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1.
Thinh Tuan Chu John W.M. Bastiaansen Elise Norberg Peer Berg 《Acta Agriculturae Scandinavica, Section A - Animal Sciences》2018,68(1):1-10
To improve genetic gain of breeding programs for village poultry production, breeding schemes with observations obtained in village production systems using individual (VIO) and group recording (VGO) were examined under different levels of genotype-by-environment-interactions (GxE). GxE was modeled by varying the correlation between traits measured in the breeding station and village environments for bodyweight (rg_BW) and egg production (rg_EP). Relative and absolute genetic gains obtained from VIO and VGO were used for comparison between the schemes. Results showed that village observations significantly improved genetic gains compared to the scheme without birds tested in the village. The improvement was only slightly larger with individual observations than with group observations. Higher rg_BW and rg_EP led to lower relative genetic gain, but a higher absolute gain of VIO and VGO. It is recommended to apply a breeding scheme using group recording of village performance when strong GxE in breeding for village poultry is expected. 相似文献
2.
M. Heidaritabar M.P.L. Calus H‐J. Megens A. Vereijken M.A.M. Groenen J.W.M. Bastiaansen 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2016,133(3):167-179
There is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non‐synonymous and non‐coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non‐synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data. 相似文献
3.
Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers 
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下载免费PDF全文 M. Heidaritabar A. Wolc J. Arango J. Zeng P. Settar J.E. Fulton N.P. O'Sullivan J.W.M. Bastiaansen R.L. Fernando D.J. Garrick J.C.M. Dekkers 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2016,133(5):334-346
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
4.
Although the sentences that we hear or read have meaning, this does not necessarily mean that they are also true. Relatively little is known about the critical brain structures for, and the relative time course of, establishing the meaning and truth of linguistic expressions. We present electroencephalogram data that show the rapid parallel integration of both semantic and world knowledge during the interpretation of a sentence. Data from functional magnetic resonance imaging revealed that the left inferior prefrontal cortex is involved in the integration of both meaning and world knowledge. Finally, oscillatory brain responses indicate that the brain keeps a record of what makes a sentence hard to interpret. 相似文献
5.
Effects of incorporating environmental cost and risk aversion on economic values of pig breeding goal traits 下载免费PDF全文
下载免费PDF全文 B.M. Ali Y. de Mey J.W.M. Bastiaansen A.G.J.M. Oude Lansink 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2018,135(3):194-207
Economic values (EVs) of traits, accounting for environmental impacts and risk preferences of farmers, are required to design breeding goals that contribute to both economic and environmental sustainability. The objective of this study was to assess the effects of incorporating environmental costs and the risk preferences of farmers on the EVs of pig breeding goal traits. A breeding goal consisting of both sow efficiency and production traits was defined for a typical Brazilian farrow‐to‐finish pig farm with 1,500 productive sows. A mean‐variance utility function was employed for deriving the EVs at finishing pig level assuming fixed slaughter weight. The inclusion of risk and risk aversion reduces the economic weights of sow efficiency traits (17%) while increasing the importance of production traits (7%). For a risk‐neutral producer, inclusion of environmental cost reduces the economic importance of sow efficiency traits (3%) while increasing the importance of production traits (1%). Genetic changes of breeding goal traits by their genetic standard deviations reduce emissions of greenhouse gases, and excretions of nitrogen and phosphorus per finished pig by up to 6% while increasing farm profit. The estimated EVs could be used to improve selection criteria and thereby contribute to the sustainability of pig production systems. 相似文献
6.
A.M. Hidalgo J.W.M. Bastiaansen M.S. Lopes M.P.L. Calus D.J. de Koning 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2016,133(6):443-451
In pig breeding, as the final product is a cross bred (CB) animal, the goal is to increase the CB performance. This goal requires different strategies for the implementation of genomic selection from what is currently implemented in, for example dairy cattle breeding. A good strategy is to estimate marker effects on the basis of CB performance and subsequently use them to select pure bred (PB) breeding animals. The objective of our study was to assess empirically the predictive ability (accuracy) of direct genomic values of PB for CB performance across two traits using CB and PB genomic and phenotypic data. We studied three scenarios in which genetic merit was predicted within each population, and four scenarios where PB genetic merit for CB performance was predicted based on either CB or a PB training data. Accuracy of prediction of PB genetic merit for CB performance based on CB training data ranged from 0.23 to 0.27 for gestation length (GLE), whereas it ranged from 0.11 to 0.22 for total number of piglets born (TNB). When based on PB training data, it ranged from 0.35 to 0.55 for GLE and from 0.30 to 0.40 for TNB. Our results showed that it is possible to predict PB genetic merit for CB performance using CB training data, but predictive ability was lower than training using PB training data. This result is mainly due to the structure of our data, which had small‐to‐moderate size of the CB training data set, low relationship between the CB training and the PB validation populations, and a high genetic correlation (0.94 for GLE and 0.90 for TNB) between the studied traits in PB and CB individuals, thus favouring selection on the basis of PB data. 相似文献
7.
Liquid crystal displays, the dominant flat panel display technology, are limited in brightness and energy efficiency because of the use of absorbing polarizers and color filters. Liquid crystal-based photoluminescent display devices have been fabricated that use thin, polarized photoluminescent layers that have highly anisotropic absorption or emission. These layers both polarize light and generate bright color. This approach can simplify device design and substantially increase device brightness, contrast, efficiency, and (in specific configurations) viewing angle. 相似文献
8.
J. de Kraker J. E. van den Ende W. A. H. Rossing C. Bastiaansen W. van der Werf 《EPPO Bulletin》2000,30(1):105-113
Development and improvement of warning systems are often done empirically, relying on extensive field testing. As this approach is both costly and time‐consuming, there is a need for a more rational and efficient alternative. In a study to explore the options for improvement of a Botrytis warning system in flower bulbs, we applied a computer‐based approach to systems design. The approach consisted of the construction and evaluation of modified versions of the warning system using epidemiological knowledge, data sets of recorded and forecast weather and a simulation model of epidemic development and fungicide spray impact. Performance of modified versions was evaluated with regard to fungicide input, efficacy of disease control and sensitivity to the prediction error in weather forecasts. This approach can be more efficient than a purely empirical one, as it enables the designer to limit the number of alternative versions to be field‐tested on the basis of explicit performance criteria. It also has the advantage that it provides insight into the potentials for improvement of the warning system. 相似文献
9.
Ciobanu DC Bastiaansen JW Lonergan SM Thomsen H Dekkers JC Plastow GS Rothschild MF 《Journal of animal science》2004,82(10):2829-2839
Suggestive QTL affecting raw firmness scores and average Instron force, tenderness, juiciness, and chewiness on cooked meat were mapped to pig chromosome 2 using a three-generation intercross between Berkshire and Yorkshire pigs. Based on its function and location, the calpastatin (CAST) gene was considered to be a good candidate for the observed effects. Several missense and silent mutations were identified in CAST and haplotypes covering most of the coding region were constructed and used for association analyses with meat quality traits. Results demonstrated that one CAST haplotype was significantly associated with lower Instron force and cooking loss and higher juiciness and, therefore, this haplotype is associated with higher eating quality. Some of the sequence variation identified may be associated with differences in phosphorylation of CAST by adenosine cyclic 3', 5'-monophosphate-dependent protein kinase and may in turn explain the meat quality phenotypic differences. The beneficial haplotype was present in all the commercial breeds tested and may provide significant improvements for the pig industry and consumers because it can be used in marker-assisted selection to produce naturally tender and juicy pork without additional processing steps. 相似文献
10.
Genomic prediction of growth in pigs based on a model including additive and dominance effects 下载免费PDF全文
下载免费PDF全文 M.S. Lopes J.W.M. Bastiaansen L. Janss E.F. Knol H. Bovenhuis 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2016,133(3):180-186
Independent of whether prediction is based on pedigree or genomic information, the focus of animal breeders has been on additive genetic effects or ‘breeding values’. However, when predicting phenotypes rather than breeding values of an animal, models that account for both additive and dominance effects might be more accurate. Our aim with this study was to compare the accuracy of predicting phenotypes using a model that accounts for only additive effects (MA) and a model that accounts for both additive and dominance effects simultaneously (MAD). Lifetime daily gain (DG) was evaluated in three pig populations (1424 Pietrain, 2023 Landrace, and 2157 Large White). Animals were genotyped using the Illumina SNP60K Beadchip and assigned to either a training data set to estimate the genetic parameters and SNP effects, or to a validation data set to assess the prediction accuracy. Models MA and MAD applied random regression on SNP genotypes and were implemented in the program Bayz. The additive heritability of DG across the three populations and the two models was very similar at approximately 0.26. The proportion of phenotypic variance explained by dominance effects ranged from 0.04 (Large White) to 0.11 (Pietrain), indicating that importance of dominance might be breed‐specific. Prediction accuracies were higher when predicting phenotypes using total genetic values (sum of breeding values and dominance deviations) from the MAD model compared to using breeding values from both MA and MAD models. The highest increase in accuracy (from 0.195 to 0.222) was observed in the Pietrain, and the lowest in Large White (from 0.354 to 0.359). Predicting phenotypes using total genetic values instead of breeding values in purebred data improved prediction accuracy and reduced the bias of genomic predictions. Additional benefit of the method is expected when applied to predict crossbred phenotypes, where dominance levels are expected to be higher. 相似文献