Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus
Common full-sib families (c2) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However,...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1081246/full |
| _version_ | 1797962271994937344 |
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| author | Nguyen Thanh Vu Nguyen Thanh Vu Nguyen Thanh Vu Tran Huu Phuc Nguyen Hong Nguyen Nguyen Hong Nguyen Nguyen Van Sang |
| author_facet | Nguyen Thanh Vu Nguyen Thanh Vu Nguyen Thanh Vu Tran Huu Phuc Nguyen Hong Nguyen Nguyen Hong Nguyen Nguyen Van Sang |
| author_sort | Nguyen Thanh Vu |
| collection | DOAJ |
| description | Common full-sib families (c2) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%–130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response. |
| first_indexed | 2024-04-11T01:10:47Z |
| format | Article |
| id | doaj.art-6a3827623963456e975bd332ed39e622 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T01:10:47Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-6a3827623963456e975bd332ed39e6222023-01-04T06:01:55ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011310.3389/fgene.2022.10812461081246Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmusNguyen Thanh Vu0Nguyen Thanh Vu1Nguyen Thanh Vu2Tran Huu Phuc3Nguyen Hong Nguyen4Nguyen Hong Nguyen5Nguyen Van Sang6School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, AustraliaCenter for Bio-Innovation, University of the Sunshine Coast, Maroochydore, QLD, AustraliaResearch Institute for Aquaculture No. 2, Ho Chi Minh City, VietnamResearch Institute for Aquaculture No. 2, Ho Chi Minh City, VietnamSchool of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, AustraliaCenter for Bio-Innovation, University of the Sunshine Coast, Maroochydore, QLD, AustraliaResearch Institute for Aquaculture No. 2, Ho Chi Minh City, VietnamCommon full-sib families (c2) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%–130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response.https://www.frontiersin.org/articles/10.3389/fgene.2022.1081246/fullgenetic improvementgenomic selectiongrowth traitsnon-additive genetic estimates and accuracy of selection responsegenetic lines |
| spellingShingle | Nguyen Thanh Vu Nguyen Thanh Vu Nguyen Thanh Vu Tran Huu Phuc Nguyen Hong Nguyen Nguyen Hong Nguyen Nguyen Van Sang Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus Frontiers in Genetics genetic improvement genomic selection growth traits non-additive genetic estimates and accuracy of selection response genetic lines |
| title | Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus |
| title_full | Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus |
| title_fullStr | Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus |
| title_full_unstemmed | Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus |
| title_short | Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus |
| title_sort | effects of common full sib families on accuracy of genomic prediction for tagging weight in striped catfish pangasianodon hypophthalmus |
| topic | genetic improvement genomic selection growth traits non-additive genetic estimates and accuracy of selection response genetic lines |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1081246/full |
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