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PubMed2002

Controlling inbreeding by constraining the average relationship between parents of young bulls entering AI progeny test programs.

In breeding is known to impair the health, fertility, and productivity of dairy cattle and other livestock species. Mating programs can address inbreeding concerns on the farm, at least in the short term, but long-term control of inbreeding in a dairy population requires consideration of relationships between young bulls entering AI progeny test programs. The present study discusses an application of optimal contribution methodology to selection of young AI bulls in the five major US dairy breeds. Elite cows and active AI sires from the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds were considered as potential bull parents. Genetic merit of selected sires and dams was maximized subject to various constraints on the mean additive genetic relationship within the selected group. Relationships between selected parents can be reduced substantially relative to current levels, but the corresponding reduction in genetic merit may be large. This loss in genetic merit occurs due to lower selection intensity, although it is mainly a reflection of a larger number of bull parents (with progeny more evenly distributed among these parents), rather than selection of genetically inferior "outcross" parents that wouldn't otherwise have been considered. Selected parents were generally older and slightly less inbred than those that would have been chosen had inbreeding been ignored. Although severe restrictions on relationships can be costly, in terms of lost genetic progress, it appears that moderate constraints can keep relationships at a manageable level without a significant loss in genetic merit. Cooperation between breed associations and several competing AI companies may be required to facilitate implementation of this methodology in dispersed populations, but if this can be accomplished, prospects for achieving a balance between inbreeding and selection seem positive.

Animals↗
PubMed2003

Analysis of the relationship between type traits, inbreeding, and functional survival in Jersey cattle using a Weibull proportional hazards model.

A Weibull proportional hazards model was used to analyze the effects of 13 linear type traits, final score, and inbreeding on the functional survival of 268,008 US Jersey cows in 2416 herds with first calving from 1981 to 2000. Functional survival was defined as the number of days from first calving until involuntary culling or censoring. The statistical model included the time-dependent effects of herd-year-season of calving, parity by stage of lactation interaction, and within-herd-year quintile for mature equivalent milk yield, as well as the time-independent effects of inbreeding, age at first calving, and linear type traits or final score (analyzed one at a time). Each type trait was divided into 10 classes, and the relative risk of involuntary culling was calculated for animals in each class after accounting for the aforementioned management factors. Type traits with the greatest contribution to the likelihood function were udder depth, fore udder attachment, front teat placement, and udder support. Cows with low scores for these traits had a risk of culling that was 1.3 to 1.8 times that of cows with intermediate scores. Cows with high scores for udder depth and udder support had a risk of culling only 0.7 to 0.85 as great as that of cows with intermediate scores. Intermediate scores were desirable for rear leg set, dairy form, and strength, but stature, rump angle, and rump width had negligible effects on survival. Cows with low final scores had a risk of culling that was 1.35 times that of cows with intermediate scores, whereas cows with high final scores had a risk of culling that was 0.8 times that of cows with intermediate scores. Animals with inbreeding coefficients greater than 10% had a slightly higher risk of culling than animals with inbreeding coefficients less than 5%.

Animals↗
PubMed2007

Nonparametric analysis of the impact of inbreeding on production in Jersey cows.

Under dominance, the relationship between a quantitative trait and the inbreeding coefficient (F) is expected to be linear. Epistasis involving dominance effects or selection against inbred individuals can produce nonlinear patterns in the form of inbreeding depression. The form of the relationship between F and yield traits was explored via local regression (LOESS). First-lactation milk, fat, and protein records from 59,778 Jersey cows with at least 6 generations of known pedigree were used. The F ranged from 0.6 to 34% and median F was 6.3%. The LOESS regressions of predicted residuals from an animal model (empirical best linear unbiased predictions, EBLUP) on F were calculated for each trait; the EBLUP model included fixed herd-year-season, age at calving and DIM effects, and random additive genetic effects. The relationship between EBLUP residuals and inbreeding was complex and nonlinear. Yields were unaffected for F 20% for fat and protein yield. For SCS, both parametric and LOESS fits were consistent with the absence of sizable dominance effects. Effects of inbreeding on performance seemed to be more complex than suggested by previous studies based on linear regression. Results should be interpreted with caution because the data were scarce at high levels of F.

Animals↗
PubMed1994

Genetic response and inbreeding with different selection methods and mating designs for nucleus breeding programs of dairy cattle.

Stochastic simulation was used to study the effect of selection and mating strategy on rates of genetic response and inbreeding with a closed nucleus breeding program for juvenile and adult schemes with 8 males and 64 females selected to produce 1024 progeny (512 females). Selection strategies considered using all available information or only individual and sibling records. Selection of sires was either unrestricted or restricted to between full-sib families. The effect of avoidance of mating of relatives to limit inbreeding was also evaluated. Four mating designs were examined: each dam was mated to 1, 2, 4, or all sires. Mating designs involving one sire per dam and more than one dam per sire were referred to as hierarchical. Use of several mates per dam resulted in a factorial mating design. Selected parents were mated either randomly, best to best, or best to worst. An index based on relative inbreeding to response ratio was used to describe the effectiveness of strategies for reducing inbreeding relative to changes in rates of genetic response. Strategies that lower index values were preferred and include selection on BLUP or approximations of BLUP and factorial mating designs that involve the random mating of dams to several sires. Factorial mating designs were effective for a range of heritabilities. Avoidance of matings of full sibs and restriction of selection of sires to between full-sib families enabled appreciable reductions in the index. Nucleus breeding programs based entirely on the selection of juveniles were not indicated because they had higher index values than adult schemes.

Animals↗
PubMed2001

[Association of microsatellite genomic heterozygosity with inbred pig performance under successive inbreeding].

Genomic scanning using microsatellites was carried out in a pig family that has undergone 5 successive generations of inbreeding. A total of 56 microsatellite markers were utilized, which were derived from swine chromosome 01, 02, 11, 13, 17, 18 and gave a considerable coverage of these chromosomes. Genomic heterozygosity was estimated as an average of marker heterozygosity over all 6 chromosomes. Analysis of variance using a generalized linear model indicated that genomic heterozygosity was positively and significantly associated with slaughter weight (SWT) and average daily slaughter gain (ADSG), but inconsistently and non-significantly associated with backfat depth (BFDP). Association effects of GH on SWT and ADSG increased from generation 1 to generation 2, and, then, reduced gradually with generations while levels of inbreeding accumulated. The maximum effect was observed in generation 2, which was estimated to be 22.43 kg for SWT and 0.132 kg/d for ADSG. The effect of marker heterozygosity on SWT and ASDG differed dramatically from chromosome to chromosome: the largest effect was observed with chromosome 13 (i.e. 6.306 kg for SWT and 0.032 kg/d for ADSG), followed by chromosome 01, 17, 18, 02 and 11. Marker heterozygosity was not found to be significantly associated with BFDP for all chromosomes. These results give rise to three implications. First, genes (e.g. QTL) contributing to traits of economic importance are not equally distributed among these chromosomes, which represents the difference in determination of quantitative traits across chromosomes or at DNA level. Second, the association of genomic or marker heterozygosity with pig performance varies from chromosome to chromosome, or with generations of inbreeding. This phenomenon provides an evidence that heterozygosity-performance association is not straight-forward, but rather complex as a result of complicated gene actions and interactions, and sometimes may even be much more complicated when confounded and misled by inabequate or improper markers utilized. Last, decreased heterozygous advantage or heterozygous disadvantage, in some cases, is very much likely as a result of the high linkage disequilibrium under high levels of inbreeding, where one or several deleterious alleles might be linked with neutural markers in much high probability.

Animals↗
PubMed2002

[Mating system and inbreeding retrogression of casuarina equisetifolia plantation, an introduced species in Xiamen].

Casuarina equisetifolia, an introduced species, is a good shelter species planted along coastlines due to its enduring sandy and saline habitats. Decline was, however, observed in C. equisetifolia plantations in many areas since 1980's. Mating system and inbreeding retrogression of a plantation of C. equisetifolia in Xiamen and their roles in the decline of C. equisetifolia forests were thus researched using allozyme technique. Multilocus outcrossing rate was 0.622, lower than that expected from related species, indicating a mixed-mating system, and more inbreeding caused through this introduction. Calculations from electrophoresis data showed that very a high inbreeding retrogression occurred in the C. equisetifolia plantation, indicating that inbreeding an its subsequent retrogression played an important role in the decline of C. equisetifolia plantation. Alleviating the decline through genotype species-introduction was also proposed.

Biological Evolution↗
PubMed2004

Inbreeding and susceptibility to osteoporosis in Croatian island isolates.

The aim of this study was to investigate a recessive genetic component in susceptibility to osteoporosis (OP) by comparing its prevalence in isolated villages of three Croatian islands: Brac, Hvar and Korcula with different levels of inbreeding. A random sample of 20-30% adults from 14 villages was obtained, including a total of 1,389 examinees. The average inbreeding coefficient (F) of examinees from each village population was estimated using Wright's path method (based on genealogical information). The morphometry of the metacarpal bones was performed on hand-wrist radiographs of both hands in all examinees. OP was defined as values of cortical index smaller than 2 standard deviations based on distribution of values in examinees of the same sex under 45 years of age. Mean values of cortical index (CI) and prevalence of OP (both standardized by age and weighted for the sample size) in each village were correlated to the mean inbreeding coefficient (F). The coefficient of correlation (r) between F values and CI was -0.28 in males (p = 0.08) and -0.42 in females (p = 0.005), and between F and OP prevalence 0.32 in males (p < 0.001) and 0.43 in females (p < 0.001). These results indicate a trend of increased susceptibility to osteoporosis with increasing level of inbreeding in isolated communities of Croatian islands.

Adult↗
PubMedDate not supplied

[Influence of inbreeding on litter size and the proportion of stillborn puppies in dachshunds].

In the present study, factors influencing the litter size of puppies and the number and the proportion of stillborn puppies per litter were analysed in normally sized German dachshounds. Data was available for litters registered from 1987 to 2002 in the German dachshound kennel club. The records studied here contained 42,855 litters. The mean litter size was 5.22 +/- 2.01 puppies. The proportion of puppies born dead per litter was 6.6%. The age of dam, the puppy's year and month of birth, the hair type and the inbreeding coefficients of the puppies, the sire and the dam were significant on the litter size and the number and the proportion of puppies born dead. The litter size decreased and the percentage of puppies born dead increased with increasing inbreeding coefficients of the puppies, dams and sires. The increase of the inbreeding coefficient of the puppies by 1% led to a 0.06% higher percentage of puppies born dead per litter. The increase of the inbreeding coefficients of the dam and the sire by 1% resulted in 0.02% and 0.007% higher percentages of puppies born dead. Young and older dams had smaller litter size than middle-aged dams. The percentage of puppies born dead per litter increased with an increasing age of the dam. In the recent birth years, the litter size and the percentage of puppies born dead increased in German dachshounds.

Animals↗
PubMedDate not supplied

Inbreeding coefficients and degree of consanguineous marriages in Spain: a review.

The contribution of consanguineous marriages corresponding to uncle-niece or aunt-nephew (C12), first cousin (C22), first cousin once removed (C23), and second cousin (C33) to the inbreeding coefficient (alpha) was analyzed from a sample of Spanish areas and periods. Multiple regressions were performed taking as independent variables the different degrees of consanguinity previously selected (C12, C22, C23, and C33) and as dependent variable the inbreeding coefficient (alpha). According to the results obtained for any degree and period, rural frequencies always surpass urban. However, the pattern is similar in both areas. In the period where consanguinity was more elevated (1890-1929) the C22/C33 ratio increased. Its variation is not due to C22 and C33 changes in the same way. In rural areas, this ratio surpasses the expected value by a factor of 2-3, but in urban areas it was 7-10 times larger, in some cases due to migration. While in rural Spain the C33 frequency was approximately 1.5 times C22, in cities C22 was 1.5 times C33. The best fit among the various types of consanguineous matings and alpha involves a lineal relationship. Regardless of the number of variables contributing significantly to alpha, C22 matings are always present. Moreover, their standardized (beta) coefficients are the highest. The above indicates that this consanguineous relationship conditions the inbreeding coefficient the most. In the period of greater consanguinity, close relationships, uncle-niece C12, and first cousin once removed (C23) make a significant contribution to alpha. In rural Spain second cousins (C33) always significantly determined alpha; however, in cities the inbreeding variation was mainly due to C12 and C23.

Consanguinity↗
PubMed1983

Inbreeding studies in Brasilian schoolchildren.

We present results of comparisons between consanguineous and control couples and their children in Southern Brasil. Multiple regression, t-test and chi 2 analyses were applied to the data. The following variables were investigated; Parents: structure of first cousin marriages, latitude and longitude of birthplaces, cohabitation time, rurality, marriage age, occupation, number of liveborn children, and frequency of twinning. Schoolchildren: clinical data as classified into 24 discontinuous traits, each one subdivided into two categories (number and severity), and seven continuous traits (weight, height, pulse rate, respiratory rate, systolic pressure, diastolic pressure, and temperature); nutrition indices and biotype; family names; intelligence tests and school performance; birth order, age, hair color, hair type, eye color, and skin color; twinning in the sibship, and infant mortality among sibs of the propositi. Our study showed a) nonrandomness of consanguineous marriages as detected on structural, racial, geographical, and temporal levels; b) a heavy mutational load of about 1.5 lethons acting on infant mortality; c) no inbreeding effect on morbidity in general (with a possible exception of "ear morbidity", including hearing deficit); d) a modest inbreeding depression on height (a decrease of 2 cm with an increase of 10% of inbreeding); 3) a suggestion of inbreeding depression on "intelligence".

Brazil↗
PubMed2006

Inbreeding and surnames: a projection into Easter Island's past.

The population of Easter Island is one of the most interesting extant human communities due to its unique demographic history, its geographic isolation, and the development of an incomparable culture characterized by the towering "Moais" and its enigmatic writing. Following the colonization of its population by Polynesians from the Mangarevan Islands in the 5th century AD, the island remained isolated up until the middle of the 20th century. Under these conditions, with endogamy levels fluctuating between 61.04-96.54% and given such a small population, a high rate of inbreeding, and consequently, an elevated level of genetic relationships would be expected. Using data from church and civil records, we calculated the consanguinity of the population of Rapa Nui. The results of this analysis do not support the hypothesis of a high level of consanguinity (alpha = 0.00028 and F(t) = 0.0007, with F(r) = 0.00586 and F(n) = -0.00519), suggesting instead the existence of a strategy used to avoid marriage between close relatives. To explain these observations, the structure and exchange dynamics of the population were studied in the tribes, known locally as "Mata." The results of this analysis suggest a tendency toward the avoidance of inbreeding within tribes, in order to decrease the rate of endogamy in each group. This is consistent with ethnographic observations from the beginning of the 20th century that support the existence of strict regulations to prevent inbreeding between closely related individuals. Furthermore, we confirm that this situation dates back to a period before the "refounding" of Easter Island. Our results demonstrate that conditions of geographical isolation are not in themselves sufficient to produce an elevated inbreeding coefficient, revealing Easter Island as an interesting example of how cultural rules can shape the genetic structure of a population.

Cluster Analysis↗
PubMed1989

Behavioral and reproductive differences in mice as a function of inbreeding.

Twenty brother-sister pairs of mice were randomly selected from a genetically heterogeneous population of mice to begin a schedule of inbreeding that lasted for six generations (F = 0 to F = .732). We examined a number of indices of reproductive behavior and found that all declined as a function of inbreeding. Specifically, there was a consistent decline in the number of fertile matings, in the number of offspring that survived to weaning, and in the weight of the pups at the time of weaning (21 days of age). We also examined a number of behaviors with the following results: there was a systematic increase in the number of trials required to learn an active avoidance task and a consistent decrease in the number of trials required to extinguish this habit. We observed a statistically significant difference in the retention of a passive avoidance habit, but these results were quite variable and not consistent across generations of inbreeding. Finally, we observed that inbreeding had little effect on measures of locomotor behavior.

Animals↗
PubMed1998

The impact of consanguinity and inbreeding on perinatal mortality in Karachi, Pakistan.

Close consanguineous unions continue to be extremely common in much of West Asia, including Pakistan. However, the impact of inbreeding on offspring mortality, particularly perinatal mortality, remains poorly documented. This paper attempts to measure the mortality risks associated with consanguinity and inbreeding while controlling for the effects of other potential confounders. The study sample comprises a multi-ethnic population residing in selected squatter settlements of Karachi. The adjusted odds ratio for perinatal mortality in the offspring of women married to their first cousins was 2.0 [95% CI 1.5, 2.6]. When parental inbreeding was also taken into account, the adjusted odds ratio for perinatal mortality increased further. Analysis of a subsample of data limited to pregnancies to women aged 35 years or above (at the time of the survey) showed that, despite adjustment for important biological and socio-demographic factors, both consanguinity and inbreeding remained important predictors of perinatal mortality in the offspring. Implications of the present study for further research are highlighted.

Adolescent↗
PubMed2001

New method of estimating inbreeding in large semi-isolated populations with application to historic Britain.

The purpose of this paper is to introduce a new method of estimating inbreeding in large, relatively isolated, populations over historic times, to demonstrate its application, and indicate some of its limitations and future developments. The method is based on the "paradox" of genealogy, and requires only that the variation of the population size be known, at least reasonably well, over an extended historic period. In this study a method has been developed to model this "paradox" which allows an estimation of the minimum level of inbreeding necessary for a given population curve in terms of values of Pearl's coefficients for each generation. As an example, the method is applied to the population of Britain. It is found that the frequency of siblings occurring in the same generation of a pedigree varies with the population size according to the Fermi-Dirac equation of statistical physics. The effect of introducing a single known estimate of inbreeding into the model is to make the otherwise diverse results for both the actual numbers of ancestors in a generation and the corresponding coefficients of inbreeding to converge.

Consanguinity↗
PubMedDate not supplied

Inbreeding and kinship in Saguenay-Lac-St-Jean: a study of newborn samples 1956-1971.

Samples of individuals born between 1956 and 1971 proportional to the population size of each parish of Saguenay-Lac-St-Jean (SLSJ) were extracted from a computerized population register. The mean inbreeding and kinship coefficients were calculated for each sample. Our results showed that inbreeding and kinship were unevenly distributed in the SLSJ region. The highest values of inbreeding and kinship were found in Bas-Saguenay, an isolated subregion of SLSJ, and in rural parishes. It was also found that the mean inbreeding and kinship coefficients had higher values in parishes that opened between 1872 and 1901 than those opened earlier or later.

Analysis of Variance↗
PubMedDate not supplied

Inbreeding and developmental stability in a small human population.

Inbreeding coefficients are reported for all members of the isolated Havasupai tribe of northern Arizona (USA), based upon pedigrees which are as deep as eight generations. Because inbreeding has been repeatedly shown to reduce developmental homeostasis in a large number of species, we ask if the degree of inbreeding in the Havasupai is associated with reduced developmental stability. Fluctuating asymmetry in two dermatoglyphic traits suggests that inbreeding significantly compromises developmental homeostasis in this population.

Analysis of Variance↗
PubMedDate not supplied

Autosomal recessive disorders in Saguenay-Lac-Saint-Jean (Quebec, Canada): estimation of inbreeding from isonymy.

The total inbreeding coefficient of a group of 574 individuals with autosomal recessive disorders (ARD) from Saguenay-Lac-Saint-Jean, a geographically isolated region of northeastern Quebec, was estimated from isonymy and compared to the mean inbreeding coefficient calculated from the genealogies. Its value was compared to that of 1722 matched controls. The total inbreeding coefficient was similar in both ARD and control groups, but higher than the values calculated from the genealogies. Most of the increase was due to the random component of inbreeding. This isonymy study confirmed that the high frequency of ARD in Saguenay-Lac-Saint-Jean is mainly the result of founder effect and genetic drift.

Case-Control Studies↗
PubMed2000

Whole-genome characterization of embryonic stage inbreeding depression in a selfed loblolly pine family.

Inbreeding depression is important in the evolution of plant populations and mating systems. Previous studies have suggested that early-acting inbreeding depression in plants is primarily due to lethal alleles and possibly epistatic interactions. Recent advances in molecular markers now make genetic mapping a powerful tool to study the genetic architecture of inbreeding depression. We describe a genome-wide evaluation of embryonic viability loci in a selfed family of loblolly pine (Pinus taeda L.), using data from AFLP markers from an essentially complete genome map. Locus positions and effects were estimated from segregation ratios using a maximum-likelihood interval mapping procedure. We identified 19 loci showing moderately deleterious to lethal embryonic effects. These loci account for >13 lethal equivalents, greater than the average of 8.5 lethal equivalents reported for loblolly pine. Viability alleles show predominantly recessive action, although potential overdominance occurs at 3 loci. We found no evidence for epistasis in the distribution of pairwise marker correlations or in the regression of fitness on the number of markers linked to deleterious alleles. The predominant role of semilethal alleles in embryonic inbreeding depression has implications for the evolution of isolated populations and for genetic conservation and breeding programs in conifers.

Crosses, Genetic↗