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1.
One widely used measure in genetic analyses of livestock species is the inbreeding coefficient. Computation costs of inbreeding coefficients are of importance for large populations. Very recently, a ‘direct’ method for computing inbreeding coefficients was modified using a relatively efficient method to construct lists of ancestors in which the integrity of chronological order within each ancestral path is kept. Using simulated data, the computational efficiency of the recently modified algorithm was investigated by comparing it with three other algorithms – the original direct algorithm, its previously modified algorithm and another direct algorithm. The recently modified algorithm became considerably faster than the original algorithm and its previous modification when the number of generations increased, and it was fast relative to the other direct algorithm when the average number of generations and family size were not large. When only animals born in the most recent year were evaluated with the knowledge of inbreeding coefficients for their ancestors, the recently modified algorithm outperformed the other algorithms, indicating its possible advantage in updating situations.  相似文献   

2.
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   

3.
The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST) and the effective population size (Ne) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (FROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (FROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.  相似文献   

4.
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   

5.
Inbreeding has detrimental effects on a number of economically important traits. W iggans et al. (1995) estimated inbreeding depression of ?29 kg, ?1.08 kg and ?0.97 kg for each 1% increase of inbreeding for the traits milk, fat and protein yield, respectively, across several dairy cattle breeds. For post-weaning gain in Hereford cattle, the depression was ?0.24 kg (G engler et al. 1998). For the number of piglets born alive, 21-day litter weight, and days to 104.5 kg, it was ?0.023, ?0.052 and 0.21, respectively (C ulbertson et al. 1998). Inbreeding also adversely impacts reproductive traits, such as delayed puberty, reduced conception rates, higher likelihood of losing established pregnancies, increased mortality of calves and lowered bull fertility (Y oung et al. 1969). National genetic evaluations involve animals with incomplete pedigrees. Regular inbreeding algorithms (RA) based on the definition of W right (1922), such as those by Q uaas (1976), calculate the inbreeding of animals with at least one parent missing as zero. Even if an animal has both parents known, its inbreeding will be underestimated if some of its ancestors are unidentified. If the proportion of missing parents is large, the inbreeding trend in a population could be seriously underestimated. Subsequently, losses from inbreeding would be underestimated, and steps to slow the increase of inbreeding, such as using sires that are less related to the general population or mating less-related animals (T oro and P erez -E nciso , 1990; G rundy et al. 1994; M euwissen and S onneson 1998; V an R aden and S mith 1999), may be delayed. In particular, use of a mating system can result in matings adjusted for both inbreeding and dominance (M isztal et al. 1999). In populations that use AI substantially, unidentified parents may not differ genetically from identified parents, on average. Therefore the real average inbreeding in animals with unidentified parent(s) may be similar to their contemporaries with both parents known. V an R aden (1992) proposed an algorithm (VRA), where the inbreeding of animals whose parent(s) are unknown is equal to the mean inbreeding of their contemporaries with known parents. Contemporaries are stratified along unknown parent groups (UPG). VRA has been applied to a few US dairy breeds (V an R aden 1992; W iggans et al. 1995). The calculated inbreeding for the youngest Holstein animals was 3.7% with RA and increased to 4.2% with VRA (V an R aden 1992). The increase was small because the number of unidentified animals was small. However, the performance of VRA in recovering inbreeding lost for a range of incomplete pedigrees has not been evaluated. The objectives of this study were (i) to determine average inbreeding coefficients when pedigrees are increasingly more incomplete; (ii) to assess the efficacy of VRA in recovering these inbreeding coefficients; and (iii) to determine the mean inbreeding using the two inbreeding algorithms in a large beef population.  相似文献   

6.
Tying‐up is a condition that primarily affects the muscles of horses. In this study, the heritability of the Tying‐up syndrome in the Thoroughbred racehorse was estimated by Bayesian analysis with Gibbs sampling based on the threshold model for binary traits. The data used were the clinical data in racehorses diagnosed by veterinarians of the Racehorse Clinics of Japan Racing Association from 2000 to 2003. The health status of the Tying‐up was treated as a binary trait. In the genetic analysis, the effect of changing the amount of the pedigree or inbreeding information on the estimation of heritability was investigated, too. The heritability estimates with non‐zero probability in the posterior densities were approximately 0.16–0.18 in minimum, suggesting that the heritability of the Tying‐up is not zero at least. The posterior density distributions of the heritability estimates were generally more pointed and sharp with using inbreeding coefficients than without using it, suggesting that more stable estimations were obtained when inbreeding coefficients were used. Among the different amounts of pedigree and inbreeding information, the heritabilities obtained with three or four generations of pedigree using inbreeding coefficients seems to be preferable, i.e. heritability of 0.42 or 0.43 for Tying‐up.  相似文献   

7.
Inbreeding coefficients of animals are required in many genetic analyses of livestock records. A modification of Colleau's indirect algorithm to compute inbreeding coefficients in large populations is presented. With overlapping generations, the modified algorithm evaluated all progeny of each sire simultaneously in one back and forth exploration of a reduced pedigree. Simulation for a relatively large number of generations, different number of sires, family sizes and mating designs showed that Colleau's algorithm was faster (from 1.2 to 143 times) than two other algorithms under comparison (Tier, modified Meuwissen and Luo), in all situations investigated. Modifying Colleau's algorithm considerably decreased computation time (from 50 to 89%), resulting in a very fast algorithm. The number of sires mostly affected computational efficiency of the modified algorithm, whereas family size and mating design had virtually no effect. In the updating situation, when only animals born in the last year were evaluated, given known inbreeding coefficients for the other, the modified algorithm was also fast compared with the other three algorithms. Memory requirements for the algorithms were also discussed.  相似文献   

8.
In real data, inbreeding is usually underestimated because of missing pedigree information. A method adapted to the dairy cattle situation is presented to approximate inbreeding when the stored population pedigree is incomplete. Missing parents in incomplete pedigrees were given a dummy identification and assigned to groups (up to nine for a given birth date of progeny). These groups were linked to contemporary reference groups with known parents. An explicit model considered that polygenic breeding values in a censored group were centred on a function of the average breeding value in the corresponding reference group and deviated independently. Inbreeding coefficients were obtained progressively over birth dates starting from founders. For each date considered, the parameters pertaining to its groups were computed using the parameters already obtained from groups belonging to the previous dates. The updating algorithms were given in detail. An indirect method was implemented to expedite mass computations of the relationship coefficients involved (MIM). MIM was compared to Van Raden's (VR) method using simulated populations with 20 overlapping generations and different rates of missing sires and dams. In the situation of random matings, the average inbreeding coefficients by date obtained by MIM were close to true values, whereas they were strongly underestimated by VR. In the situation of assortative matings, MIM gave average inbreeding coefficients moderately underestimated, whereas those of VR's method were still strongly underestimated. The main conclusion of this study adapted to the situation of dairy cattle with incomplete pedigrees was that corrections for inbreeding and coancestry coefficients are more efficient with an explicit appropriate genetic model than without.  相似文献   

9.
Using pedigree data, the inbreeding coefficients of 715 Austrian dual‐purpose Simmental (Fleckvieh) bulls stationed in two artificial insemination (AI) centres in Upper and Lower Austria were calculated and incorporated in statistical models for the analysis of semen quality. Five semen quality parameters (volume, concentration, motility, number of spermatozoa per ejaculate and percentage of viable spermatozoa) of approximately 30 000 ejaculates, used in two separate data sets, were investigated. The mixed model included the fixed effects age class of the bull, bull handler, semen collector, month and year of collection, number of collection per bull and day, time interval since last collection, the linear continuous effect of the inbreeding coefficient of the bull, interactions between age class and month, and age class and interval since last collection, respectively, as well as the random effect of the bull and the random residual effect. Non‐linear effects of inbreeding were significant for motility only. Despite the quite low inbreeding coefficients (mean 1.3%), all semen quality traits showed inbreeding depression, in four of the five traits significantly in at least one of the data sets. The magnitude of inbreeding depression was small, which might partly be caused by the low inbreeding levels and a potential pre‐selection of the bulls in the AI centres. However, monitoring of inbreeding depression on fertility traits is recommended to avoid unrecognized deterioration of such traits.  相似文献   

10.
Model-based accuracy, defined as the theoretical correlation between true and estimated breeding value, can be obtained for each individual as a function of its prediction error variance (PEV) and inbreeding coefficient F, in BLUP, GBLUP and SSGBLUP genetic evaluations. However, for computational convenience, inbreeding is often ignored in two places. First, in the computation of reliability = 1-PEV/(1 + F). Second, in the set-up, using Henderson's rules, of the inverse of the pedigree-based relationship matrix A . Both approximations have an effect in the computation of model-based accuracy and result in wrong values. In this work, first we present a reminder of the theory and extend it to SSGBLUP. Second, we quantify the error of ignoring inbreeding with real data in three scenarios: BLUP evaluation and SSGBLUP in Uruguayan dairy cattle, and BLUP evaluations in a line of rabbit closed for >40 generations with steady increase of inbreeding up to an average of 0.30. We show that ignoring inbreeding in the set-up of the A- inverse is equivalent to assume that non-inbred animals are actually inbred. This results in an increase of apparent PEV that is negligible for dairy cattle but considerable for rabbit. Ignoring inbreeding in reliability = 1-PEV/(1 + F) leads to underestimation of reliability for BLUP evaluations, and this underestimation is very large for rabbit. For SSGBLUP in dairy cattle, it leads to both underestimation and overestimation of reliability, both for genotyped and non-genotyped animals. We strongly recommend to include inbreeding both in the set-up of A- inverse and in the computation of reliability from PEVs.  相似文献   

11.
Analysis of variance (ANOVA) and symmetric differences squared (SDS) methods for estimating genetic and environmental variances and covariances associated with beef cattle weaning weight were compared via simulation. Simulation was based on the pedigree and record structure of 503 beef weaning weights collected over 19 yr from a university herd. The SDS methodology was used with four models. The simplest model included direct (g) and maternal (gm) additive genetic effects, genetic covariance between direct and maternal additive genetic effects (sigma ggm), permanent maternal environmental effects (m) and temporary environmental effects (e). The second model also allowed for a nonzero environmental covariance (sigma mem) between dam and offspring weaning weights. Models 3 and 4 were models 1 and 2, respectively, expanded to include a grandmaternal genetic effect (gn) and covariances sigma ggn and sigma gmgn. Two ANOVA solution sets for the parameters of model 4 were obtained using sire, dam, maternal grandsire, maternal grandam and phenotypic variances and offspring-dam (covOD), offspring-sire (covOS), offspring-grandam (covOGD), and offspring-maternal half-aunt or uncle (covOMH) covariances. Four ANOVA solution sets for the parameters of model 2 were obtained using sire, dam, within dam and maternal grandsire variances, covOD and either covOS or covOGD. Two sets of 1,000 replicates of the data were simulated. These data were used to compare precision and accuracy of SDS and ANOVA estimators, to estimate correlations among SDS and ANOVA estimators, and to study the importance of taking inbreeding into account with SDS methodology. All ANOVA estimators for rho ggm were biased downward. The SDS procedure had a clear advantage over ANOVA. Averages of SDS estimates were closer to parameter values used to simulate the data and their standard deviations were generally smaller. The standard deviations of both SDS and ANOVA estimates of rho ggm were very large. It is important to allow for a nonzero sigma mem (at least when it is negative) when using SDS methods; otherwise estimators of sigma 2gm and sigma ggm are biased upward and downward, respectively.  相似文献   

12.
在项目搭建的“奶牛精细养殖综合技术平台”上，将对动物个体祖先谱系的跟踪问题转化为满二叉树的数据结构后，选用前序遍历搜索算法，编写了追溯奶牛个体面向4代祖先的自定义“找祖先”函数，利用平台系统设定参数产生的模拟数据，实现了4代以内祖先的谱系跟踪，同时还提供雌性祖先的生产性能数据；以跟踪的谱系数据为基础，将“找祖先”函数和计算近交系数的原理相结合，实现了某个体与指定公牛（或母牛）交配后裔的近交系数监测，以控制近亲繁殖。研究还进一步指出，只要改变寻找祖先的起点，就能实现超过4代的祖先谱系分析。但是，个体谱系高世代（中亲或远亲）追踪必须以超越时空的、完整的奶牛繁殖档案数据库为基础，因此建议尽快建立我国奶牛繁殖科学数据库。  相似文献   

13.
We have evaluated the use of genomic coancestry coefficients based on shared segments for the maintenance of genetic diversity through optimal contributions methodology for populations of three different Austrian cattle breeds. This coancestry measure has been compared with the genomic coancestry coefficient calculated on a SNP‐by‐SNP basis and with pedigree‐based coancestry. The regressions of the shared segments coancestry on the other two coefficients suggest that the former mainly reflect Identity By Descent but with the advantage over pedigree‐based coancestry of providing the realized Identity By Descent rather than an expectation. The effective population size estimated from the rate of coancestry based on shared segments was very similar to those obtained with the other coefficients and of small magnitude (from 26.24 to 111.90). This result highlights the importance of implementing active management strategies to control the increase of inbreeding and the loss of genetic diversity in livestock breeds, even when the population size is reasonably large. One problem for the implementation of coancestry based on shared segments is the need of estimating the gametic phases of the SNPs which, given the techniques used to obtain the genotypes, are a priori unknown. This study shows, through computer simulations, that using estimates of gametic phases for computing coancestry based on shared segments does not lead to a significant loss in the diversity maintained. This has been shown to be true even when the size of the population is very small as it is usually the case in populations subjected to conservation programmes.  相似文献   

14.
Two methods are presented for estimating variances and covariances from beef cattle field data using multiple-trait sire models. Both methods require that the first trait have no missing records and that the contemporary groups for the second trait be subsets of the contemporary groups for the first trait; however, the second trait may have missing records. One method uses pseudo expectations involving quadratics composed of the solutions and the right-hand sides of the mixed model equations. The other method is an extension of Henderson's Simple Method to the multiple trait case. Neither of these methods requires any inversions of large matrices in the computation of the parameters; therefore, both methods can handle very large sets of data. Four simulated data sets were generated to evaluate the methods. In general, both methods estimated genetic correlations and heritabilities that were close to the Restricted Maximum Likelihood estimates and the true data set values, even when selection within contemporary groups was practiced. The estimates of residual correlations by both methods, however, were biased by selection. These two methods can be useful in estimating variances and covariances from multiple-trait models in large populations that have undergone a minimal amount of selection within contemporary groups.  相似文献   

15.
一个适于大型畜群近交程度分析的SAS过程   总被引：1，自引：0，他引：1  
近交程度分析是家畜育种中一项重要的工作。SAS统计分析系统(6．11版本以上)中提供了一个可用于大型畜群近交程度分析的INBREED过程。本文详细介绍了INBREED过程的使用方法,并以实际数据为例对程序的编写以及运行结果的分析等进行了详尽的阐述。  相似文献   

16.
Life data statistical methods are proposed for the analysis of dairy cattle production data representing the time from one event to another. The Kaplan-Meier estimator of survival is described and its applications to dairy cattle data are exemplified with data sets of replacement times, time from calving to first case of mastitis and time from calving to first insemination. All data sets include censored data from cows for which the event had not been observed at the end of lactation or data collection period. A method for modifying replacement times to a standard calving interval is presented. A simple non-parametric test of homogeneity in two samples is described.  相似文献   

17.
Our aim was to ascertain inbreeding depression in the Spanish Purebred horses for eight body measurements. A total of 16,472 individuals were measured for height at withers, height at chest, leg length, body length, width of chest, heart girth circumference, knee perimeter and cannon bone circumference. Three different multivariate animal models including, respectively, no measure of inbreeding, individual inbreeding coefficients (Fi) or individual increase in inbreeding coefficients (ΔFi) as linear covariates were used. Significant inbreeding depression was assessed. Even though the models including measures of inbreeding fitted better with data, no effect on estimates of genetic parameters was assessed. However, the inclusion of inbreeding measures affected the ranking order according to the Expected Breeding Values (EBV). Due to the better fit with data and nice properties (the adjustment of individual inbreeding coefficients with the pedigree depth and linear behaviour) the use of ΔFi in the evaluation models can be recommended for morphological traits in horses.  相似文献   

18.
Bayesian analysis via Gibbs sampling, restricted maximum likelihood (REML), and Method R were used to estimate variance components for several models of simulated data. Four simulated data sets that included direct genetic effects and different combinations of maternal, permanent environmental, and dominance effects were used. Parents were selected randomly, on phenotype across or within contemporary groups, or on BLUP of genetic value. Estimates by Bayesian analysis and REML were always empirically unbiased in large data sets. Estimates by Method R were biased only with phenotypic selection across contemporary groups; estimates of the additive variance were biased upward, and all the other estimates were biased downward. No empirical bias was observed for Method R under selection within contemporary groups or in data without contemporary group effects. The bias of Method R estimates in small data sets was evaluated using a simple direct additive model. Method R gave biased estimates in small data sets in all types of selection except BLUP. In populations where the selection is based on BLUP of genetic value or where phenotypic selection is practiced mostly within contemporary groups, estimates by Method R are likely to be unbiased. In this case, Method R is an alternative to single-trait REML and Bayesian analysis for analyses of large data sets when the other methods are too expensive to apply.  相似文献   

19.
Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.  相似文献   

20.
The correlation between pedigree and genomic-based inbreeding coefficients is usually discussed in the literature. However, some of these correlations could be spurious. Using partial correlations and information theory, it is possible to distinguish a significant association between two variables which is independent from associations with a third variable. The objective of this study is to implement partial correlations and information theory to assess the relationship between different inbreeding coefficients using a selected population of rabbits. Data from pedigree and genomic information from a 200K SNP chip were available. After applying filtering criteria, the data set comprised 437 animals genotyped for 114,604 autosomal SNP. Fifteen pedigree- and genome-based inbreeding coefficients were estimated and used to build a network. Recent inbreeding coefficient based on runs of homozygosity had 9 edges linking it with different inbreeding coefficients. Partial correlations and information theory approach allowed to infer meaningful associations between inbreeding coefficients and highlighted the importance of the recent inbreeding based on runs of homozygosity, but a good proxy of it could be those pedigree-based definitions reflecting recent inbreeding.  相似文献   

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