Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings
Abstract Background The gilthead sea bream (Sparus aurata) has long been considered resistant to viral nervous necrosis (VNN), until recently, when significant mortalities caused by a reassortant nervous necrosis virus (NNV) strain were reported. Selective breeding to enhance resistance against NNV...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2023-04-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-023-00796-0 |
| _version_ | 1797850215418429440 |
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| author | Sara Faggion Paolo Carnier Rafaella Franch Massimiliano Babbucci Francesco Pascoli Giulia Dalla Rovere Massimo Caggiano Hervé Chavanne Anna Toffan Luca Bargelloni |
| author_facet | Sara Faggion Paolo Carnier Rafaella Franch Massimiliano Babbucci Francesco Pascoli Giulia Dalla Rovere Massimo Caggiano Hervé Chavanne Anna Toffan Luca Bargelloni |
| author_sort | Sara Faggion |
| collection | DOAJ |
| description | Abstract Background The gilthead sea bream (Sparus aurata) has long been considered resistant to viral nervous necrosis (VNN), until recently, when significant mortalities caused by a reassortant nervous necrosis virus (NNV) strain were reported. Selective breeding to enhance resistance against NNV might be a preventive action. In this study, 972 sea bream larvae were subjected to a NNV challenge test and the symptomatology was recorded. All the experimental fish and their parents were genotyped using a genome-wide single nucleotide polymorphism (SNP) array consisting of over 26,000 markers. Results Estimates of pedigree-based and genomic heritabilities of VNN symptomatology were consistent with each other (0.21, highest posterior density interval at 95% (HPD95%): 0.1–0.4; 0.19, HPD95%: 0.1–0.3, respectively). The genome-wide association study suggested one genomic region, i.e., in linkage group (LG) 23 that might be involved in sea bream VNN resistance, although it was far from the genome-wide significance threshold. The accuracies (r) of the predicted estimated breeding values (EBV) provided by three Bayesian genomic regression models (Bayes B, Bayes C, and Ridge Regression) were consistent and on average were equal to 0.90 when assessed in a set of cross-validation (CV) procedures. When genomic relationships between training and testing sets were minimized, accuracy decreased greatly (r = 0.53 for a validation based on genomic clustering, r = 0.12 for a validation based on a leave-one-family-out approach focused on the parents of the challenged fish). Classification of the phenotype using the genomic predictions of the phenotype or using the genomic predictions of the pedigree-based, all data included, EBV as classifiers was moderately accurate (area under the ROC curve 0.60 and 0.66, respectively). Conclusions The estimate of the heritability for VNN symptomatology indicates that it is feasible to implement selective breeding programs for increased resistance to VNN of sea bream larvae/juveniles. Exploiting genomic information offers the opportunity of developing prediction tools for VNN resistance, and genomic models can be trained on EBV using all data or phenotypes, with minimal differences in classification performance of the trait phenotype. In a long-term view, the weakening of the genomic ties between animals in the training and test sets leads to decreased genomic prediction accuracies, thus periodical update of the reference population with new data is mandatory. |
| first_indexed | 2024-04-09T18:56:47Z |
| format | Article |
| id | doaj.art-213f1521814d4111a02ec1e062b5f398 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-04-09T18:56:47Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-213f1521814d4111a02ec1e062b5f3982023-04-09T11:06:18ZdeuBMCGenetics Selection Evolution1297-96862023-04-0155111210.1186/s12711-023-00796-0Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settingsSara Faggion0Paolo Carnier1Rafaella Franch2Massimiliano Babbucci3Francesco Pascoli4Giulia Dalla Rovere5Massimo Caggiano6Hervé Chavanne7Anna Toffan8Luca Bargelloni9Department of Comparative Biomedicine and Food Science, University of PadovaDepartment of Comparative Biomedicine and Food Science, University of PadovaDepartment of Comparative Biomedicine and Food Science, University of PadovaDepartment of Comparative Biomedicine and Food Science, University of PadovaDivision of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe)Department of Comparative Biomedicine and Food Science, University of PadovaPanittica Italia Società Agricola S.R.L.Panittica Italia Società Agricola S.R.L.Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe)Department of Comparative Biomedicine and Food Science, University of PadovaAbstract Background The gilthead sea bream (Sparus aurata) has long been considered resistant to viral nervous necrosis (VNN), until recently, when significant mortalities caused by a reassortant nervous necrosis virus (NNV) strain were reported. Selective breeding to enhance resistance against NNV might be a preventive action. In this study, 972 sea bream larvae were subjected to a NNV challenge test and the symptomatology was recorded. All the experimental fish and their parents were genotyped using a genome-wide single nucleotide polymorphism (SNP) array consisting of over 26,000 markers. Results Estimates of pedigree-based and genomic heritabilities of VNN symptomatology were consistent with each other (0.21, highest posterior density interval at 95% (HPD95%): 0.1–0.4; 0.19, HPD95%: 0.1–0.3, respectively). The genome-wide association study suggested one genomic region, i.e., in linkage group (LG) 23 that might be involved in sea bream VNN resistance, although it was far from the genome-wide significance threshold. The accuracies (r) of the predicted estimated breeding values (EBV) provided by three Bayesian genomic regression models (Bayes B, Bayes C, and Ridge Regression) were consistent and on average were equal to 0.90 when assessed in a set of cross-validation (CV) procedures. When genomic relationships between training and testing sets were minimized, accuracy decreased greatly (r = 0.53 for a validation based on genomic clustering, r = 0.12 for a validation based on a leave-one-family-out approach focused on the parents of the challenged fish). Classification of the phenotype using the genomic predictions of the phenotype or using the genomic predictions of the pedigree-based, all data included, EBV as classifiers was moderately accurate (area under the ROC curve 0.60 and 0.66, respectively). Conclusions The estimate of the heritability for VNN symptomatology indicates that it is feasible to implement selective breeding programs for increased resistance to VNN of sea bream larvae/juveniles. Exploiting genomic information offers the opportunity of developing prediction tools for VNN resistance, and genomic models can be trained on EBV using all data or phenotypes, with minimal differences in classification performance of the trait phenotype. In a long-term view, the weakening of the genomic ties between animals in the training and test sets leads to decreased genomic prediction accuracies, thus periodical update of the reference population with new data is mandatory.https://doi.org/10.1186/s12711-023-00796-0 |
| spellingShingle | Sara Faggion Paolo Carnier Rafaella Franch Massimiliano Babbucci Francesco Pascoli Giulia Dalla Rovere Massimo Caggiano Hervé Chavanne Anna Toffan Luca Bargelloni Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings Genetics Selection Evolution |
| title | Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings |
| title_full | Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings |
| title_fullStr | Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings |
| title_full_unstemmed | Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings |
| title_short | Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings |
| title_sort | viral nervous necrosis resistance in gilthead sea bream sparus aurata at the larval stage heritability and accuracy of genomic prediction with different training and testing settings |
| url | https://doi.org/10.1186/s12711-023-00796-0 |
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