Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon
Genomic selection has a great potential in aquaculture breeding since many important traits are not directly measured on the candidates themselves. However, its implementation has been hindered by staggering genotyping costs because of many individual genotypes. In this study, we explored the potent...
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Online Access: | http://dx.doi.org/10.3389/fgene.2022.896774 https://www.frontiersin.org/articles/10.3389/fgene.2022.896774/full |
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crfrontiers:10.3389/fgene.2022.896774 2024-09-15T17:56:34+00:00 Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon Dagnachew, Binyam Aslam, Muhammad Luqman Hillestad, Borghild Meuwissen, Theo Sonesson, Anna European Commission 2022 http://dx.doi.org/10.3389/fgene.2022.896774 https://www.frontiersin.org/articles/10.3389/fgene.2022.896774/full unknown Frontiers Media SA https://creativecommons.org/licenses/by/4.0/ Frontiers in Genetics volume 13 ISSN 1664-8021 journal-article 2022 crfrontiers https://doi.org/10.3389/fgene.2022.896774 2024-08-20T04:05:28Z Genomic selection has a great potential in aquaculture breeding since many important traits are not directly measured on the candidates themselves. However, its implementation has been hindered by staggering genotyping costs because of many individual genotypes. In this study, we explored the potential of DNA pooling for creating a reference population as a tool for genomic selection of a binary trait. Two datasets from the SalmoBreed population challenged with salmonid alphavirus, which causes pancreas disease, were used. Dataset-1, that includes 855 individuals (478 survivors and 377 dead), was used to develop four DNA pool samples (i.e., 2 pools each for dead and survival). Dataset-2 includes 914 individuals (435 survivors and 479 dead) belonging to 65 full-sibling families and was used to develop in-silico DNA pools. SNP effects from the pool data were calculated based on allele frequencies estimated from the pools and used to calculate genomic breeding values (GEBVs). The correlation between SNP effects estimated based on individual genotypes and pooled data increased from 0.3 to 0.912 when the number of pools increased from 1 to 200. A similar trend was also observed for the correlation between GEBVs, which increased from 0.84 to 0.976, as the number of pools per phenotype increased from 1 to 200. For dataset-1, the accuracy of prediction was 0.71 and 0.70 when the DNA pools were sequenced in 40× and 20×, respectively, compared to an accuracy of 0.73 for the SNP chip genotypes. For dataset-2, the accuracy of prediction increased from 0.574 to 0.691 when the number of in-silico DNA pools increased from 1 to 200. For this dataset, the accuracy of prediction using individual genotypes was 0.712. A limited effect of sequencing depth on the correlation of GEBVs and prediction accuracy was observed. Results showed that a large number of pools are required to achieve as good prediction as individual genotypes; however, alternative effective pooling strategies should be studied to reduce the number of pools ... Article in Journal/Newspaper Atlantic salmon Frontiers (Publisher) Frontiers in Genetics 13 |
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description |
Genomic selection has a great potential in aquaculture breeding since many important traits are not directly measured on the candidates themselves. However, its implementation has been hindered by staggering genotyping costs because of many individual genotypes. In this study, we explored the potential of DNA pooling for creating a reference population as a tool for genomic selection of a binary trait. Two datasets from the SalmoBreed population challenged with salmonid alphavirus, which causes pancreas disease, were used. Dataset-1, that includes 855 individuals (478 survivors and 377 dead), was used to develop four DNA pool samples (i.e., 2 pools each for dead and survival). Dataset-2 includes 914 individuals (435 survivors and 479 dead) belonging to 65 full-sibling families and was used to develop in-silico DNA pools. SNP effects from the pool data were calculated based on allele frequencies estimated from the pools and used to calculate genomic breeding values (GEBVs). The correlation between SNP effects estimated based on individual genotypes and pooled data increased from 0.3 to 0.912 when the number of pools increased from 1 to 200. A similar trend was also observed for the correlation between GEBVs, which increased from 0.84 to 0.976, as the number of pools per phenotype increased from 1 to 200. For dataset-1, the accuracy of prediction was 0.71 and 0.70 when the DNA pools were sequenced in 40× and 20×, respectively, compared to an accuracy of 0.73 for the SNP chip genotypes. For dataset-2, the accuracy of prediction increased from 0.574 to 0.691 when the number of in-silico DNA pools increased from 1 to 200. For this dataset, the accuracy of prediction using individual genotypes was 0.712. A limited effect of sequencing depth on the correlation of GEBVs and prediction accuracy was observed. Results showed that a large number of pools are required to achieve as good prediction as individual genotypes; however, alternative effective pooling strategies should be studied to reduce the number of pools ... |
author2 |
European Commission |
format |
Article in Journal/Newspaper |
author |
Dagnachew, Binyam Aslam, Muhammad Luqman Hillestad, Borghild Meuwissen, Theo Sonesson, Anna |
spellingShingle |
Dagnachew, Binyam Aslam, Muhammad Luqman Hillestad, Borghild Meuwissen, Theo Sonesson, Anna Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon |
author_facet |
Dagnachew, Binyam Aslam, Muhammad Luqman Hillestad, Borghild Meuwissen, Theo Sonesson, Anna |
author_sort |
Dagnachew, Binyam |
title |
Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon |
title_short |
Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon |
title_full |
Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon |
title_fullStr |
Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon |
title_full_unstemmed |
Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon |
title_sort |
use of dna pools of a reference population for genomic selection of a binary trait in atlantic salmon |
publisher |
Frontiers Media SA |
publishDate |
2022 |
url |
http://dx.doi.org/10.3389/fgene.2022.896774 https://www.frontiersin.org/articles/10.3389/fgene.2022.896774/full |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Frontiers in Genetics volume 13 ISSN 1664-8021 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3389/fgene.2022.896774 |
container_title |
Frontiers in Genetics |
container_volume |
13 |
_version_ |
1810432769712455680 |