdominant case the number of stable internal equilibria decreased from two to one with only a slight degree of inbreeding. Equilibrium frequencies of stable internal equilibria and stability of fixation equilibria were also affected by the degree of inbreeding. For strictly advantageous alleles, inbreeding had the same qualitative effect on the fixation probability and mean fixation time as predicted in simpler selection models.

Alleles↗

PubMed1994

Purging inbreeding depression and the probability of extinction: full-sib mating.

Inbreeding depression has been a topic of interest in recent years from a number of perspectives, particularly in the captive breeding of endangered species. Generally, the goal of captive breeding is to avoid the detrimental effects of inbreeding depression and to retain genetic variation for future adaptation. However, an important component of another suggested approach to captive breeding is to purge rapidly the population of its genetic load so that its long-term fitness is not compromised. I have examined the effectiveness of purging the genetic load by documenting both the reduction in inbreeding depression and the increase of the probability of extinction when there is continuous full-sib mating. When the genetic load is the result of lethals, the inbreeding depression is quickly purged without a high probability of extinction, except when the total genetic load is high. On the other hand, if the load is due to detrimentals of relatively small effect, the genetic load becomes fixed, the mean fitness is reduced, and the probability of extinction may be greatly increased. In other words, the success of such a programme to purge genetic load without an increase in the probability of extinction is highly dependent upon the genetic basis of inbreeding depression, information that is not readily available for most species.

Adaptation, Physiological↗

PubMed1995

Heat-shock tolerance and inbreeding in Drosophila buzzatii.

The effect of inbreeding on survival after a short-term heat shock was tested for two age groups of the cactophilic fruit fly, Drosophila buzzatii, reared under nonstress conditions. Four inbreeding levels (F = 0, F = 0.25, F = 0.375, F = 0.5) were generated by outcrossing or full-sib mating. All flies were conditioned at 36.5 degrees C for 75 min prior to exposure to stress, to activate the synthesis of heat-shock proteins. These proteins are known to protect cells against stress damage. The younger group of flies were exposed to a thermal stress of 40.7 degrees C for 88 min, 103 min, or 118 min and the older flies to the same temperature only for 88 min or 103 min, as the survival of older flies after heat stress was much lower than that of the younger flies. Survival after heat shock declined with increased inbreeding in both age groups. For the younger flies, the slope of the regression line, F, on survival was lower at higher stress levels. For the older flies, inbreeding effects were similar at both stress levels. Mortality without stress also differed significantly among inbreeding groups, mainly because of a large difference between the F = 0.5 group and all others.

Adaptation, Physiological↗