| 1. |
- Michenet, Alexis, et al.
(författare)
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International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight
- 2022
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Ingår i: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 54
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Mohammed Abdallah, Sallam, et al.
(författare)
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Across-countries genomic prediction using national breeding values or multitrait across-countries evaluation breeding values
- 2022
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 105, s. 3282-3295
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Tidskriftsartikel (refereegranskat)abstract
- In across-country genomic predictions for dairy cattle, 2 kinds of bull information can be used as dependent variables. The first is estimated breeding value (EBV) from the national genetic evaluations, assuming genetic correlations between countries are less than 1. The second is EBV from multitrait across-countries evaluation (MACE), assuming genetic correlations between countries equal 1. In the present study, the level of bias and reliability of a cross-countries genomic prediction using national EBV or MACE EBV as the dependent variable were investigated. Data from Brown Swiss Organizations joining the InterGenomics Service by Inter bull Centre (Uppsala, Sweden) were used. National and MACE EBV of 3 traits (protein yield, cow conception rate, and calving interval) from 7, 5, and 4 countries, respectively, were used, resulting in 16 trait-country combinations. Genotypes for 45,473 SNP markers and deregressed (national or MACE) EBV of 7,490; 5,833; and 5,177 bulls were used in analysis of protein yield, cow conception rate, and calving interval, respectively. For most of trait-country combinations, the use of MACE EBV via single-trait approach resulted in less biased and more reliable across-countries genomic predictions. In case some of the MACE EBV might have been inflated, the resulting single-trait genomic predictions were inflated as well. For these specific cases, the use of national EBV via multitrait approach provided less bias and more reliable across-countries genomic predictions.
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| 3. |
- Savoia, Simone
(författare)
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Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population
- 2023
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Ingår i: Genetics Selection Evolution. - 0999-193X .- 1297-9686. ; 55
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 4. |
- Savoia, Simone
(författare)
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Phenotypic and genetic variation of ultraviolet-visible-infrared spectral wavelengths of bovine meat
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Spectroscopic predictions can be used for the genetic improvement of meat quality traits in cattle. No information is however available on the genetics of meat absorbance spectra. This research investigated the phenotypic variation and the heritability of meat absorbance spectra at individual wavelengths in the ultraviolet-visible and near-infrared region (UV-Vis-NIR) obtained with portable spectrometers. Five spectra per instrument were taken on the ribeye surface of 1185 Piemontese young bulls from 93 farms (13,182 Herd-Book pedigree relatives). Linear animal model analyses of 1481 single-wavelengths from UV-Vis-NIRS and 125 from Micro-NIRS were carried out separately. In the overlapping regions, the proportions of phenotypic variance explained by batch/date of slaughter (14 +/- 6% and 17 +/- 7%,), rearing farm (6 +/- 2% and 5 +/- 3%), and the residual variances (72 +/- 10% and 72 +/- 5%) were similar for the UV-Vis-NIRS and Micro-NIRS, but additive genetics (7 +/- 2% and 4 +/- 2%) and heritability (8.3 +/- 2.3% vs 5.1 +/- 0.6%) were greater with the Micro-NIRS. Heritability was much greater for the visible fraction (25.2 +/- 11.4%), especially the violet, blue and green colors, than for the NIR fraction (5.0 +/- 8.0%). These results allow a better understanding of the possibility of using the absorbance of visible and infrared wavelengths correlated with meat quality traits for the genetic improvement in beef cattle.
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