Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population
ABSTRACT: The validation of estimated breeding values from single-step genomic BLUP (ssGBLUP) is an important topic, as more and more countries and animal populations are currently changing their genomic prediction to single-step. The objective of this work was to compare different methods to valida...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | Journal of Dairy Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S002203022300543X |
| _version_ | 1797390634645979136 |
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| author | Judith Himmelbauer Hermann Schwarzenbacher Christian Fuerst Birgit Fuerst-Waltl |
| author_facet | Judith Himmelbauer Hermann Schwarzenbacher Christian Fuerst Birgit Fuerst-Waltl |
| author_sort | Judith Himmelbauer |
| collection | DOAJ |
| description | ABSTRACT: The validation of estimated breeding values from single-step genomic BLUP (ssGBLUP) is an important topic, as more and more countries and animal populations are currently changing their genomic prediction to single-step. The objective of this work was to compare different methods to validate single-step genomic breeding values (GEBV). The investigations were carried out using a simulation study based on the German-Austrian-Czech Fleckvieh population. To test the validation methods under different conditions, several biased and unbiased scenarios were simulated. The application of the widely used Interbull GEBV test to the single-step method is only possible to a limited extent, partly because of genomic preselection, which biases conventional estimated breeding values. Alternative validation methods considered in the study are the linear regression method proposed by Legarra and Reverter, the improved genomic validation including additional regressions as suggested by VanRaden and an adaptation of the Interbull GEBV test using daughter yield deviations (DYD) from ssGBLUP instead of pedigree BLUP. The comparison of the different methods for the different scenarios showed that for males the methods based on GEBV estimate the dispersion more accurate and less biased compared with the GEBV test using DYD from ssGBLUP, whereas the standard Interbull GEBV test is highly affected by genomic preselection for males. For females, the GEBV test using yield deviations from ssGBLUP results in better estimations for the true dispersion. |
| first_indexed | 2024-03-08T23:13:45Z |
| format | Article |
| id | doaj.art-b9cb491b5a23478b93d41e67283bd17a |
| institution | Directory Open Access Journal |
| issn | 0022-0302 |
| language | English |
| last_indexed | 2024-03-08T23:13:45Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Dairy Science |
| spelling | doaj.art-b9cb491b5a23478b93d41e67283bd17a2023-12-15T07:22:00ZengElsevierJournal of Dairy Science0022-03022023-12-011061290269043Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle populationJudith Himmelbauer0Hermann Schwarzenbacher1Christian Fuerst2Birgit Fuerst-Waltl3ZuchtData EDV-Dienstleistungen GmbH, 1200 Vienna, Austria; University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; Corresponding authorZuchtData EDV-Dienstleistungen GmbH, 1200 Vienna, AustriaZuchtData EDV-Dienstleistungen GmbH, 1200 Vienna, AustriaUniversity of Natural Resources and Life Sciences, Vienna, 1180 Vienna, AustriaABSTRACT: The validation of estimated breeding values from single-step genomic BLUP (ssGBLUP) is an important topic, as more and more countries and animal populations are currently changing their genomic prediction to single-step. The objective of this work was to compare different methods to validate single-step genomic breeding values (GEBV). The investigations were carried out using a simulation study based on the German-Austrian-Czech Fleckvieh population. To test the validation methods under different conditions, several biased and unbiased scenarios were simulated. The application of the widely used Interbull GEBV test to the single-step method is only possible to a limited extent, partly because of genomic preselection, which biases conventional estimated breeding values. Alternative validation methods considered in the study are the linear regression method proposed by Legarra and Reverter, the improved genomic validation including additional regressions as suggested by VanRaden and an adaptation of the Interbull GEBV test using daughter yield deviations (DYD) from ssGBLUP instead of pedigree BLUP. The comparison of the different methods for the different scenarios showed that for males the methods based on GEBV estimate the dispersion more accurate and less biased compared with the GEBV test using DYD from ssGBLUP, whereas the standard Interbull GEBV test is highly affected by genomic preselection for males. For females, the GEBV test using yield deviations from ssGBLUP results in better estimations for the true dispersion.http://www.sciencedirect.com/science/article/pii/S002203022300543Xgenetic evaluationsingle-step genomic best linear unbiased predictorbias |
| spellingShingle | Judith Himmelbauer Hermann Schwarzenbacher Christian Fuerst Birgit Fuerst-Waltl Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population Journal of Dairy Science genetic evaluation single-step genomic best linear unbiased predictor bias |
| title | Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population |
| title_full | Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population |
| title_fullStr | Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population |
| title_full_unstemmed | Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population |
| title_short | Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population |
| title_sort | comparison of different validation methods for single step genomic evaluations based on a simulated cattle population |
| topic | genetic evaluation single-step genomic best linear unbiased predictor bias |
| url | http://www.sciencedirect.com/science/article/pii/S002203022300543X |
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