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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
BACKGROUND: International 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 co...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10258954/ https://www.ncbi.nlm.nih.gov/pubmed/37308814 http://dx.doi.org/10.1186/s12711-023-00813-2 |
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author | Bonifazi, Renzo Calus, Mario P. L. ten Napel, Jan Veerkamp, Roel F. Biffani, Stefano Cassandro, Martino Savoia, Simone Vandenplas, Jérémie |
author_facet | Bonifazi, Renzo Calus, Mario P. L. ten Napel, Jan Veerkamp, Roel F. Biffani, Stefano Cassandro, Martino Savoia, Simone Vandenplas, Jérémie |
author_sort | Bonifazi, Renzo |
collection | PubMed |
description | BACKGROUND: International 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 (EBV(INT) and EBV(NAT), 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’ EBV(INT) 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. METHODS: Publishable sires’ international information, i.e. EBV(INT) 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. RESULTS: Overall, 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. CONCLUSIONS: Our 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’ EBV(INT) from pedigree-based or single-step based international beef cattle evaluations into national evaluations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-023-00813-2. |
format | Online Article Text |
id | pubmed-10258954 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-102589542023-06-13 Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population Bonifazi, Renzo Calus, Mario P. L. ten Napel, Jan Veerkamp, Roel F. Biffani, Stefano Cassandro, Martino Savoia, Simone Vandenplas, Jérémie Genet Sel Evol Research Article BACKGROUND: International 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 (EBV(INT) and EBV(NAT), 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’ EBV(INT) 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. METHODS: Publishable sires’ international information, i.e. EBV(INT) 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. RESULTS: Overall, 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. CONCLUSIONS: Our 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’ EBV(INT) from pedigree-based or single-step based international beef cattle evaluations into national evaluations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-023-00813-2. BioMed Central 2023-06-12 /pmc/articles/PMC10258954/ /pubmed/37308814 http://dx.doi.org/10.1186/s12711-023-00813-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Bonifazi, Renzo Calus, Mario P. L. ten Napel, Jan Veerkamp, Roel F. Biffani, Stefano Cassandro, Martino Savoia, Simone Vandenplas, Jérémie Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population |
title | Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population |
title_full | Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population |
title_fullStr | Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population |
title_full_unstemmed | Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population |
title_short | Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population |
title_sort | integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the italian limousin population |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10258954/ https://www.ncbi.nlm.nih.gov/pubmed/37308814 http://dx.doi.org/10.1186/s12711-023-00813-2 |
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