Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon
Summary Farmed Atlantic salmon ( Salmo salar ) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome‐wide association and genomic prediction can now be impl...
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crwiley:10.1111/age.12513 2024-10-13T14:06:02+00:00 Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon Kijas, J. Elliot, N. Kube, P. Evans, B. Botwright, N. King, H. Primmer, C. R. Verbyla, K. 2016 http://dx.doi.org/10.1111/age.12513 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fage.12513 https://onlinelibrary.wiley.com/doi/pdf/10.1111/age.12513 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Animal Genetics volume 48, issue 2, page 237-241 ISSN 0268-9146 1365-2052 journal-article 2016 crwiley https://doi.org/10.1111/age.12513 2024-09-17T04:52:53Z Summary Farmed Atlantic salmon ( Salmo salar ) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome‐wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNP s in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage disequilibrium ( LD ) and imputation accuracy. Genetic diversity in Tasmanian Atlantic salmon was lower than observed within European populations when compared using four diversity metrics. The distribution of allele frequencies also showed a clear difference, with the Tasmanian animals carrying an excess of low minor allele frequency variants. The strength of observed LD was high at short distances (<25 kb) and remained above background for marker pairs separated by large chromosomal distances (hundreds of kb), in sharp contrast to the European Atlantic salmon tested. Genotypes were used to evaluate the accuracy of imputation from low density (0.5 to 5 K) up to increased density SNP sets (78 K). This revealed high imputation accuracies (0.89–0.97), suggesting that the use of low density SNP sets will be a successful approach for genomic prediction in this population. The long‐range LD , comparatively low genetic diversity and high imputation accuracy in Tasmanian salmon is consistent with known aspects of their population history, which involved a small founding population and an absence of subsequent introgression. The findings of this study represent an important first step towards the design of methods to apply genomics in this economically important population. Article in Journal/Newspaper Atlantic salmon Salmo salar Wiley Online Library Animal Genetics 48 2 237 241 |
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Wiley Online Library |
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English |
description |
Summary Farmed Atlantic salmon ( Salmo salar ) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome‐wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNP s in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage disequilibrium ( LD ) and imputation accuracy. Genetic diversity in Tasmanian Atlantic salmon was lower than observed within European populations when compared using four diversity metrics. The distribution of allele frequencies also showed a clear difference, with the Tasmanian animals carrying an excess of low minor allele frequency variants. The strength of observed LD was high at short distances (<25 kb) and remained above background for marker pairs separated by large chromosomal distances (hundreds of kb), in sharp contrast to the European Atlantic salmon tested. Genotypes were used to evaluate the accuracy of imputation from low density (0.5 to 5 K) up to increased density SNP sets (78 K). This revealed high imputation accuracies (0.89–0.97), suggesting that the use of low density SNP sets will be a successful approach for genomic prediction in this population. The long‐range LD , comparatively low genetic diversity and high imputation accuracy in Tasmanian salmon is consistent with known aspects of their population history, which involved a small founding population and an absence of subsequent introgression. The findings of this study represent an important first step towards the design of methods to apply genomics in this economically important population. |
format |
Article in Journal/Newspaper |
author |
Kijas, J. Elliot, N. Kube, P. Evans, B. Botwright, N. King, H. Primmer, C. R. Verbyla, K. |
spellingShingle |
Kijas, J. Elliot, N. Kube, P. Evans, B. Botwright, N. King, H. Primmer, C. R. Verbyla, K. Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon |
author_facet |
Kijas, J. Elliot, N. Kube, P. Evans, B. Botwright, N. King, H. Primmer, C. R. Verbyla, K. |
author_sort |
Kijas, J. |
title |
Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon |
title_short |
Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon |
title_full |
Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon |
title_fullStr |
Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon |
title_full_unstemmed |
Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon |
title_sort |
diversity and linkage disequilibrium in farmed tasmanian atlantic salmon |
publisher |
Wiley |
publishDate |
2016 |
url |
http://dx.doi.org/10.1111/age.12513 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fage.12513 https://onlinelibrary.wiley.com/doi/pdf/10.1111/age.12513 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Animal Genetics volume 48, issue 2, page 237-241 ISSN 0268-9146 1365-2052 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/age.12513 |
container_title |
Animal Genetics |
container_volume |
48 |
container_issue |
2 |
container_start_page |
237 |
op_container_end_page |
241 |
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1812812066413608960 |