Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China
Abstract Background At the beginning of genomic selection, some Chinese companies genotyped pigs with different single nucleotide polymorphism (SNP) arrays. The obtained genomic data are then combined and to do this, several imputation strategies have been developed. Usually, only additive genetic e...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | deu |
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BMC
2022-10-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-022-00760-4 |
| _version_ | 1811336457893183488 |
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| author | Quanshun Mei Zulma G. Vitezica Jielin Li Shuhong Zhao Andres Legarra Tao Xiang |
| author_facet | Quanshun Mei Zulma G. Vitezica Jielin Li Shuhong Zhao Andres Legarra Tao Xiang |
| author_sort | Quanshun Mei |
| collection | DOAJ |
| description | Abstract Background At the beginning of genomic selection, some Chinese companies genotyped pigs with different single nucleotide polymorphism (SNP) arrays. The obtained genomic data are then combined and to do this, several imputation strategies have been developed. Usually, only additive genetic effects are considered in genetic evaluations. However, dominance effects that may be important for some traits can be fitted in a mixed linear model as either ‘classical’ or ‘genotypic’ dominance effects. Their influence on genomic evaluation has rarely been studied. Thus, the objectives of this study were to use a dataset from Canadian Yorkshire pigs to (1) compare different strategies to combine data from two SNP arrays (Affymetrix 55K and Illumina 42K) and identify the most appropriate strategy for genomic evaluation and (2) evaluate the impact of dominance effects (classical’ and ‘genotypic’) and inbreeding depression effects on genomic predictive abilities for average daily gain (ADG), backfat thickness (BF), loin muscle depth (LMD), days to 100 kg (AGE100), and the total number of piglets born (TNB) at first parity. Results The reliabilities obtained with the additive genomic models showed that the strategy used to combine data from two SNP arrays had little impact on genomic evaluations. Models with classical or genotypic dominance effect showed similar predictive abilities for all traits. For ADG, BF, LMD, and AGE100, dominance effects accounted for a small proportion (2 to 11%) of the total genetic variance, whereas for TNB, dominance effects accounted for 11 to 20%. For all traits, the predictive abilities of the models increased significantly when genomic inbreeding depression effects were included in the model. However, the inclusion of dominance effects did not change the predictive ability for any trait except for TNB. Conclusions Our study shows that it is feasible to combine data from different SNP arrays for genomic evaluation, and that all combination methods result in similar accuracies. Regardless of how dominance effects are fitted in the genomic model, there is no impact on genetic evaluation. Models including inbreeding depression effects outperform a model with only additive effects, even if the trait is not strongly affected by dominant genes. |
| first_indexed | 2024-04-13T17:39:46Z |
| format | Article |
| id | doaj.art-79c0ec3746384759b636023dc6873d32 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-04-13T17:39:46Z |
| publishDate | 2022-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-79c0ec3746384759b636023dc6873d322022-12-22T02:37:14ZdeuBMCGenetics Selection Evolution1297-96862022-10-0154111210.1186/s12711-022-00760-4Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in ChinaQuanshun Mei0Zulma G. Vitezica1Jielin Li2Shuhong Zhao3Andres Legarra4Tao Xiang5Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityINRAE, INP, UMR 1388 GenPhySEKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityINRAE, INP, UMR 1388 GenPhySEKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityAbstract Background At the beginning of genomic selection, some Chinese companies genotyped pigs with different single nucleotide polymorphism (SNP) arrays. The obtained genomic data are then combined and to do this, several imputation strategies have been developed. Usually, only additive genetic effects are considered in genetic evaluations. However, dominance effects that may be important for some traits can be fitted in a mixed linear model as either ‘classical’ or ‘genotypic’ dominance effects. Their influence on genomic evaluation has rarely been studied. Thus, the objectives of this study were to use a dataset from Canadian Yorkshire pigs to (1) compare different strategies to combine data from two SNP arrays (Affymetrix 55K and Illumina 42K) and identify the most appropriate strategy for genomic evaluation and (2) evaluate the impact of dominance effects (classical’ and ‘genotypic’) and inbreeding depression effects on genomic predictive abilities for average daily gain (ADG), backfat thickness (BF), loin muscle depth (LMD), days to 100 kg (AGE100), and the total number of piglets born (TNB) at first parity. Results The reliabilities obtained with the additive genomic models showed that the strategy used to combine data from two SNP arrays had little impact on genomic evaluations. Models with classical or genotypic dominance effect showed similar predictive abilities for all traits. For ADG, BF, LMD, and AGE100, dominance effects accounted for a small proportion (2 to 11%) of the total genetic variance, whereas for TNB, dominance effects accounted for 11 to 20%. For all traits, the predictive abilities of the models increased significantly when genomic inbreeding depression effects were included in the model. However, the inclusion of dominance effects did not change the predictive ability for any trait except for TNB. Conclusions Our study shows that it is feasible to combine data from different SNP arrays for genomic evaluation, and that all combination methods result in similar accuracies. Regardless of how dominance effects are fitted in the genomic model, there is no impact on genetic evaluation. Models including inbreeding depression effects outperform a model with only additive effects, even if the trait is not strongly affected by dominant genes.https://doi.org/10.1186/s12711-022-00760-4 |
| spellingShingle | Quanshun Mei Zulma G. Vitezica Jielin Li Shuhong Zhao Andres Legarra Tao Xiang Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China Genetics Selection Evolution |
| title | Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China |
| title_full | Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China |
| title_fullStr | Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China |
| title_full_unstemmed | Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China |
| title_short | Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China |
| title_sort | impacts of additive dominance and inbreeding depression effects on genomic evaluation by combining two snp chips in canadian yorkshire pigs bred in china |
| url | https://doi.org/10.1186/s12711-022-00760-4 |
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