Selective genotyping strategies for a sib test scheme of a broiler breeder program
Abstract Background In broiler breeding, genotype-by-environment interaction is known to result in a genetic correlation between body weight measured in bio-secure and commercial environments that is substantially less than 1. Thus, measuring body weights on sibs of selection candidates in a commerc...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2023-03-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-023-00785-3 |
| _version_ | 1797865811946242048 |
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| author | Charlie A. de Hollander Vivian P. Breen John Henshall Fernando B. Lopes Mario PL. Calus |
| author_facet | Charlie A. de Hollander Vivian P. Breen John Henshall Fernando B. Lopes Mario PL. Calus |
| author_sort | Charlie A. de Hollander |
| collection | DOAJ |
| description | Abstract Background In broiler breeding, genotype-by-environment interaction is known to result in a genetic correlation between body weight measured in bio-secure and commercial environments that is substantially less than 1. Thus, measuring body weights on sibs of selection candidates in a commercial environment and genotyping them could increase genetic progress. Using real data, the aim of this study was to evaluate which genotyping strategy and which proportion of sibs placed in the commercial environment should be genotyped to optimize a sib-testing breeding program in broilers. Phenotypic body weight and genomic information were collected on all sibs raised in a commercial environment, which allowed to retrospectively analyze different sampling strategies and genotyping proportions. Results Accuracies of genomic estimated breeding values (GEBV) obtained with the different genotyping strategies were assessed by computing their correlation with GEBV obtained when all sibs in the commercial environment were genotyped. Results showed that, compared to random sampling (RND), genotyping sibs with extreme phenotypes (EXT) resulted in higher GEBV accuracy across all genotyping proportions, especially for genotyping proportions of 12.5% or 25%, which resulted in correlations of 0.91 vs 0.88 for 12.5% and 0.94 vs 0.91 for 25% genotyped. Including pedigree on birds with phenotype in the commercial environment that were not genotyped increased accuracy at lower genotyping proportions, especially for the RND strategy (correlations of 0.88 vs 0.65 at 12.5% and 0.91 vs 0.80 at 25%), and a smaller but still substantial increase in accuracy for the EXT strategy (0.91 vs 0.79 for 12.5% and 0.94 vs 0.88 for 25% genotyped). Dispersion bias was virtually absent for RND if 25% or more birds were genotyped. However, GEBV were considerably inflated for EXT, especially when the proportion genotyped was low, which was further exacerbated if the pedigree of non-genotyped sibs was excluded. Conclusions When less than 75% of all animals placed in a commercial environment are genotyped, it is recommended to use the EXT strategy, because it yields the highest accuracy. However, caution should be taken when interpreting the resulting GEBV because they will be over-dispersed. When 75% or more of the animals are genotyped, random sampling is recommended because it yields virtually no bias of GEBV and results in similar accuracies as the EXT strategy. |
| first_indexed | 2024-04-09T23:14:52Z |
| format | Article |
| id | doaj.art-0c75314b5e594b818898c2b480849216 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-04-09T23:14:52Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-0c75314b5e594b818898c2b4808492162023-03-22T10:03:30ZdeuBMCGenetics Selection Evolution1297-96862023-03-0155111010.1186/s12711-023-00785-3Selective genotyping strategies for a sib test scheme of a broiler breeder programCharlie A. de Hollander0Vivian P. Breen1John Henshall2Fernando B. Lopes3Mario PL. Calus4Cobb Vantress, IncCobb Vantress, IncCobb Vantress, IncCobb Vantress, IncAnimal Breeding and Genomics, Wageningen University and ResearchAbstract Background In broiler breeding, genotype-by-environment interaction is known to result in a genetic correlation between body weight measured in bio-secure and commercial environments that is substantially less than 1. Thus, measuring body weights on sibs of selection candidates in a commercial environment and genotyping them could increase genetic progress. Using real data, the aim of this study was to evaluate which genotyping strategy and which proportion of sibs placed in the commercial environment should be genotyped to optimize a sib-testing breeding program in broilers. Phenotypic body weight and genomic information were collected on all sibs raised in a commercial environment, which allowed to retrospectively analyze different sampling strategies and genotyping proportions. Results Accuracies of genomic estimated breeding values (GEBV) obtained with the different genotyping strategies were assessed by computing their correlation with GEBV obtained when all sibs in the commercial environment were genotyped. Results showed that, compared to random sampling (RND), genotyping sibs with extreme phenotypes (EXT) resulted in higher GEBV accuracy across all genotyping proportions, especially for genotyping proportions of 12.5% or 25%, which resulted in correlations of 0.91 vs 0.88 for 12.5% and 0.94 vs 0.91 for 25% genotyped. Including pedigree on birds with phenotype in the commercial environment that were not genotyped increased accuracy at lower genotyping proportions, especially for the RND strategy (correlations of 0.88 vs 0.65 at 12.5% and 0.91 vs 0.80 at 25%), and a smaller but still substantial increase in accuracy for the EXT strategy (0.91 vs 0.79 for 12.5% and 0.94 vs 0.88 for 25% genotyped). Dispersion bias was virtually absent for RND if 25% or more birds were genotyped. However, GEBV were considerably inflated for EXT, especially when the proportion genotyped was low, which was further exacerbated if the pedigree of non-genotyped sibs was excluded. Conclusions When less than 75% of all animals placed in a commercial environment are genotyped, it is recommended to use the EXT strategy, because it yields the highest accuracy. However, caution should be taken when interpreting the resulting GEBV because they will be over-dispersed. When 75% or more of the animals are genotyped, random sampling is recommended because it yields virtually no bias of GEBV and results in similar accuracies as the EXT strategy.https://doi.org/10.1186/s12711-023-00785-3 |
| spellingShingle | Charlie A. de Hollander Vivian P. Breen John Henshall Fernando B. Lopes Mario PL. Calus Selective genotyping strategies for a sib test scheme of a broiler breeder program Genetics Selection Evolution |
| title | Selective genotyping strategies for a sib test scheme of a broiler breeder program |
| title_full | Selective genotyping strategies for a sib test scheme of a broiler breeder program |
| title_fullStr | Selective genotyping strategies for a sib test scheme of a broiler breeder program |
| title_full_unstemmed | Selective genotyping strategies for a sib test scheme of a broiler breeder program |
| title_short | Selective genotyping strategies for a sib test scheme of a broiler breeder program |
| title_sort | selective genotyping strategies for a sib test scheme of a broiler breeder program |
| url | https://doi.org/10.1186/s12711-023-00785-3 |
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