Oppfatningen av en voksenjobb. En kvalitativ studie om serveringsarbeideres holdninger til fagorganisering

SOS360MASV-SO

Sparse single-step genomic blup in crossbreeding schemes

The algorithm for proven and young animals (APY) efficiently computes an approximated inverse of the genomic relationship matrix, by dividing genotyped animals in the so-called core and noncore animals. The APY leads to computationally feasible single-step genomic Best Linear Unbiased Prediction (ssGBLUP) with a large number of genotyped animals and was successfully applied to real single-breed or line datasets. This study aimed to assess the quality of genomic estimated breeding values (GEBV) when using the APY (GEBVAPY), in comparison to GEBV when using the directly inverted genomic relationship matrix (GEBVDIRECT), for situations based on crossbreeding schemes, including F1 and F2 crosses, such as the ones for pigs and chickens. Based on simulations of a 3-way crossbreeding program, we compared different approximated inverses of a genomic relationship matrix, by varying the size and the composition of the core group. We showed that GEBVAPY were accurate approximations of GEBVDIRECT for multivariate ssGBLUP involving different breeds and their crosses. GEBVAPY as accurate as GEBVDIRECT were obtained when the core groups included animals from different breed compositions and when the core groups had a size between the numbers of the largest eigenvalues explaining 98% and 99% of the variation in the raw genomic relationship matrix.</p

Evaluatie fokprogramma voor kortere staarten bij schapenrassen met ontheffing van het coupeerverbod

Three sheep breeds have in the Netherlands an temporary exempt from the ban on tail docking. In this report the breeding policy of the past decade is evaluated. All three herd books have set up breeding value estimation. This is done most effectively for the Suffolk and the Clun Forest, both breeds have lowered the mean tail length at birth to about 17 cm, and this is about 2 cm less

Impact of Interbeef on national beef cattle evaluations

Submitted 2020-07-02 | Accepted 2020-08-22 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.144-155International evaluation models for beef cattle allow to compare animals’ estimated breeding values (EBV) across different countries, thanks to sires having offspring in more than one country. In this study we aimed to provide an up-to-date picture of the Interbeef international beef cattle evaluations from a national perspective, considering both large and small populations. Limousin age-adjusted weaning weight (AWW) phenotypes were available for 3,115,598 animals from 10 European countries, born between 1972 and 2017. EBV and reliabilities were obtained using a multi-trait animal model including maternal effects where AWW from different countries are modelled as different traits. We investigated the country of origin of the sires with internationally publishable EBV and, among them, the country of origin of the top 100 sires for each country scale. All countries had 20 to 28,557 domestic sires whose EBV were publishable, according to Interbeef’s rules, on the scale of other countries. All countries, except one, had domestic sires that ranked among the top 100 sires on other country scales. Across countries, inclusion of information from relatives recorded in other countries increased the reliability of EBV for domestic animals on average by 9.6 percentage points for direct EBV, and 8.3 percentage points for maternal EBV. In conclusion, international evaluations provide small countries access to a panel of elite foreign sires with EBV on their country scale and a more accurate estimation of EBV of domestic animals, while large countries obtain EBV for their sires on the scale of different countries which helps to better promote them.Keywords: international breeding values, genotype-by-environment interaction, Interbeef, reliabilities, weaning weightReferencesBonifazi, R., Vandenplas, J., Napel, J. ten, Matilainen, K., Veerkamp, R. F., & Calus, M. P. L. (2020). Impact of sub-setting the data of the main Limousin beef cattle population on the estimates of across-country genetic correlations. Genetics Selection Evolution, 52(1), 32. https://doi.org/10.1186/s12711-020-00551-9Bouquet, A., Venot, E., Laloë, D., Forabosco, F., Fogh, A., Pabiou, T., Coffey, M., Eriksson, J-A., Renand, G., & Phocas, F. (2009). Genetic Structure of the European Limousin Cattle Metapopulation Using Pedigree Analyses. Interbull Bullettin, 40, 98–103.Durr, J., & Philipsson, J. (2012). International cooperation: The pathway for cattle genomics. Animal Frontiers, 2(1), 16–21. https://doi.org/10.2527/af.2011-0026Fikse, W. F., & Philipsson, J. (2007). Development of international genetic evaluations of dairy cattle for sustainable breeding programs. Animal Genetic Resources, (41), 29–43. https://doi.org/10.1017/S1014233900002315Goddard, M. (1985). A method of comparing sires evaluated in different countries. Livestock Production Science, 13(4), 321–331. https://doi.org/10.1016/0301-6226(85)90024-7Interbeef. (2020). Interbeef Working Group, ICAR. Retrieved August 20, 2020, from https://www.icar.org/index.php/technical-bodies/working-groups/interbeef-working-group/Jorjani, H., Emanuelson, U., & Fikse, W. F. (2005). Data Subsetting Strategies for Estimation of Across-Country Genetic Correlations. Journal of Dairy Science, 88(3), 1214–1224. https://doi.org/10.3168/jds.S0022-0302(05)72788-0Journaux, L., Wickham, B., Venot, E., & Pabiou, T. (2006). Development of Routine International Genetic Evaluation Services for Beef Cattle as an Extension of Interbull ’s Services. Interbull Bulletin, 35(1), 146–152.MiX99 Development Team. (2017). MiX99: A software package for solving large mixed model equations. Release XI/2017.Moore, S. G., & Hasler, J. F. (2017). A 100-Year Review: Reproductive technologies in dairy science. Journal of Dairy Science, 100(12), 10314–10331. https://doi.org/10.3168/jds.2017-13138Mrode, R. A., & Thompson, R. (2005). Linear models for the prediction of animal breeding values: Second Edition. In Linear Models For the Prediction of Animal Breeding Values: Second Edition.Philipsson, J. (2011). Interbull Developments, Global Genetic Trends and Role in the Era of Genomics. Interbull Bulletin, 44, i–xiii.Phocas, F., Donoghue, K., & Graser, H. U. (2005). Investigation of three strategies for an international genetic evaluation of beef cattle weaning weight. Genetics Selection Evolution, 37(4), 361–380. https://doi.org/10.1051/gse:2005006Quintanilla, R., Laloë, D., & Renand, G. (2002a). Heterogeneity of variances across regions for weaning weight in Charolais breed. 7th World Congress on Genetics Applied to Livestock Production, 19–23. Montpellier, France.Quintanilla, R., Laloë, D., & Renand, G. (2002b). Heteroskedasticity and genotype by environment interaction across European countries for weaning weight in Charolais breed. Proceedings of the 33rd Biennial Session of ICAR, 147–150. Interlaken, Switzerland: EAAP publication N. 107, 2003.Renand, G., Laloë, D., Quintanilla, R., & Fouilloux, M. N. (2003). A first attempt of an international genetic evaluation of beef breeds in Europe. Interbull Bulletin, 31, 151–155.Robinson, G. K. (1986). That BLUP Is a Good Thing: The Estimation of Random Effects. Statistical Science, 6(1), 15–51.Schaeffer, L. R. (1994). Multiple-Country Comparison of Dairy Sires. Journal of Dairy Science, 77(9), 2671–2678. https://doi.org/10.3168/jds.S0022-0302(94)77209-XTier, B., & Meyer, K. (2004). Approximating prediction error covariances among additive genetic effects within animals in multiple-trait and random regression models. Journal of Animal Breeding and Genetics, 121(2), 77–89. https://doi.org/10.1111/j.1439-0388.2003.00444.xVenot, E., Fouilloux, M. N., Forabosco, F., Fogh, A., Pabiou, T., Moore, K., Eriksson, J-A., Renand, G., Laloë, D.(2009). Interbeef genetic evaluation of Charolais and Limousine weaning weights. Interbull Bulletin, 40, 61–67.Venot, E., Pabiou, T., Hjerpe, E., Nilforooshan, M. M. A., Launay, A., & Wickham, B. W. W. (2014). Benefits ofInterbeef international genetic evaluations for weaning weight. 10th World Congress of Genetics Applied to Livestock Production.Venot, E, Pabiou, T., Guerrier, J., Cromie, A., Journaux, L., Flynn, J., & Wickham, B. (2007). Interbeef in Practice: Example of a Joint Genetic Evaluation between France, Ireland and United Kingdom for Pure Bred Limousine Weaning Weights. Interbull Bulletin, 36, 41–47.Venot, E, Pabiou, T., Wickham, B., & Journaux, L. (2006). First Steps Towards a European Joint Genetic Evaluation of the Limousine Breed. Interbull Bulletin, 35, 141–145.Venot, Eric, Fouilloux, M. N., Sullivan, P., & Laloë, D. (2008). Level of Connectedness and Reliability in International Beef Evaluation. Interbull Bulletin, 38(June 2008), 3–7.Vishwanath, R. (2003). Artificial insemination: The state of the art. Theriogenology, 59(2), 571–584. https://doi.org/10.1016/S0093-691X(02)01241-4Wickham, B. W., & Durr, J. W. (2011). A new international infrastructure for beef cattle breeding. Animal Frontiers, 1(2), 53–59. https://doi.org/10.2527/af.2011-0019Wilmink, J. B. M., Meijering, A., & Engel, B. (1986). Conversion of breeding values for milk from foreign populations. Livestock Production Science, 14(3), 223–229. https://doi.org/10.1016/0301-6226(86)90081-3

Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction

In the last decade, a number of methods have been suggested to deal with large amounts of genetic data in genomic predictions. Yet, steadily growing population sizes and the suboptimal use of computational resources are pushing the practical application of these approaches to their limits. As an extension to the C/CUDA library miraculix, we have developed tailored solutions for the computation of genotype matrix multiplications which is a critical bottleneck in the empirical evaluation of many statistical models. We demonstrate the benefits of our solutions at the example of single-step models which make repeated use of this kind of multiplication. Targeting modern Nvidia® GPUs as well as a broad range of CPU architectures, our implementation significantly reduces the time required for the estimation of breeding values in large population sizes. miraculix is released under the Apache 2.0 license and is freely available at https://github.com/alexfreudenberg/miraculix

Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population

BackgroundInternational evaluations combine data from different countries allowing breeders to have access to larger panels of elite bulls and to increase the accuracy of estimated breeding values (EBV). However, international and national evaluations can use different sources of information to compute EBV (EBVINT and EBVNAT, respectively), leading to differences between them. Choosing one of these EBV results in losing the information that is contained only in the discarded EBV. Our objectives were to define and validate a procedure to integrate publishable sires' EBVINT and their associated reliabilities computed from pedigree-based or single-step international beef cattle evaluations into national evaluations to obtain "blended" EBV. The Italian (ITA) pedigree-based national evaluation was used as a case study to validate the integration procedure.MethodsPublishable sires' international information, i.e. EBVINT and their associated reliabilities, was included in the national evaluation as pseudo-records. Data were available for 444,199 individual age-adjusted weaning weights of Limousin cattle from eight countries and 17,607 genotypes from four countries (ITA excluded). To mimic differences between international and national evaluations, international evaluations included phenotypes (and genotypes) of animals born prior to January 2019, while national evaluations included ITA phenotypes of animals born until April 2019. International evaluations using all available information were considered as reference scenarios. Publishable sires were divided into three groups: sires with >= 15, < 15 and no recorded offspring in ITA.ResultsOverall, for these three groups, integrating either pedigree-based or single-step international information into national pedigree-based evaluations improved the similarity of the blended EBV with the reference EBV compared to national evaluations without integration. For instance, the correlation with the reference EBV for direct (maternal) EBV went from 0.61 (0.79) for a national evaluation without integration to 0.97 (0.88) when integrating single-step international information, on average across all groups of publishable sires.ConclusionsOur proposed one-animal-at-a-time integration procedure yields blended EBV that are in close agreement with full international EBV for all groups of animals analysed. The procedure can be directly applied by countries since it does not rely on specific software and is computationally inexpensive, allowing straightforward integration of publishable sires' EBVINT from pedigree-based or single-step based international beef cattle evaluations into national evaluations

International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight

Background Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations. Methods Weaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUP(INT)) and an international pedigree-based BLUP evaluation (PBLUPINT). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method. Results On average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUP(INT) showed the highest accuracies of EBV and, compared to PBLUPINT, led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUP(INT) were observed for all countries. Overall, ssSNPBLUP(INT) level and dispersion bias remained similar or slightly reduced compared to PBLUPINT and national scenarios. Conclusions International single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds

Klimaatslimme melkveehouderij : een routekaart voor implementatie van mitigatie- en adaptatiemaatregelen

The aim of this study was to describe the challenges faced by the Dutch dairy sector in terms of climate change mitigation and adaptation, and to show possible pathways for implementation of mitigation and adaptation options towards 2030 and 2050. With regard to mitigation, the dairy sector has to comply with targets for mitigation of greenhouse gas emissions in sectoral, national and European legislation. With regard to adaptation, dairy farms are expected to benefit from increasing temperatures and CO2 concentrations, but this may be counteracted by increases in extreme weather events and animal and plant diseases and plagues. A roadmap is shown with phased implementation of mitigation- and adaptation options, based on their effectiveness, costs, readiness for practical implementation, and interaction with other aspects of sustainability

Physical discrimination between human T-lymphocyte subpopulations by means of light scattering, revealing two populations of T8-positive cells

Light-scattering properties of human T-lymphocyte subpopulations selected by immunofluorescence were studied. Based on differences in orthogonal light scattering, two subpopulations of T8-positive cells can be distinguished. The first population (T8a) has the same orthogonal light-scattering properties as T4-positive cells, whereas the orthogonal light scattering of the second population (T8b) was about 70% larger. Orthogonal light scattering of Leu7-positive lymphocytes resembles that of the T8b population. We have studied the occurrence of the subpopulation in healthy individuals and we discuss their possible functional identification. Light-scattering properties of lymphocyte subpopulations in two patients with B-cell chronic lymphatic leukemia suggest that this observation is of clinical interest