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1.
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   

2.
The amount of variance captured in genetic estimations may depend on whether a pedigree‐based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree‐based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population‐trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree‐based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree‐based relationship matrix. The ratio of the genomic to pedigree‐based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress.  相似文献   

3.
The breeding of the dog breed Elo was started in 1987. This dog breed was established by using 16 dogs of nine different breeds. All pedigree information of the dogs from 1987 to 2002 was included for the analysis of the proportion of genes of the different founder breeds, of the inbreeding coefficient, and relationship coefficients. Additionally, the number of died puppies per litter were investigated. The Eurasian dog breed contributed about 48% of the genes in the whole Elo dog population. Old English sheepdog and Chow Chow contributed about 23% and 10% of the genes. The other dog breeds were of minor importance. The mean inbreeding and relationship coefficients of the whole Elo dog population were 12.04% and 19.22%, respectively. With the exception of 3.5% of animals, all Elo dogs were related to each other. The mean litter size was 6.39 puppies. The percentage of stillborn puppies per litter averaged at 9.47%. The inbreeding coefficients of the puppies and of their dams, the age of the sire and the dam at the time of birth of the puppies, the litter size, the puppies' year of birth and the proportion of genes of the Chow Chow showed a significant effect on the number of stillborn puppies per litter. The heritability for the frequency of stillborn puppies was estimated using a linear animal model. After transformation of the linear estimates to the underlying liability scale, the heritability amounted to h2 = 0.15.  相似文献   

4.
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   

5.
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   

6.
Repeatability and phenotypic correlations were estimated for saltwater crocodile reproductive traits. No pedigree information was available to estimate heritability or genetic correlations, because the majority of breeder animals on farms were wild‐caught. Moreover, as the age of the female breeders could not be accounted for, egg‐size measurements were used as proxies. The reproductive traits investigated were clutch size (total number of eggs laid), number of viable eggs, number of eggs that produced a live, healthy hatchling, hatchability, average snout–vent length of the hatchlings and time of nesting. A second data set was also created comprising binary data of whether or not the female nested. Repeatability estimates ranged from 0.24 to 0.68 for the measurable traits, with phenotypic correlations ranging from ?0.15 to 0.86. Repeatability for whether a female nested or not was 0.58 on the underlying scale. Correlations could not be estimated between the measurement and binary traits because of confounding. These estimates are the first published for crocodilian reproduction traits.  相似文献   

7.
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   

8.
Information about genetic parameters is essential for selection decisions and genetic evaluation. These estimates are population specific; however, there are few studies with dairy cattle populations reared under tropical and sub‐tropical conditions. Thus, the aim was to obtain estimates of heritability and genetic correlations for milk yield and quality traits using pedigree and genomic information from a Holstein population maintained in a tropical environment. Phenotypic records (n = 36 457) of 4203 cows as well as the genotypes for 57 368 single nucleotide polymorphisms from 755 of these cows were used. Covariance components were estimated using the restricted maximum likelihood method under a mixed animal model, considering a pedigree‐based relationship matrix or a combined pedigree‐genomic matrix. High heritabilities (around 0.30) were estimated for lactose and protein content in milk whereas moderate values (between 0.19 and 0.26) were obtained for percentages of fat, saturated fatty acids and palmitic acid in milk. Genetic correlations ranging from −0.38 to −0.13 were determined between milk yield and composition traits. The smaller estimates compared to other similar studies can be due to poor environmental conditions, which may reduce genetic variability. These results highlight the importance in using genetic parameters estimated in the population under evaluation for selection decisions.  相似文献   

9.
The objectives of this study were to 1) evaluate the genetic diversity of Navajo-Churro sheep using pedigree information; 2) examine the distribution of the Navajo-Churro population; and 3) evaluate the effect of breeder dynamics on genetic conservation of the breed. Pedigree data and breeder information (city and state) were obtained from the Navajo-Churro Sheep Breed Association. Inbreeding coefficients were calculated for each individual animal using pedigree information. A geographic information system program was used to divide the United States into four regions and overlay breeder locations, flock size, and flock inbreeding level. The small correlation between level of inbreeding and flock size (r = -0.07, P = 0.07) indicated that inbreeding levels are not different across flock sizes. The mean flock inbreeding levels ranged from 0 to 11% across regions. The level of inbreeding did not differ among regions (P = 0.15), except for Region 4 (Kansas and Missouri; P = 0.001). The number of breeders registering sheep averaged 34 per year. Most of the breeders were transient, with only eight breeders maintaining ownership for more than 7 yr. Average inbreeding level for 2000 was found to be 1.2%, with a linear increase in inbreeding of 0.1%/yr over the period studied, suggesting a minimal loss of genetic diversity for the Navajo-Churro. However, given the relatively small effective population size (92) and the transient nature of the breeders, development of an ex situ cryo-preserved germplasm bank may be the best long-term strategy for maintaining this breed's genetic diversity.  相似文献   

10.
Bayesian estimation via Gibbs sampling, REML, and Method R were compared for their empirical sampling properties in estimating genetic parameters from data subject to parental selection using an infinitesimal animal model. Models with and without contemporary groups, random or nonrandom parental selection, two levels of heritability, and none or 15% randomly missing pedigree information were considered. Nonrandom parental selection caused similar effects on estimates of variance components from all three methods. When pedigree information was complete, REML and Bayesian estimation were not biased by nonrandom parental selection for models with or without contemporary groups. Method R estimates, however, were strongly biased by nonrandom parental selection when contemporary groups were in the model. The bias was empirically shown to be a consequence of not fully accounting for gametic phase disequilibrium in the subsamples. The joint effects of nonrandom parental selection and missing pedigree information caused estimates from all methods to be highly biased. Missing pedigree information did not cause biased estimates in random mating populations. Method R estimates usually had greater mean square errors than did REML and Bayesian estimates.  相似文献   

11.
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   

12.
First parity calving difficulty scores from Italian Piemontese cattle were analysed using a threshold mixed effects model. The model included the fixed effects of age of dam and sex of calf and their interaction and the random effects of sire, maternal grandsire, and herd‐year‐season. Covariances between sire and maternal grandsire effects were modelled using a numerator relationship matrix based on male ancestors. Field data consisted of 23 953 records collected between 1989 and 1998 from 4741 herd‐year‐seasons. Variance and covariance components were estimated using two alternative approximate marginal maximum likelihood (MML) methods, one based on expectation‐maximization (EM) and the other based on Laplacian integration. Inferences were compared to those based on three separate runs or sequences of Markov Chain Monte Carlo (MCMC) sampling in order to assess the validity of approximate MML estimates derived from data with similar size and design structure. Point estimates of direct heritability were 0.24, 0.25 and 0.26 for EM, Laplacian and MCMC (posterior mean), respectively, whereas corresponding maternal heritability estimates were 0.10, 0.11 and 0.12, respectively. The covariance between additive direct and maternal effects was found to be not different from zero based on MCMC‐derived confidence sets. The conventional joint modal estimates of sire effects and associated standard errors based on MML estimates of variance and covariance components differed little from the respective posterior means and standard deviations derived from MCMC. Therefore, there may be little need to pursue computation‐intensive MCMC methods for inference on genetic parameters and genetic merits using conventional threshold sire and maternal grandsire models for large datasets on calving ease.  相似文献   

13.
This study evaluated the differences between linear and non‐linear modelled heritability estimates of racing performance based on lifetime earnings (LE) and lifetime ranking (LR) in Japanese Thoroughbred racehorses. The heritability estimate (h2 = 0.25) obtained from a non‐linear model based on formal Japan Racing Association ranking was much higher than that obtained from a linear model based on the original trait phenotype (h2 = 0.11). The linear models showed slightly higher heritability estimates under the trait categorizations than under the original phenotypes, while the non‐linear categorical trait models showed much higher heritability estimates than the linear models, especially for binary trait categorizations (h2 = 0.34) with non‐winning and winning horses. The binary trait categorizations were consistent with the case and control classifications in the previous genome‐wide association study (GWAS), which identified possible sequence variants on ECA18 that affect racing performance in Japanese Thoroughbred racehorses. Those findings suggested that the different heritability estimates obtained from several trait categorizations would reflect the possible presence of susceptibility gene segregations in the analyzed population, indicating that heritability estimates from non‐linear models are useful for the selection of case and control populations in GWAS.  相似文献   

14.
The consequences of assuming a zero environmental covariance between a binary trait 'test-status' and a continuous trait on the estimates of genetic parameters by restricted maximum likelihood and Gibbs sampling and on response from genetic selection when the true environmental covariance deviates from zero were studied. Data were simulated for two traits (one that culling was based on and a continuous trait) using the following true parameters, on the underlying scale: h2 = 0.4; r(A) = 0.5; r(E) = 0.5, 0.0 or -0.5. The selection on the continuous trait was applied to five subsequent generations where 25 sires and 500 dams produced 1500 offspring per generation. Mass selection was applied in the analysis of the effect on estimation of genetic parameters. Estimated breeding values were used in the study of the effect of genetic selection on response and accuracy. The culling frequency was either 0.5 or 0.8 within each generation. Each of 10 replicates included 7500 records on 'test-status' and 9600 animals in the pedigree file. Results from bivariate analysis showed unbiased estimates of variance components and genetic parameters when true r(E) = 0.0. For r(E) = 0.5, variance components (13-19% bias) and especially (50-80%) were underestimated for the continuous trait, while heritability estimates were unbiased. For r(E) = -0.5, heritability estimates of test-status were unbiased, while genetic variance and heritability of the continuous trait together with were overestimated (25-50%). The bias was larger for the higher culling frequency. Culling always reduced genetic progress from selection, but the genetic progress was found to be robust to the use of wrong parameter values of the true environmental correlation between test-status and the continuous trait. Use of a bivariate linear-linear model reduced bias in genetic evaluations, when data were subject to culling.  相似文献   

15.
The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (FPED), or runs of homozygosity (ROH; FROH) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each breed. VdB showed higher inbreeding coefficients compared to SAR, with both breeds showing lower estimates as the minimum ROH length increased. Significant inbreeding depression was found only for milk yield, with a loss of around 7 g/day (for SAR) and 9 g/day (VdB) for a 1% increase of FROH. The present study confirms how the use of genomic information can be used to manage intra-breed diversity and to calculate the effects of inbreeding on phenotypic traits.  相似文献   

16.
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   

17.
Estimates of genetic parameters resulting from various analytical models for birth weight (BWT, n = 4,155), 205-d weight (WWT, n = 3,884), and 365-d weight (YWT, n = 3,476) were compared. Data consisted of records for Line 1 Hereford cattle selected for postweaning growth from 1934 to 1989 at ARS-USDA, Miles City, MT. Twelve models were compared. Model 1 included fixed effects of year, sex, age of dam; covariates for birth day and inbreeding coefficients of animal and of dam; and random animal genetic and residual effects. Model 2 was the same as Model 1 but ignored inbreeding coefficients. Model 3 was the same as Model 1 and included random maternal genetic effects with covariance between direct and maternal genetic effects, and maternal permanent environmental effects. Model 4 was the same as Model 3 but ignored inbreeding. Model 5 was the same as Model 1 but with a random sire effect instead of animal genetic effect. Model 6 was the same as Model 5 but ignored inbreeding. Model 7 was a sire model that considered relationships among males. Model 8 was a sire model, assuming sires to be unrelated, but with dam effects as uncorrelated random effects to account for maternal effects. Model 9 was a sire and dam model but with relationships to account for direct and maternal genetic effects; dams also were included as uncorrelated random effects to account for maternal permanent environmental effects. Model 10 was a sire model with maternal grandsire and dam effects all as uncorrelated random effects. Model 11 was a sire and maternal grandsire model, with dams as uncorrelated random effects but with sires and maternal grandsires assumed to be related using male relationships. Model 12 was the same as Model 11 but with all pedigree relationships from the full animal model for sires and maternal grandsires. Rankings on predictions of breeding values were the same regardless of whether inbreeding coefficients for animal and dam were included in the models. Heritability estimates were similar regardless of whether inbreeding effects were in the model. Models 3 and 9 best fit the data for estimation of variances and covariances for direct, maternal genetic, and permanent environmental effects. Other models resulted in changes in ranking for predicted breeding values and for estimates of direct and maternal heritability. Heritability estimates of direct effects were smallest with sire and sire-maternal grandsire models.  相似文献   

18.
AIM: To investigate, in a pilot study, a possible genetic component to type 2 diabetes mellitus (T2D) in Burmese cats in New Zealand by analysing pedigree data.

METHODS: Pedigrees were obtained for 305 Burmese cats living in New Zealand; diabetes was diagnosed in 19 of these due to presence of polyuria and polydipsia, persistent concentrations of glucose in plasma >16?mmol/L and glucosuria prior to insulin treatment. Pedigrees were also submitted for 16 cats with no clinical signs of T2D. The remaining 270 cats were unobserved relatives of these individuals. Inbreeding coefficients and heritability were calculated, and a single major locus model segregation analysis was conducted using pedigree analysis software.

RESULTS: Nineteen cats were diagnosed with T2D. Males (n = 14) and females (n = 5) were both affected, suggesting that the gene or genes causing diabetes are autosomal rather than sex-linked. Examination of the pedigree revealed few signs of fully penetrant dominant gene action: diabetes was ostensibly rarely seen in sequential generations and nearly always skipped at least one and often more generations; apparently unaffected offspring of apparently unaffected parents sometimes produced affected progeny. The mean relatedness of the affected animals within the core pedigree (16 diabetic cats) was 0.049, and mean inbreeding 0.033. Based on 100,000 permutations of the trait values, the expected relatedness of a random sample of 16 animals taken from the phenotyped animals would be 0.013 (SD 0.007) (permutation p = 0.0009). The observed inbreeding was also significant (permutation p= 0.02).

Heritability was estimated to be 9 (95% CI = 0–57)% assuming all animals with unknown status were unaffected. The best fitting genetic model was a major gene model with dominant expression with the risk allele frequency at 15% with 60% penetrance.

CONCLUSIONS: In this pilot study the increased inbreeding in the cases, lack of likely sampling bias, the increased frequency of T2D in Burmese, and small number of breed founders are consistent with the involvement of a major locus in diabetes in Burmese cats with a significant risk allele prevalence. However, low case numbers meant this could not be unambiguously confirmed. A genome-wide association study may be useful for investigating the genetic cause of T2D.  相似文献   

19.
OBJECTIVE: To determine prevalence, level of inbreeding, heritability, and mode of inheritance for rupture of the cranial cruciate ligament (RCCL) in Newfoundlands. DESIGN: Retrospective and recruitment study. ANIMALS: 574 client-owned Newfoundlands. PROCEDURE: Medical records from January 1, 1996, to December 31, 2002, were evaluated for prevalence of RCCL. A pedigree was constructed by use of recruited Newfoundlands with RCCL status based on results of veterinary examination; level of inbreeding, heritability, and mode of inheritance were calculated. RESULTS: Hospital prevalence for RCCL was 22%; dogs in the pedigree from the recruitment study had a mean level of inbreeding of 1.19 x 10(4), heritability of 0.27, and a possible recessive mode of inheritance with 51% penetrance for RCCL. CONCLUSIONS AND CLINICAL RELEVANCE: Identification of a genetic basis for RCCL in Newfoundlands provided evidence that investigators can now focus on developing methods to identify carriers to reduce the prevalence of RCCL.  相似文献   

20.
The present study investigated the effects of the choices of animals of reference populations on long‐term responses to genomic selection. Simulated populations comprised 300 individuals and 10 generations of selection practiced for a trait with heritability of 0.1, 0.3 or 0.5. Thirty individuals were randomly selected in the first five generations and selected by estimated breeding values from best linear unbiased prediction (BLUP) and genomic BLUP in the subsequent five generations. The reference populations comprise all animals for all generations (scenario 1), all animals for 6‐10 generations (scenario 2) and 2‐6 generations (scenario 3), and half of the animals for all generations (scenario 4). For all heritability levels, the genetic gains in generation 10 were similar in scenarios 1 and 2. Among scenarios 2 to 4, the highest genetic gains were obtained in scenario 2, with heritabilities of 0.1 and 0.3 as well as scenario 4 with heritability of 0.5. The inbreeding coefficients in scenarios 1, 2 and 4 were lower than those in BLUP, especially within cases with low heritability. These results indicate an appropriate choice of reference population can improve genetic gain and restrict inbreeding even when the reference population size is limited.  相似文献   

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