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PubMed1995

Comparison of evaluation-selection systems for maximizing genetic response at the same level of inbreeding.

Use of improved methods of genetic evaluation and intense selection lead to higher rates of genetic change but also lead to higher rates of inbreeding. A number of methods have been proposed to attain high rates of genetic response with moderate or low inbreeding (i.e., restrict the number of close relatives selected, use false high heritability in the genetic evaluation, use assortative mating, adjust estimated breeding values for the relationship with those already selected, avoid matings of related individuals, and increase the number of parents selected). These various methods were compared here using stochastic simulation of an infinitesimal genetic model. The results were studied graphically plotting response against inbreeding, so allowing comparison of the methods at each of a range of inbreeding levels. None of the methods was best over all conditions. At high rates of inbreeding and with a fixed number of sires, several of the methods gave large decreases in inbreeding for small losses in response. However, these were matched by simply increasing the number of sires selected. There is an optimum response-inbreeding "front" attained by several methods, and this front seems hard to breach. Characterization of the front would be useful in designing selection programs.

Algorithms↗
PubMed1998

Effects of inbreeding and heterozygosity on preweaning traits in a closed population of Herefords under selection.

Records of five inbred lines at the Livestock and Range Research Laboratory were used to evaluate effects of inbreeding and heterozygosity on preweaning traits. Members of each line were descendants of a single founder Hereford bull. A total of 8,065 records of birth weight and 7,380 records of preweaning daily gain and weaning weight were analyzed by derivative-free REML using a model that included fixed effects of sex, combination of year and month of birth and parity of dam, with covariates for direct and maternal genetic fractions of inheritance from the genetic groups, inbreeding, and heterozygosity fractions. Heterozygosity fractions were computed for crosses between lines. The random model effects were direct and maternal genetic and uncorrelated maternal permanent environmental and temporary environmental. Direct inbreeding and heterozygosity fractions averaged .098 and .343, and maternal inbreeding and heterozygosity fractions averaged .075 and .294. Regression coefficients of traits on direct and maternal inbreeding fractions were -5.8 +/- 1.1 and -4.7 +/- 1.3 for birth weight, -.189 +/- .031 and -.252 +/- .039 for preweaning daily gain, and -44.5 +/- 6.6 and -56.1 +/- 8.4 kg for weaning weight. Estimates for direct heritability, maternal heritability, and direct-maternal genetic correlations were .37, .12, and -.01 for birth weight; .16, .25, and -.27 for daily gain; and .17, .26, and -.21 for weaning weight. Results suggest that heterosis represents recovery of accumulated inbreeding depression. Results also indicate that selection can overcome inbreeding depression and antagonism exists between direct and maternal genetic effects for preweaning traits.

Animals↗
PubMed2002

Inbreeding effects on the parameters of the growth function in three strains of Iberian pigs.

The growth performance of inbred pigs coming from full-sib matings was compared to that of contemporary animals coming from the same sires mated to control dams. The animals belong to three strains of Iberian pigs with different histories of previous inbreeding. The data consisted of 1,615 weight records between 50 and 250 d of age from 229 pigs. The statistical model assumed the two parameters that describe the linear growth function (a = intercept, b = slope) as different traits (weight at 120 d and daily gain) and the analysis was carried out in a Bayesian framework via Gibbs sampling. The means of the posterior distribution of heritabilities, common litter environmental coefficients, and genetic correlation were 0.328 (h(2)a), 0.332 (h2b), 0.084 (c(2)a), 0.060 (c(2)b) and 0.973 (rhoG). Inbreeding depression, expressed as the performance decrease relative to the mean, per 10% increase of the inbreeding coefficient, was -3.18, -2.31 and -5.37% for weight at 120 d (a), and -3.16, -2.08 and -6.49% for daily gain (b) in each of the three strains. The results indicate that the inbreeding effects are dependent on the level of previous inbreeding, the more previous inbreeding, the less inbreeding depression.

Animals↗
PubMed2004

Effect of inbreeding on the incidence of retained placenta in Friesian horses.

This study was motivated by the hypothesis that the incidence of retained placenta (RP) in Friesian horses is associated with inbreeding. The objectives were to 1) calculate the inbreeding rate in the total registered Friesian horse population; 2) study the association of the inbreeding coefficient of the foal and the mare with the incidence of RP; and 3) study the heritability of RP in Friesian mares after normal foalings. Data from the total registered Friesian horse population from 1879 to 2000 (52,392 individuals) were collected from the registration files of the Friesian Horse Studbook. In 1999 and 2000, 495 parturitions in 436 mares were studied. From 1979 to 2000, the inbreeding rate of the total population was 1.9% per generation. The regression coefficients for the regression of the incidence of RP on inbreeding coefficients of the foal and the mare were 0.12 +/- 0.052 and -0.016 +/- 0.019, respectively. Mean heritability estimates of RP as a foal trait and as a mare trait were 0.046 +/- 0.088 and 0.105 +/- 0.123, respectively. It was concluded that, in order to avoid a further increase in the incidence of RP in Friesian mares, a decrease in the inbreeding rate by increasing the effective breeding population is required. Furthermore, the findings indicate that the high incidence of RP in Friesian horses is at least partly a result of inbreeding.

Animals↗
PubMed1989

Effects of inbreeding and heterosis in Hereford females on fertility, calf survival and preweaning growth.

Effects of inbreeding and heterosis and the difference between them were estimated by comparing linecross (L), topcross (T), inbred (I) and control line (C) Hereford females for reproductive and preweaning growth traits of their progeny. Inbred females (average inbreeding coefficient = 26.5%) originated from four single-sire inbred lines. Control females (average inbreeding coefficient = 6.9%) were produced by a four-sire, 60-cow line. Linecross females were produced from all possible reciprocal crosses of the I lines. Topcross females were produced by mating I bulls to C cows. Differences in pregnancy rate among these lines were not detected. Effects of maternal heterosis were positive for both prenatal and postnatal survival. The weaning rate by L females exceeded the weaning rate by I females as a result. Prenatal survival was reduced in calves from I females relative to those from C females, resulting in corresponding differences in birth and weaning rates. Differences in the magnitudes of maternal heterosis and inbreeding effects were not detected, except for birth weight. For birth weight the effect of maternal inbreeding was of greater magnitude than the effect of maternal heterosis. Within the I and C lines regressions of pregnancy rate, prenatal survival, birth rate, postnatal survival, weaning rate, weaning weight/cow exposed, birth weight and weaning weight on the inbreeding coefficients of the cows indicated significant inbreeding depression on all traits except pregnancy rate and postnatal survival.

Animals↗
PubMed1984

Inbreeding of artificially bred dairy cattle in the northeastern United States.

Inbreeding coefficients of artificially bred Ayrshire, Guernsey, Holstein, Jersey, and Brown Swiss cows were calculated from relationships between sires and maternal male ancestors. Percentages of inbred cows and average inbreeding coefficients of inbred cows were: Ayrshire, 26 and 11%; Guernsey, 11 and 4%; Holstein, 31 and 1%; Jersey 23 and 2%; and Brown Swiss, 23 and 2%. Percentages of inbred cows and average inbreeding coefficients of all cows increased over time whereas average coefficients of inbred cows decreased over time. These temporal trends may be due in part to having more pedigree information available for cows born in later years. Effects of inbreeding on milk and fat yields of first lactation (2 times milked, 305-day mature equivalent), 48-mo stayability, and first calving interval were estimated with a model including effects for fixed herd-year-seasons, fixed sire and maternal grandsire groups, random sires and maternal grandsires within groups, and random residual. Regression coefficients of milk (kg), fat (kg), 48-mo stayability (proportion of cows surviving to 48 mo of age), and calving interval (days) on inbreeding coefficient (%) were: Ayrshire -27.1, -1.2, -.005, .23; Guernsey -19.3, -.97, -.007, .27; Holstein -21.1, -.78, -.003, .09; Jersey -14.8, -.80, -.002, .63; and Brown Swiss -39.5, -1.36; -.011, .03. There is no cause for concern over current inbreeding, but active inbreeding is not recommended.

Animals↗
PubMed2002

Strong inbreeding depression in a Daphnia metapopulation.

The deleterious effects of inbreeding have long been known, and inbreeding can increase the risk of extinction for local populations in metapopulations. However, other consequences of inbreeding in metapopulations are still not well understood. Here we show the presence of strong inbreeding depression in a rockpool metapopulation of the planktonic freshwater crustacean Daphnia magna, which reproduces by cyclical parthenogenesis. We conducted three experiments in real and artificial rockpools to quantify components of inbreeding depression in the presence and the absence of competition between clonal lines of selfed and outcrossed genotypes. In replicated asexual populations, we recorded strong selection against clones produced by selfing in competition with clones produced by outcrossing. In contrast, inbreeding depression was much weaker in single-clone populations, that is, in the absence of competition between inbred and outbred clones. The finding of a competitive advantage of the outbred genotypes in this metapopulation suggests that if rockpool populations are inbred, hybrid offspring resulting from crosses between immigrants and local genotypes might have a strong selective advantage. This would increase the effective gene flow in the metapopulation. However, the finding of low inbreeding depression in the monoclonal populations suggests that inbred and outbred genotypes might have about equal chances of establishing new populations.

Animals↗
PubMed2003

Inbreeding, developmental stabilty, and canalization in the sand cricket Gryllus firmus.

Inbreeding, the mating of close relatives, is known to have deleterious effects on fitness traits in organisms. Developmental stability (DS) and canalization may represent two processes that allow an organism to maintain a stable development that will produce the fittest phenotype. Inbreeding is thus expected to affect either DS or canalization. We tested if inbreeding affects DS and canalization using an inbreeding experiment on the cricket Gryllus firmus. We compared mean length, fluctuating asymmetry (as an index of DS), and morphological variation (as an index of canalization) of four limb traits between seven highly inbred lines, their F1 crosses, and outbred lines originated from the same stock population and maintained in the same environmental conditions. We show evidence for moderate inbreeding depression on the four measures of leg length. The nonsystematic difference in fluctuating asymmetry indices between breed types indicates that inbreeding or heterozygosity did not affect DS, or that fluctuating asymmetry is not a reliable index of DS. In contrast, inbreeding appears to affect canalization, as shown by the significantly higher variation in inbred lines compared to other lines. Identical low variation values in the crossbred and outbred lines indicate that heterozygosity could affect canalization. High variation in morphological variation and fluctuating asymmetry within crossbred or inbred lines, however, suggest the effect of recessive deleterious alleles on both canalization and DS. Although the strong correlation in morphological variation among traits suggests that identical genetic mechanisms govern canalization for all the limb traits, the absence of significant correlation in fluctuating asymmetry among traits causes us to reject this hypothesis for DS. For most of the traits, morphological variation and fluctuating asymmetry were not significantly correlated, which support the hypothesis that canalization and DS consist in two distinct mechanisms.

Analysis of Variance↗
PubMed2004

Five reasons why inbreeding may have considerable effect on post-reproductive human health.

As the genetic architecture of common complex diseases of late onset is emerging through intensive research, it is intriguing to assess the predicted effect of inbreeding on those diseases. In this paper, we propose five reasons why we believe inbreeding may have a considerable effect on post-reproductive human health. (i) The joint effect of inbreeding depression on all polygenic quantitative phenotypes that confer risk for late-onset diseases is predicted to be multiplicative rather than additive. (ii) The "genetic load" of rare "Mendelian" variants with large deleterious effects in post-reproductive adults is unknown, but could be much greater than expected as these variants were invisible to selection through human history. (iii) Deleterious effects resulting from autozygosity in hundreds of affected rare recessive variants of small effect under common disease/rare variant (CD/RV) hypothesis could result in epistatic effects that could jointly impair capacity to compensate against environmental risks. (iv) Heterozygote advantage in loci under balancing selection could be reduced by inbreeding. (v) Published empirical evidence in animals and humans consistently report large inbreeding effects on late-onset traits. Since inbreeding is common in many populations and the effects of inbreeding depression could substantially contribute to disease burden and reduced life expectancy we believe there is now a clear need for further genetic epidemiological research in humans to investigate this issue.

Animals↗
PubMed1998

Relationships among parental inbreeding, parental behaviour and offspring viability in oldfield mice

Studies of inbreeding depression have traditionally suffered from two weaknesses. First, they usually confound offspring deficiencies with parental ones; second, they neglect the possible role of behaviour in inbreeding depression. In the present study, I examined the relationship among parental inbreeding, offspring viability and parental behaviour in two subspecies of the monogamous oldfield mouse, Peromyscus polionotus. Parental inbreeding was separated from any offspring inbreeding effects through both experimental design and analysis. Dams performed more parental behaviour than did sires, and maternal behaviour had a stronger effect on offspring survival than did paternal behaviour. Maternal behaviour was more buffered to the effects of inbreeding than was paternal behaviour; that is, parental behaviour of inbred females was not compromised. In contrast, inbred males showed substantial deficits in parental behaviour, but this did not put their offspring at risk. Although inbred females had lower reproductive success than outbred females, this effect was not manifest in terms of lower offspring viability. Therefore, inbreeding depression manifests itself through deficits on traits of adult females other than maternal care. A possible physiological basis for these findings is hypothesized.Copyright 1998 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed2004

Minimising inbreeding in small populations by rotational mating with frozen semen.

Mating plans are investigated in order to minimize inbreeding in small populations when frozen semen is available. For a single dam line it was found that specific sire rotations minimized the asymptotic level of inbreeding when semen is used repeatedly from certain generations. When semen of N foundation (G0) sires is used rotationally over generations it is shown that the inbreeding level asymptotes to 1/(2(N+1) - 2). However, if only G0 sires are used then all genes will eventually descend from the founder sires. Inbreeding can be reduced further by using sires from generation one (G1) and later as this retains genes from the founder dams in the long-term gene pool. If semen from NG0 sires and N unrelated G1 sons is used rotationally then inbreeding asymptotes to (2(N-1) + 1)/(2(2N+1) - 2). When there are more founder dams than sires, the asymptotic inbreeding can be reduced even further by using the semen of half-sib G1 sires in rotation. Optimal rotations using full-sib G1 sires or generation 2 (or later) sires will lower the asymptotic inbreeding also, but generally not by much. It was found that when unlimited frozen semen from a specified group of sires was available, the optimal mating plan was achieved by selecting each generation the sire with the least co-ancestry with the current female of the dam line.

Algorithms↗
PubMed2004

Does heterozygosity estimate inbreeding in real populations?

Many recent studies report that individual heterozygosity at a handful of apparently neutral microsatellite markers is correlated with key components of fitness, with most studies invoking inbreeding depression as the likely underlying mechanism. The implicit assumption is that an individual's inbreeding coefficient can be estimated reliably using only 10 or so markers, but the validity of this assumption is unclear. Consequently, we have used individual-based simulations to examine the conditions under which heterozygosity and inbreeding are likely to be correlated. Our results indicate that the parameter space in which this occurs is surprisingly narrow, requiring that inbreeding events are both frequent and severe, for example, through selfing, strong population structure and/or high levels of polygyny. Even then, the correlations are strong only when large numbers of loci (~200) can be deployed to estimate heterozygosity. With the handful of markers used in most studies, correlations only become likely under the most extreme scenario we looked at, namely 20 demes of 20 individuals coupled with strong polygyny. This finding is supported by the observation that heterozygosity is only weakly correlated among markers within an individual, even in a dataset comprising 400 markers typed in diverse human populations, some of which favour consanguineous marriages. If heterozygosity and inbreeding coefficient are generally uncorrelated, then heterozygosity-fitness correlations probably have little to do with inbreeding depression. Instead, one would need to invoke chance linkage between the markers used and one or more gene(s) experiencing balancing selection. Unfortunately, both explanations sit somewhat uncomfortably with current understanding. If inbreeding is the dominant mechanism, then our simulations indicate that consanguineous mating would have to be vastly more common than is predicted for most realistic populations. Conversely, if heterosis provides the answer, there need to be many more polymorphisms with major fitness effects and higher levels of linkage disequilibrium than are generally assumed.

Computer Simulation↗
PubMed2003

Effects of inbreeding on coastal Douglas fir growth and yield in operational plantations: a model-based approach.

In advanced generation seed orchards, tradeoffs exist between genetic gain obtained by selecting the best related individuals for seed orchard populations, and potential losses due to subsequent inbreeding between these individuals. Although inbreeding depression for growth rate is strong in most forest tree species at the individual tree level, the effect of a small proportion of inbreds in seed lots on final stand yield may be less important. The effects of inbreeding on wood production of mature stands cannot be assessed empirically in the short term, thus such effects were simulated for coastal Douglas fir [ Pseudotsuga menziesii var. menziesii (Mirb.) Franco] using an individual-tree growth and yield model TASS (Tree and Stand Simulator). The simulations were based on seed set, nursery culling rates, and 10-year-old field test performance for trees resulting from crosses between unrelated individuals and for inbred trees produced through mating between half-sibs, full-sibs, parents and offspring and self-pollination. Results indicate that inclusion of a small proportion of related clones in seed orchards will have relatively low impacts on stand yields due to low probability of related individuals mating, lower probability of producing acceptable seedlings from related matings than from unrelated matings, and a greater probability of competition-induced mortality for slower growing inbred individuals than for outcrossed trees. Thus, competition reduces the losses expected due to inbreeding depression at harvest, particularly on better sites with higher planting densities and longer rotations. Slightly higher breeding values for related clones than unrelated clones would offset or exceed the effects of inbreeding resulting from related matings. Concerns regarding the maintenance of genetic diversity are more likely to limit inclusion of related clones in orchards than inbreeding depression for final stand yield.

Analysis of Variance↗
PubMed1990

Prediction of rates of inbreeding in selected populations.

A method is presented for the prediction of rate of inbreeding for populations with discrete generations. The matrix of Wright's numerator relationships is partitioned into 'contribution' matrices which describe the contribution of the Mendelian sampling of genes of ancestors in a given generation to the relationship between individuals in later generations. These contributions stabilize with time and the value to which they stabilize is shown to be related to the asymptotic rate of inbreeding and therefore also the effective population size, Ne approximately 2N/(mu 2r + sigma 2r), where N is the number of individuals per generation and mu r and sigma 2r are the mean and variance of long-term relationships or long-term contributions. These stabilized values are then predicted using a recursive equation via the concept of selective advantage for populations with hierarchical mating structures undergoing mass selection. Account is taken of the change in genetic parameters as a consequence of selection and also the increasing 'competitiveness' of contemporaries as selection proceeds. Examples are given and predicted rates of inbreeding are compared to those calculated in simulations. For populations of 20 males and 20, 40, 100 or 200 females the rate of inbreeding was found to increase by as much as 75% over the rate of inbreeding in an unselected population depending on mating ratio, selection intensity and heritability of the selected trait. The prediction presented here estimated the rate of inbreeding usually within 5% of that calculated from simulation.

Animals↗
PubMed2002

The use of frozen semen to minimize inbreeding in small populations.

In this study, we compared the average coancestry and inbreeding levels for two genetic conservation schemes in which frozen semen from a gene bank is used to reduce the inbreeding in a live population. For a simple scheme in which only semen of generation-0 (G0) sires is used, the level of inbreeding asymptotes to 1/(2N), where N is the number of newborn sires in the base generation and rate of inbreeding goes to zero. However, when only sires of G0 are selected, all genes will eventually descend from the founder sires and all genes from the founder dams are lost. We propose an alternative scheme in which N sires from generation 1 (G1), as well as the N sires from G0, have semen conserved, and the semen of G0 and G1 sires is used for dams of odd and even generation numbers, respectively. With this scheme, the level of inbreeding asymptotes to 1/(3N) and the genes of founder dams are also conserved, because 50% of the genes of sires of G1 are derived from the founder dams. A computer simulation study shows that this is the optimum design to minimize inbreeding, even if semen from later generations is available.

Animals↗
PubMed2003

Outcrossing rate and inbreeding depression in the herbaceous autotetraploid, Campanula americana.

Polyploidy in angiosperms is frequently associated with an increase in self-compatibility. Self-fertilization can enhance polyploid establishment, and theory predicts reduced inbreeding depression in polyploids relative to diploids. Therefore, we may expect mating systems that promote self-fertilization or mixed-mating in polyploid species. However, few studies have measured polyploid mating systems and inbreeding depression. We report the outcrossing rate and inbreeding depression for Campanula americana, a self-compatible protandrous herb. Allozyme genotypes suggest that C. americana is an autotetraploid with tetrasomic inheritance. We found that the multilocus outcrossing rate, t(m)=0.938, did not differ from unity. This result was unexpected since previous work demonstrated that pollinators frequently move from male- to female-phase flowers on the same plant, that is, geitonogamy. Self and outcross pollinations were conducted for three populations. Offspring were germinated in controlled conditions and grown to maturity in pots in nature. Inbreeding depression was not significant for most seed and germination characters. However, all later life traits except flowering date differed between inbred and outcrossed individuals resulting in a 26% reduction in cumulative fitness for inbred plants. Limited early- and moderate later-life inbreeding depression suggest that it is buffered by the higher levels of heterozygosity found in an autotetraploid. C. americana appears to have a flexible mating system where within flower protandry and/or cryptic self-incompatibility result in a high outcrossing rate when pollinators are abundant, but self-compatibility and limited inbreeding depression maintain reproductive success when mates are limited.

Campanulaceae↗
PubMed2001

Inbreeding depression in two populations of Arenaria uniflora (Caryophyllaceae) with contrasting mating systems.

I used parallel family-structured crossing designs to investigate the relative performance of self and outcross progeny in selfing and predominantly outcrossing populations of the annual plant Arenaria uniflora. The selfer population experienced much lower inbreeding depression (delta = 0.05 +/- 0.02 SE) than the outcrossers (delta = 0.19 +/- 0.02 SE). The negative association between genetic load and selfing rate suggests that purgable partially recessive alleles are the primary source of inbreeding depression, as does its late expression in both populations. Inbreeding depression in the selfer population, which naturally consists of highly inbred lines, was used to calculate the mean dominance (h = 0.33) and incidence rate (U = 0.30) of deleterious mutations. In the outcrosser population, significant variation among individuals in the expression of inbreeding depression may reflect lineage-specific differences in inbreeding history or, more probably, random variation in mutational load. The low (<< 0.5) inbreeding depression of outcrossers suggests that the maintenance of a mixed mating system in some A. uniflora populations and the evolution of nearly cleistogamous self-pollination in others may reflect local pollinator-mediated selection for selfing rather than the constant 3:2 genetic advantage invoked by many models.

Analysis of Variance↗
PubMed2002

The effects of inbreeding on testicular sperm concentration in Peromyscus polionotus.

Inbreeding effects on fitness have most often been quantified via juvenile mortality. However, inbred adults may suffer from inbreeding depression if their fertility or fecundity is compromised as a consequence of inbreeding. Here, the effects of inbreeding on male fertility in oldfield mice, Peromyscus polionotus, were examined. Testicular sperm concentration was assessed in 93 males, 68 of which were paired for breeding. Forty of the 68 paired males failed to produce offspring. Total testicular sperm count, sperm count (g testis)(-1), and testis mass all declined significantly with increasing inbreeding coefficient. Sperm concentration did not significantly impact reproductive success. Although sperm concentration in males of most species can decline to low levels before reproductive impairment is detectable, the declines in testicular sperm concentration found here suggest that inbreeding can affect fertility in adult males. Furthermore, monitoring testicular sperm concentration could provide a mechanism to monitor potential declines in reproductive performance before population-level reproductive success is irreparably impaired. The implications for the management of small, captive and wild populations may be substantial.

Animals↗