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1.
The epistatic kinship describes the probability that chromosomal segments of length x in Morgan are identical by descent. It is an extension from the single locus consideration of the kinship coefficient to chromosomal segments. The parameter reflects the number of meioses separating individuals or populations. Hence it is suggested as a measure to quantify the genetic distance of subpopulations that have been separated only few generations ago. Algorithms for the epistatic kinship and the extension of the rules to set up the rectangular relationship matrix are presented. The properties of the epistatic kinship based on pedigree information were investigated theoretically. Pedigree data are often missing for small livestock populations. Therefore, an approach to estimate epistatic kinship based on molecular marker data are suggested. For the epistatic kinship based on marker information haplotypes are relevant. An easy and fast method that derives haplotypes and the respective frequencies without pedigree information was derived based on sampled full‐sib pairs. Different parameters of the sampling scheme were tested in a simulation study. The power of the method decreases with increasing segment length and with increasing number of segments genotyped. Further, it is shown that the efficiency of the approach is influenced by the number of animals genotyped and the polymorphism of the markers. It is discussed that the suggested method has a considerable potential to allow a phylogenetic differentiation between close populations, where small sample size can be balanced by the number, the length, and the degree of polymorphism of the chromosome segments considered.  相似文献   

2.
Coefficients of inbreeding are commonly used in mixed-model methods for forming inverses of Wright's numerator relationship matrix and transformation matrices used in variance component estimation and national cattle evaluation. Computation of exact coefficients of inbreeding from very large data sets has been believed to be too expensive or too difficult a task to perform. Approximate methods have been used instead. The effects of using approximation methods for inbred data that appear in national cattle data sets are demonstrated. An algorithm is given for the computation of inbreeding coefficients for large data sets. The algorithm feasibly computes inbreeding coefficients for large data sets even on small computing architectures.  相似文献   

3.
Non-additive genetic effects are usually ignored in animal breeding programs due to data structure (e.g., incomplete pedigree), computational limitations and over-parameterization of the models. However, non-additive genetic effects may play an important role in the expression of complex traits in livestock species, such as fertility and reproduction traits. In this study, components of genetic variance for additive and non-additive genetic effects were estimated for a variety of fertility and reproduction traits in Holstein cattle using pedigree and genomic relationship matrices. Four linear models were used: (a) an additive genetic model; (b) a model including both additive and epistatic (additive by additive) genetic effects; (c) a model including both additive and dominance effects; and (d) a full model including additive, epistatic and dominance genetic effects. Nine fertility and reproduction traits were analysed, and models were run separately for heifers (N = 5,825) and cows (N = 6,090). For some traits, a larger proportion of phenotypic variance was explained by non-additive genetic effects compared with additive effects, indicating that epistasis, dominance or a combination thereof is of great importance. Epistatic genetic effects contributed more to the total phenotypic variance than dominance genetic effects. Although these models varied considerably in the partitioning of the components of genetic variance, the models including a non-additive genetic effect did not show a clear advantage over the additive model based on the Akaike information criterion. The partitioning of variance components resulted in a re-ranking of cows based solely on the cows’ additive genetic effects between models, indicating that adjusting for non-additive genetic effects could affect selection decisions made in dairy cattle breeding programs. These results suggest that non-additive genetic effects play an important role in some fertility and reproduction traits in Holstein cattle.  相似文献   

4.
The influence of selection and epistasis on inbreeding depression estimates   总被引：1，自引：0，他引：1  
Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coefficients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coefficients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coefficient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was difficult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.  相似文献   

5.
The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47 794 l and a pedigree of 14 622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection.  相似文献   

6.
The inbreeding coefficients are considered in breeding decisions, and the inverse numerator relationship matrix A ?1 is a prerequisite for breeding value estimation. Polyandry and haploid males are among the specifics of relationships between honey bees. Brascamp and Bijma (2014) averaged out the manifold possible relationships among honey bees that appear to have the same parents in a pedigree and assigned a single entry in A to animals that behave as a unit, for example, the workers of a hive. Their methods of calculation connected full‐sibs in the variance matrix of the Mendelian sampling terms D , via nonzero off‐diagonal elements. This impedes the inversion of A and the closely connected calculation of inbreeding coefficients, because efficient algorithms for this task take D to be a diagonal matrix. Memory limitations necessitate their use for large data sets. We adapted the quickest of them to the block diagonal matrix D , that is postulated for the honey bee. To our knowledge, the presented algorithm is the first one that facilitates the method of Brascamp and Bijma (2014) on large data sets.  相似文献   

7.
利用RAD-seq简化基因组测序鉴定狼山鸡保种群个体基因组SNP标记,计算个体(间)分子近交系数和分子亲缘系数,结合系谱信息组建高、低近交两个试验组。分析后代繁殖性状近交衰退系数,评价近交对繁殖性状的影响。结果显示:利用FROH、FGRM、FHOM和FUNI四种分子近交系数结合亲缘系数kin估算的后代分子近交系数较为一致。低近交组后代的平均分子近交系数小于0.04,高近交组(6个家系)后代的平均分子近交系数介于0.14~0.25。近交对各繁殖性状的效应表现并不一致。高近交组后代母鸡开产日龄、300日龄产蛋数发生显著衰退(P<0.05,P<0.01),且与分子近交系数呈显著相关(P<0.05,P<0.01);开产体重和开产蛋重未发生显著性衰退(P>0.05)。研究结果为进一步探讨狼山鸡繁殖性状近交衰退分子机制提供了基础。  相似文献   

8.
ABSTRACT

The Fjord horse originates from Norway but forms a global population due to several small populations in foreign countries. There exists no information about the additive relationship and the genetic variance between these subpopulations. By collecting blood samples from Norwegian and Swedish Fjord horses, a sample of 311 Norwegian and 102 Swedish horses gave 485,918 SNPs available for analysis. Their inbreeding coefficients were calculated and compared to the pairwise coancestry and the shared genomic segments. The effective population size was almost similar with the two methods in the Norwegian Fjord horse population (63 and 71), but very different in the Swedish population (269 and 1136) and unprecise due to a much smaller number of observations. The study showed that coancestry from shared genomic segments can be used to estimate additive genetic relationship and genetic variation within and between the global populations of the Fjord horse.  相似文献   

9.
Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi‐generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP‐derived metrics of homozygosity (r = 0.814–0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality‐checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.  相似文献   

10.
本文对亲缘协方差的来源及相关公式了进行了系统推导,并概括了应用亲缘协方差公式 计算动物亲缘系数及近交系数的规则。文章提示亲缘方差法的基础仍在于莱特的通径亲缘系数法。本法的优势在于能对种群的个体进行化的操作运算、简捷、快速、准确,并特别适合于利用计算机求解。但莱特的通径系数法则适于针对种群中的辊个体进行计算。故三种方法各有其适用的场合,应分别情况灵活加以把握和应用。  相似文献   

11.
In this study, the effect of different measurements of ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models were used to estimate the effect of ancestral inbreeding, and the estimated regression coefficient of phenotypic data on different measurements of ancestral inbreeding was used to quantify the effect of ancestral inbreeding. The first model included only one measurement of inbreeding, whereas the second model included the classical inbreeding coefficients and one alternative inbreeding coefficient. The third model included the classical inbreeding coefficients, the interaction between classical inbreeding and ancestral inbreeding, and the classical inbreeding coefficients of the dam. Phenotypic data for this study were collected from February 1998 to December 2008 on three large commercial milk farms. During this time, 36 477 calving events were recorded. All calves were weighed after birth, and 8.08% of the calves died within 48 h after calving. Calving ease was recorded on a scale between 1 and 4 (1 = easy birth, 4 = surgery), and 69.95, 20.91, 8.92 and 0.21% of the calvings were scored with 1, 2, 3 and 4, respectively. The average inbreeding coefficient of inbred animals was 0.03, and average ancestral inbreeding coefficients were 0.08 and 0.01, depending on how ancestral inbreeding was calculated. Approximately 26% of classically non‐inbred animals showed ancestral inbreeding. Correlations between different inbreeding coefficients ranged between 0.46 and 0.99. No significant effect of ancestral inbreeding was found for calving ease, because the number of animals with reasonable high level of ancestral inbreeding was too low. Significant effects of ancestral inbreeding were estimated for birthweight and stillbirth. Unfavourable effects of ancestral inbreeding were observed for birthweight. However, favourable purging effects were estimated for stillbirth, indicating that purging could be partly beneficial for genetic improvement of stillbirth.  相似文献   

12.
(Co)variance components, direct and maternal breed additive, dominance, and epistatic loss effects on preweaning weight gain of beef cattle were estimated. Data were from 478,466 animals in Ontario, Canada, from 1986 to 1999, including records of both purebred and crossbred animals from Angus, Blonde d'Aquitaine, Charolais, Gelbvieh, Hereford, Limousin, Maine-Anjou, Salers, Shorthorn, and Simmental breeds. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effects. Estimates of direct and maternal additive genetic, maternal permanent environmental and residual variances, expressed as proportions of the phenotypic variance, were 0.32, 0.20, 0.12, and 0.52, respectively. Correlation between direct and maternal additive genetic effects was -0.63. Breed ranking was similar to previous studies, but estimates showed large SE. The favorable effects of direct and maternal dominance (P < 0.05) on preweaning gain were equivalent to 1.3 and 2.3% of the phenotypic mean of purebred calves, respectively. The same features for direct and maternal epistatic loss effects were -2.2% (P < 0.05) and -0.1% (P > 0.05). The large SE of breed effects were likely due to multicollinearity among predictor variables and deficiencies in the dataset to separate direct and maternal effects and may result in a less reliable ranking of the animals for across breed comparisons. Further research to identify the causes of the instability of estimates of breed additive, dominance, and epistatic loss genetic effects, and application of alternative statistical methods is recommended.  相似文献   

13.
For models with only additive direct genetic effects, the rules of Westell combined with the Q-P transformation can be used to calculate the coefficients of mixed-model equations corresponding to the inverse elements of the numerator relationship matrix and group effects that are used to account for selection on ancestors that do not have records. Groups generally can be assigned on the basis of most recent ancestors without records. When maternal effects are in the model, most recent female ancestors without records contribute maternal effects to their progeny. If the vectors for additive direct and maternal effects do not include the same animals, numerator relationship matrices for direct and maternal effects and between direct and maternal effects are different. Even if they are the same, the Q-P transformation and Westell's rules do not lead to simplification for calculation of the coefficient matrix unless group assignment is the same for direct and maternal effects. This result can be achieved by including each female ancestor with offspring having records in both vectors and by assigning both of her parents to the same group she would have been assigned for a model including only direct effects. This strategy is equivalent to assigning group effects similarly for both direct and maternal effects and allows making use of the computational efficiency available from the Q-P transformation and Westell's rules, which are similar to Henderson's rules for calculating the inverse of the numerator relationship matrix.  相似文献   

14.
The aim of this study was to separate marked additive genetic variability for three quantitative traits in chickens into components associated with classes of minor allele frequency (MAF), individual chromosomes and marker density using the genomewide complex trait analysis (GCTA) approach. Data were from 1351 chickens measured for body weight (BW), ultrasound of breast muscle (BM) and hen house egg production (HHP), each bird with 354 364 SNP genotypes. Estimates of variance components show that SNPs on commercially available genotyping chips marked a large amount of genetic variability for all three traits. The estimated proportion of total variation tagged by all autosomal SNPs was 0.30 (SE 0.04) for BW, 0.33 (SE 0.04) for BM, and 0.19 (SE 0.05) for HHP. We found that a substantial proportion of this variation was explained by low frequency variants (MAF <0.20) for BW and BM, and variants with MAF 0.10–0.30 for HHP. The marked genetic variance explained by each chromosome was linearly related to its length (R2 = 0.60) for BW and BM. However, for HHP, there was no linear relationship between estimates of variance and length of the chromosome (R2 = 0.01). Our results suggest that the contribution of SNPs to marked additive genetic variability is dependent on the allele frequency spectrum. For the sample of birds analysed, it was found that increasing marker density beyond 100K SNPs did not capture additional additive genetic variance.  相似文献   

15.
Data of the Elsenburg Dormer sheep stud, which was kept closed since inception, were collected over a period of 62 years (1941–2002). The breed is a composite, resulting from a cross of Dorset Horn rams with South African Mutton Merino ewes. These data were analysed to quantify the increase in actual level of inbreeding and to investigate the effect of inbreeding on phenotypic values, genetic parameters and estimated breeding values. After editing 11954 pedigree, 11721 birth weight (BW) and survival, 9205 weaning weight (WW) and 7504 reproduction records were available for analysis. The mean level of inbreeding (F) of all animals over all years was 16%; 14% for dams and 16% for sires. Mean, minimum and maximum F for the lambs in 1997 (when 3 rams from outside were introduced) were 22%, 21% and 24% respectively. Estimates of inbreeding depression for individual inbreeding of 1% were − 0.006 kg for birth and − 0.093 kg for weaning weight respectively. These were the only estimates that were significantly (P < 0.01) different from zero. No significant effects of inbreeding on the other traits were found. There were virtually no differences in the genetic parameters estimated when fitting the two models (inclusion or exclusion of inbreeding coefficients as covariates). Estimates of the phenotypic variance differed slightly for WW between the two models. Ranking of animals were studied for weaning weight when the two models were considered. The high correlation coefficients (0.990) indicate that the use of inbreeding coefficients did not cause important changes in ranking of animals and sires for WW. It was concluded that slow inbreeding (rate of inbreeding of approximately 1.53% per generation over 19 generations) allows natural selection to operate and to remove the less fit animals. At any given mean level of F, less inbreeding depression would then be expected among the individuals who accumulated the inbreeding over a larger number of generations. Nevertheless, inbreeding coefficients should be considered when mating decisions are made, to limit the possible deleterious effects of inbreeding on productive and reproductive traits and to detect animals “resilient to” higher levels of inbreeding.  相似文献   

16.
Severity of inbreeding depression depends on the hidden (i.e., recessive) genetic load carried by a population. If the load is distributed unevenly among founder genomes, or founder-lines were exposed to variable amounts of selection, descendants from different founders may be differentially affected by inbreeding. Between-founder heterogeneity in inbreeding depression for production traits and somatic cell score in milk (SCS) was studied using records from 59,788 Jersey cows. Inbreeding coefficients (F) were partitioned into components due to four founders, plus a remainder. A two-stage statistical analysis was performed. First, empirical best linear unbiased predictions (EBLUP) of residuals for milk, fat and protein yield, and for SCS, were computed using linear models including fixed effects of herd–year–season, age at calving and days in milk, and random additive genetic effects of individual cows. Second, models with total and partial inbreeding coefficients as predictor variables were fitted to EBLUP residuals, for each trait. Tests of differences between slopes indicated that regressions of milk, fat and protein yield on partial inbreeding coefficients were heterogeneous; SCS did not exhibit inbreeding depression. Hence, alleles contributing to inbreeding depression for production in this Jersey population seem to be associated with specific founders. This indicates that a homogeneous effect of inbreeding on production may be an incorrect statistical specification in genetic evaluation models that attempt to account for inbreeding depression. Furthermore, the observed variability between effects of partial inbreeding due to different founders implies that inbreeding effects on yield traits may be due to alleles with major effects.  相似文献   

17.
OBJECTIVE: To determine relative impact of genetic, common-litter, and within-litter factors on puppy mortality. ANIMALS: 2,622 Boxer puppies of 413 litters born during a 14-month period. PROCEDURE: For each puppy, pedigree was determined, and litter in which it was born was registered. Overall mortality and mortality per specific cause of death were analyzed by use of a model that included an additive genetic effect, common-litter effect, within-litter effect, and regression of mortality on inbreeding coefficient. Relative importance of the effects was determined from estimates of the variance in mortality explained by each factor. RESULTS: 22% of the puppies died before reaching 7 weeks old. Stillbirth was the most frequent cause of death, followed by infection. Most observed differences were attributable to within-litter factors, which explained 67% of the variance in death attributable to infection and < or = 96% of the variance in death attributable to asphyxia. Common-litter factors were more important than additive genetic factors. Variance attributed to common-litter factors ranged from 2% for cheiloschisis, palatoschisis, or cheilopalatoschisis to 30% for death attributable to infection, and variance attributed to additive genetic factors ranged from 0% for asphyxia to 14% for euthanatized because of white color. Inbreeding coefficient had a significant effect on death attributable to infection, which increased 0.26% for each percentage increase of inbreeding. CONCLUSIONS AND CLINICAL RELEVANCE: Additive genetic factors have less impact on preweaning mortality than common-litter factors, which in turn have less impact than within-litter factors. Mortality attributable to infection increases significantly with increases in inbreeding.  相似文献   

18.
Breeding circles allow genetic management in closed populations without pedigrees. In a breeding circle, breeding is split over sub‐populations. Each sub‐population receives breeding males from a single sub‐population and supplies breeding males to one other sub‐population. Donor‐recipient combinations of sub‐populations remain the same over time. Here, we derive inbreeding levels both mathematically and by computer simulation and compare them to actual inbreeding rates derived from DNA information in a real sheep population. In Veluws Heideschaap, a breeding circle has been in operation for over 30 years. Mathematically, starting with inbreeding levels and kinships set to zero, inbreeding rates per generation (ΔF) initially were 0.29%–0.47% within flocks but later converged to 0.18% in all flocks. When, more realistically, inbreeding levels at the start were high and kinship between flocks low, inbreeding levels immediately dropped to the kinship levels between flocks and rates more gradually converged to 0.18%. In computer simulations with overlapping generations, inbreeding levels and rates followed the same pattern, but converged to a lower ΔF of 0.12%. ΔF was determined in the real population with a 12 K SNP chip in recent generations. ΔF in the real population was 0.29%, based on markers to 0.41% per generation based on heterozygosity levels. This is two to three times the theoretically derived values. These increased rates in the real population are probably due to selection and/or the presence of dominant rams siring a disproportionate number of offspring. When these were simulated, ΔF agreed better: 0.35% for selection, 0.38% for dominant rams and 0.67% for both together. The realized inbreeding rates are a warning that in a real population inbreeding rates in a breeding circle can be higher than theoretically expected due to selection and dominant rams. Without a breeding circle, however, inbreeding rates would have been even higher.  相似文献   

19.
This study compares two genetic management scenarios for species kept in herds, such as deer. The simulations were designed so that their results can be extended to a wide range of zoo populations. In the first scenario, the simulated populations of size 3 × 20, 6 × 40 or 20 × 60 (herds × animals in herd) were managed with a rotational mating (RM) scheme in which 10%, 20% or 50% of males were selected for breeding and moved between herds in a circular fashion. The second scenario was based on optimal contribution theory (OC). OC requires an accurate pedigree to calculate kinship; males were selected and assigned numbers of offspring to minimize kinship in the next generation. RM was efficient in restriction of inbreeding and produced results comparable with OC. However, RM can result in genetic adaptation of the population to the zoo environment, in particular when 20% or less males are selected for rotation and selection of animals is not random. Lowest rates of inbreeding were obtained by combining OC with rotation of males as in the RM scheme. RM is easy to implement in practice and does not require pedigree data. When full pedigree is available, OC management is preferable.  相似文献   

20.
Variance and covariance components were estimated for weaning weight from Senepol field data for use in the reduced animal model for a maternally influenced trait. The 4,634 weaning records were used to evaluate 113 sires and 1,406 dams on the island of St. Croix. Estimates of direct additive genetic variance (sigma 2A), maternal additive genetic variance (sigma 2M), covariance between direct and maternal additive genetic effects (sigma AM), permanent maternal environmental variance (sigma 2PE), and residual variance (sigma 2 epsilon) were calculated by equating variances estimated from a sire-dam model and a sire-maternal grandsire model, with and without the inverse of the numerator relationship matrix (A-1), to their expectations. Estimates were sigma 2A, 139.05 and 138.14 kg2; sigma 2M, 307.04 and 288.90 kg2; sigma AM, -117.57 and -103.76 kg2; sigma 2PE, -258.35 and -243.40 kg2; and sigma 2 epsilon, 588.18 and 577.72 kg2 with and without A-1, respectively. Heritability estimates for direct additive (h2A) were .211 and .210 with and without A-1, respectively. Heritability estimates for maternal additive (h2M) were .47 and .44 with and without A-1, respectively. Correlations between direct and maternal (IAM) effects were -.57 and -.52 with and without A-1, respectively.  相似文献   

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