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1.
We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross‐breed. Elite nucleus herds had access to high‐quality feed, and production herds were fed low‐quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (rg = 0.2), medium (rg = 0.5) and high (rg = 0.8). In our alternative breeding schemes, different proportion of production animals were recorded for feed efficiency and genotyped with high‐density panel of genetic markers. Genomic breeding value of the selection candidates for feed efficiency was estimated based on three different approaches. In one approach, genomic breeding value was estimated including nucleus animals in the reference population. In the second approach, the reference population was containing a mixture of nucleus and production animals. In the third approach, the reference population was only consisting of production herds. Using a mixture reference population, we generated 40–115% more genetic gain in the production environment as compared to only using nucleus reference population that were fed high‐quality feed sources when the production animals were offspring of the nucleus animals. When the production animals were grand offspring of the nucleus animals, 43–104% more genetic gain was generated. Similarly, a higher genetic gain generated in the production environment when mixed reference population was used as compared to only using production animals. This was up to 19 and 14% when the production animals were offspring and grand offspring of nucleus animals, respectively. Therefore, in genomic selection pig breeding programmes, feed efficiency traits could be improved by properly designing the reference population.  相似文献   

2.
《Livestock Science》2006,99(1):69-77
Economic values or weights measure the net economic gain per unit genetic increase of a given trait. These were derived for sow productivity traits for use as weighting factors in a dam line selection index used by purebred or nucleus dam line breeders. The profit function approach was used in order to provide flexibility to alternative production systems, market requirements or population trait levels. The approach accounted for constraints on perinatal survival rate imposed by larger birth litter sizes. The effect of accounting for these constraints was to reduce the economic value of birth litter size as the population average increased; without this, the economic weight for litter size was constant. Weights for the other traits were not affected. Economic weights were calculated for both the 100 kg finished pig and the 25 kg feeder pig market, and for a range of average birth litter sizes, with constant values for all other traits, using average market conditions, prices and costs in Canada as an example. The relative importance of litter size for the finished pig market decreased from 64% of the total breeding value when average litter size was 8 pigs to 29% when average litter size was 20 pigs, whereas that of perinatal survival increased from 17% to 42%, and that of survival to weaning increased from 7% to 18%. The relative importance of litter size for the feeder pig market also decreased from 45% to 15% as average litter size increased from 8 to 20 pigs, whereas that of piglet weaning weight increased from 22% to 41%, that of perinatal survival increased from 12% to 22% and that of survival to weaning increased from 5% to 9%. The relative importance of age at puberty and weaning to conception interval were both less than 8% of the total in both markets at all litter sizes. These results show that economic weights for litter size designed for populations with relatively small litter sizes should be reduced when the average litter size becomes large and more emphasis should be placed on other traits, particularly perinatal survival.  相似文献   

3.
采用计算机随机模拟方法模拟了在一个闭锁群体内连续对单个性状进行 1 5个世代选择的情况。选择过程中世代不重叠 ,每个世代的种畜根据动物模型最佳线性无偏预测 (BLUP)法估计的育种值进行选留 ,并在此基础上系统地比较了不同群体规模、公母比例和性状遗传力对群体遗传方差和近交系数变化的影响。结果表明 ,扩大育种群规模、增加公畜比例以及对低遗传力性状进行选择时 ,群体遗传方差降低的速度和近交系数上升的速度会更慢 ,在长期选择时可望获得更大的持续进展和适宜的近交增量  相似文献   

4.
Different modes of selection in dogs were studied with a special focus on the availability of disease information. Canine hip dysplasia (CHD) in the German shepherd dog was used as an example. The study was performed using a simulation model, comparing cases when selection was based on phenotype, true or predicted breeding value, or genomic breeding value. The parameters in the simulation model were drawn from the real population data. The data on all parents and 40% of their progeny were assumed to be available for the genetic evaluation carried out by Gibbs sampling. With respect to the use of disease records on progeny, three scenarios were considered: random exclusion of disease data (no restrictions, N), general exclusion of disease data (G) and exclusion of disease data for popular sires (P). One round of selection was considered, and the response was expressed as change of mean CHD score, proportion of dogs scored as normal, proportion of dogs scored as clearly affected and true mean breeding value in progeny of popular sires in comparison with all sires. When no restrictions on data were applied, selection on breeding value was three times more efficient than when some systematic exclusion was practised. Higher selection response than in the exclusion cases was achieved by selecting on the basis of genomic breeding value and CHD score. Genomic selection would therefore be the method of choice in the future.  相似文献   

5.
An important prerequisite for high prediction accuracy in genomic prediction is the availability of a large training population, which allows accurate marker effect estimation. This requirement is not fulfilled in case of regional breeds with a limited number of breeding animals. We assessed the efficiency of the current French routine genomic evaluation procedure in four regional breeds (Abondance, Tarentaise, French Simmental and Vosgienne) as well as the potential benefits when the training populations consisting of males and females of these breeds are merged to form a multibreed training population. Genomic evaluation was 5–11% more accurate than a pedigree‐based BLUP in three of the four breeds, while the numerically smallest breed showed a < 1% increase in accuracy. Multibreed genomic evaluation was beneficial for two breeds (Abondance and French Simmental) with maximum gains of 5 and 8% in correlation coefficients between yield deviations and genomic estimated breeding values, when compared to the single‐breed genomic evaluation results. Inflation of genomic evaluation of young candidates was also reduced. Our results indicate that genomic selection can be effective in regional breeds as well. Here, we provide empirical evidence proving that genetic distance between breeds is only one of the factors affecting the efficiency of multibreed genomic evaluation.  相似文献   

6.
The measures used to control the epidemics of foot-and-mouth disease in Canada in 1951/52 (29 outbreaks) were compared with those used in the epidemic in Hampshire in 1967 (29 outbreaks). In both epidemics the disease spread more from premises where the disease was reported late and the imposition of quarantine or restrictions on infected premises was delayed. In Hampshire, area restrictions were imposed, susceptible livestock on infected premises and on premises in direct contact were slaughtered, and contacts were traced. In Canada, the initial diagnosis was vesicular stomatitis, no area restrictions were imposed, no tracing was carried out and the animals on infected premises were allowed to recover. However, apart from the disease's spread through infected meat and by unknown or airborne routes, it did not spread from infected premises once quarantine was imposed, partly owing to the low population density of livestock in the area. The effects of the slaughter of infected premises and direct contacts in the Fareham area of Hampshire in 1967 and in the Chathill area of Northumberland in 1966 were compared with what might have happened if, in addition, culling on contiguous premises or culling on premises within 3 km or emergency vaccination had been put into effect. The slaughter of cattle, sheep, goats and pigs on premises within 3 km two days after confirmation of the first outbreak would have resulted in fewer outbreaks and a shorter period to complete slaughter, but more animals would have been slaughtered. In the Chathill area, the slaughter of sheep, goats and pigs only on premises within 3 km two days after confirmation of the first outbreak would not have resulted in fewer outbreaks and more animals would have been slaughtered. Fewer premises and animals would have been slaughtered by a contiguous cull than by a 3 km cull but more than by the slaughter of infected premises and direct contacts. Emergency vaccination within 3 km, providing protection at four days (but not to animals already infected before the development of immunity), would have resulted in the fewest animals being slaughtered and could have reduced the number of outbreaks in the Fareham area by one and in the Chathill area by two or three. All the procedures would have had a greater effect the sooner they were introduced. However, with many foci of infection, priorities for action would have had to have been established. Earlier tracing of the last outbreak in the Fareham area could have shortened the Hampshire epidemic. Surveillance of a farm identified as at risk through animal movements and by the use of an airborne-prediction model could have eliminated the source of further outbreaks in the Chathill area.  相似文献   

7.
36 intact male and 69 female lambs of two breeds (n = 63 Merinoland; n = 42 Rh?n) aged 12 weeks were orally infected with 5000 infective-stage larvae, L3, of the nematode Haemonchus contortus. After 4 and 8 weeks faecal egg counts (FEC), haematocrit values and plasma testosterone levels were determined. All lambs were slaughtered at 20 weeks of age. The gastrointestinal tracts were examined for the presence of adult stages of H. contortus. Male lambs showed significantly higher log FEC (p < 0.001), higher mean establishment rates (p < 0.05), higher worm burdens (p < 0.01) and lower haematocrit values (p < 0.001) when compared with female lambs. Correlations between economically important traits (body weight, daily weight gain) and parasitological parameters were significantly higher in male animals. Testosterone level was 4 weeks after infection significantly positive correlated with worm burden. The results suggest that female lambs are more resistant against an experimental H. contortus infection when compared with male lambs. Testosterone seems to play an important role in resistance. This approach can be of importance if parasite resistance is incorporated into breeding programs and the estimated breeding values for rams are only based on male offspring information. Therefore male breeding values are probably not representative for the whole population.  相似文献   

8.
Excessive inbreeding rates and small effective population sizes are an important problem in many populations of dogs. Proper genetic management of these populations can decrease the problem, and several measures are available. However, the effectiveness of these measures is not clear beforehand. Therefore, a simulation model was developed to test measures that aim to decrease the rate of inbreeding. The simulation program was used to evaluate inbreeding restriction measures in the Dutch golden retriever dog population. This population consisted of approximately 600 dams and 150 sires that produce 300 litters each year. The five most popular sires sire approximately 25% of the litters in a year. Simulations show that the small number of popular sires and their high contribution to the next generation are the main determinants of the inbreeding rates. Restricting breeding to animals with a low average relatedness to all other animals in the population was the most effective measure and decreased the rate of inbreeding per generation from 0.41 to 0.12%. Minimizing co‐ancestry of parents was not effective in the long run, but decreased variation in inbreeding rates. Restricting the number of litters per sire generally decreased the generation interval because sires were replaced more quickly, once they met their restriction. In some instances, this lead to an increase in inbreeding rates because the next generations were more related. The simulation tool proved to be a powerful and educational tool for deciding which breeding restrictions to apply, and can be effective in different breeds and species as well.  相似文献   

9.
Population structure of Reyna Creole cattle in Nicaragua   总被引：1，自引：1，他引：0  
Reyna Creole cattle originated from Bos taurus cattle brought to Latin America during the Spanish colonization in the fifteenth century and are the only remaining local breed in Nicaragua. However, the current genetic status of this breed is unknown. Therefore, the population structure of three recorded Reyna Creole herds in Nicaragua was studied to estimate their level of inbreeding, effective population size, and generation intervals. Data from 2,609 animals born between 1958 and 2007 were analyzed. A pedigree completeness index higher than 0.8 was required to obtain reliable estimates of the level of inbreeding, and this criterion was met for 367 animals (14%) in two herds. The average level of inbreeding was 13.0%, with values ranging from 0% to 43.8% for individual animals. One of the herds had an average inbreeding level of 21.6%, primarily due to long periods in which the same bulls were used for mating, leading to excessive frequencies of matings between closely related animals. The effective population size differed between years and ranged from 28 to 46 animals, showing that the Reyna Creole cattle breed is endangered, close to critical status. The average generation interval was 6.9 years with values as high as 19.1 years for some sires that were used for artificial insemination over a long period of time. Due to the high level of inbreeding and small population size, urgent actions are required for the development of a breeding program to protect the breed and support its sustainable utilization.  相似文献   

10.
Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single‐nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic‐based [genomic best linear unbiased prediction (GBLUP)‐REML and BayesC] and pedigree‐based (PBLUP‐REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP‐REML across traits, from 0 to 0.03 with GBLUP‐REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic‐based methods were small (0.01–0.05), with GBLUP‐REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP‐REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population.  相似文献   

11.
The objective of this paper was to investigate, for various scenarios at low and high marker density, the accuracy of imputing genotypes when using a multivariate mixed model framework using information from 2, 4, or 10 surrounding markers. This model predicts genotypes at a locus, using genotypes at nearby loci as correlated traits, and the additive genetic relationship matrix to use information from genotyped relatives. For 2 scenarios this method was compared with the population-based imputation algorithms FastPHASE and Beagle. Accuracies of imputation were obtained with Monte Carlo simulation and predicted with selection index theory, using input from the simulated data. Five different scenarios of missing genotypes were considered: 1) genotypes of some loci are missing due to genotyping errors, 2) juvenile selection candidates are genotyped using a smaller SNP panel, 3) some animals in the pedigree of a breeding population are not genotyped, 4) juvenile selection candidates are not genotyped, and 5) 1 generation of animals in the top of the pedigree are not genotyped. Surrounding marker information did not improve accuracy of imputation when animals whose genotypes were imputed were not genotyped for those surrounding markers. When those animals were genotyped for surrounding markers, results indicated a limited gain when linkage disequilibrium (LD) between SNP was low, but a substantial increase in accuracy when LD between SNP was high. For scenario 1, using 1 vs. 11 SNP, accuracy was respectively 0.75 and 0.81 at low, and 0.75 and 0.93 at high density. For scenario 2, using 1 vs. 11 SNP, accuracy was, respectively, 0.70 and 0.73 at low, and 0.71 and 0.84 at high density. Beagle outperformed the other methods at high SNP density, whereas the multivariate mixed model was clearly superior when SNP density was low and animals where genotyped with a reduced SNP panel. The results showed that extending the univariate gene content method to a multivariate BLUP model with inclusion of surrounding marker information only yields greater imputation accuracy when the animals with imputed loci are at least genotyped for some SNP that are in LD with the SNP to be imputed. The equation derived from selection index theory accurately predicted the accuracy of imputation using the multivariate mixed model framework.  相似文献   

12.
Population structure, performance testing and breeding scheme of the sire breed Piétrain in Bavaria were analyzed as a basis for further optimization studies of the breeding programme. To evaluate the current breeding programme, genetic trends and effective population size were estimated. Four data sets were used which contained breeding animals born between 1981 and 2005, estimated breeding values of traits in the breeding goal, records from young boars in field test and records from purebred and crossbred progeny on test stations. The population is subdivided in many small herds. That has disadvantages with respect to a uniform breeding goal used across herds and with respect to selection intensity and the avoidance of inbreeding. The idealized selection practice consists of three selection stages. On the first two stages information from half and full sibs on test stations is most important so that the risk of co-selecting related animals is increased. The breeding scheme is a mixture of a half sib design and a progeny testing design, but both have disadvantages. Nevertheless, genetic trends are in the desired directions. To improve accuracy and intensity of selection, only AI-boars should be used instead of natural service sires. Though the effective population size is high, the recent trend of inbreeding shows that the extensive use of popular AI-boars can lead to a rapid increase of inbreeding.  相似文献   

13.
基因组选择(GS)是近些年发展起来的一项新型育种技术,目前已在动植物育种实践中应用。本研究通过在1 068头杜洛克公猪群体中使用不同密度的SNP芯片进行全基因组选择效果比较分析。结果发现:使用基因型填充后芯片以及高密度SNP芯片所获得的估计基因组育种值(GEBV)之间可以达到99%的相关,并发现个体间亲缘关系的远近对同群体内基因型填充结果的准确率影响不大。由此可见,与目标性状紧密相关的低密度SNP芯片可用于实际育种工作,在降低使用成本的同时并不影响全基因组选择效果,为实质性进行猪分子育种提供了一条可行途径。  相似文献   

14.
Rates of gain and feed efficiency are important traits in most breeding programs for growing farm animals. The rate of gain (GAIN) is usually expressed over a certain age period and feed efficiency is often expressed as residual feed intake (RFI), defined as observed feed intake (FI) minus expected feed intake based on live weight (WGT) and GAIN. However, the basic traits recorded are always WGT and FI and other traits are derived from these basic records. The aim of this study was to develop a procedure for simultaneous analysis of the basic records and then derive linear traits related to feed efficiency without retorting to any approximation. A bivariate longitudinal random regression model was employed on 13,791 individual longitudinal records of WGT and FI from 2,827 bulls of six different beef breeds tested for their own performance in the period from 7 to 13 mo of age. Genetic and permanent environmental covariance functions for curves of WGT and FI were estimated using Gibbs sampling. Genetic and permanent covariance functions for curves of GAIN were estimated from the first derivative of the function for WGT and finally the covariance functions were extended to curves for RFI, based on the conditional distribution of FI given WGT and GAIN. Furthermore, the covariance functions were extended to include GAIN and RFI defined over different periods of the performance test. These periods included the whole test period as normally used when predicting breeding values for GAIN and RFI for beef bulls. Based on the presented method, breeding values and genetic parameters for derived traits such as GAIN and RFI defined longitudinally or integrated over (parts of) of the test period can be obtained from a joint analysis of the basic records. The resulting covariance functions for WGT, FI, GAIN, and RFI are usually singular but the method presented here does not suffer from the estimation problems associated with defining these traits individually before the genetic analysis. All the results are thus estimated simultaneously, and the set of parameters is consistent.  相似文献   

15.
The formulas given in literature for the construction of restricted indexes were designed only for the imposition of a single restriction (zero, fixed, or proportional). This study presents both the theory and the methods of a simultaneous procedure for constructing indexes with single or multiple restriction(s). Numerical examples are given to verify the theoretical development and to demonstrate the implementation of the procedure. The simultaneous procedure presented brings the construction of various restricted indexes into a simple computational scheme. In addition to the use of the proposed procedure to handle multiple traits, it can be used to modify the growth curve of meat animals or the lactation curve of dairy animals, which generally requires simultaneous imposition of different restrictions on different stages of the curves. A misconception in the literature is that the variance of an index (b'Pb) is not equal to the covariance between an index and its net merit (b'Ga) when the index is a restricted one. This study showed generally that b'Pb and b'Ga are equal in the restricted or unrestricted case only when elements of b represent the original solutions from the index equations and are not equal when elements of b are expressed in terms of proportions.  相似文献   

16.
Genetic improvement of pigs in tropical developing countries has focused on imported exotic populations which have been subjected to intensive selection with attendant high population‐wide linkage disequilibrium (LD). Presently, indigenous pig population with limited selection and low LD are being considered for improvement. Given that the infrastructure for genetic improvement using the conventional BLUP selection methods are lacking, a genome‐wide selection (GS) program was proposed for developing countries. A simulation study was conducted to evaluate the option of using 60 K SNP panel and observed amount of LD in the exotic and indigenous pig populations. Several scenarios were evaluated including different size and structure of training and validation populations, different selection methods and long‐term accuracy of GS in different population/breeding structures and traits. The training set included previously selected exotic population, unselected indigenous population and their crossbreds. Traits studied included number born alive (NBA), average daily gain (ADG) and back fat thickness (BFT). The ridge regression method was used to train the prediction model. The results showed that accuracies of genomic breeding values (GBVs) in the range of 0.30 (NBA) to 0.86 (BFT) in the validation population are expected if high density marker panels are utilized. The GS method improved accuracy of breeding values better than pedigree‐based approach for traits with low heritability and in young animals with no performance data. Crossbred training population performed better than purebreds when validation was in populations with similar or a different structure as in the training set. Genome‐wide selection holds promise for genetic improvement of pigs in the tropics.  相似文献   

17.
Data on performance of animals are, in several situations, collected at the group rather than individual level. Genetic evaluations in farm animals, however, are based on phenotypic information collected at the individual level. Therefore, it would be very attractive to extend genetic evaluations by incorporating information collected at the group level. In this paper we show the use of data collected at the group level for the estimation of variance components and the prediction of breeding values. We outline a general procedure that can be applied in different farm animal species. In the present work this procedure was applied to BW, for which pooled, as well as individual, observations were available, thus allowing for a comparison of the estimates, and to egg production, for which only pooled data were available. For BW at 19 and 27 wk the estimated heritabilities based on individual observations were very similar to those based on pooled observations. For BW at 43 and 51 wk, heritability estimates based on individual and pooled data were different, which can be caused by the emergence of competition effects. The accuracy of EBV predicted from pooled observations was about 70 to 80% of the accuracy of EBV predicted from individual observations. This result quantifies the loss deriving from the use of pooled instead of individual observations. Results show that estimation of variance components and breeding values from pooled data instead of individual observations is theoretically and practically feasible.  相似文献   

18.
National cattle evaluation programs for weaning weight in most beef breed associations involve implementation of the maternal animal model to predict direct and maternal EPD. With this model, direct breeding values are predicted for all animals with records or pedigree ties to animals with records, or both. Even though maternal genetic value is expressed only in animals that become dams, these effects are transmitted by all parents and inherited from parents by all animals, leading to maternal breeding values being predicted for all animals as well. A small example data set was simulated involving 12 parents, 8 nonparents, and 13 animals with weaning weight records. The pedigree was developed to include paternal and maternal half-sib families, full-sibs, and some inbreeding, similar to field populations of beef cattle. Assembly of the mixed model equations and solutions for the maternal animal model are illustrated explicitly to assist animal breeding students in their understanding of the properties of the maternal animal model and to explicitly implement the model. Model parameters and moments, fixed contemporary group solutions, adjustment of breeding values for merit of mates, interpretation of maternal permanent environmental effect solutions, and alternatives for the assembly of the equations are shown. This example should lead to increased student and producer understanding of genetic improvement programs for weaning weight in beef cattle.  相似文献   

19.
In livestock populations, estimation of breeding values for selection requires a matrix describing the additive relationship between individuals in the population. This matrix can be derived from pedigree information. In some livestock populations, pedigree information may be unavailable, incomplete, or in error. Here we use simulated data to demonstrate that marker-derived relationship matrices can be used to predict breeding values and estimate additive variance components, provided the markers are sufficiently dense. The approach is demonstrated for an Angus data set with 9,323 SNP markers genotyped.  相似文献   

20.
Lemurs are a diverse group of primates comprised of five families, all of which are found only on Madagascar and the Comoro Islands. Of the 60 known species, 17 are endangered and 5 of these are considered critically endangered. The effects of inbreeding on population health and viability have been well described; though negative inbreeding effects can be ameliorated through the introduction of new genetic material. Introduction of new individuals into a population can be extremely challenging because of the highly social nature of lemurs. Semen collection in lemur species is notoriously challenging, as the ejaculate forms a coagulum. During normal breeding, the coagulum forms a copulatory plug in the female. However, this coagulum can present a life-threatening situation when retained in the urethra abnormally following electroejaculation. This study investigates the use of ascorbic acid in preventing urethral blockage in two lemur species during semen collection, demonstrates successful collection of semen by electroejaculation from two species of lemur during the breeding season, and discusses removal of urethral plugs subsequent to semen collection. Semen was collected successfully from all animals. Urethral plugs formed during each collection and were abnormally retained in 2/11 collections. Both plugs were successfully and immediately removed with the use of retropulsion through a urethral catheter. Although the results of this study are encouraging, more investigation is required to establish whether or not this procedure can be safely performed in the field.  相似文献   

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