Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf
Genomic selection can accelerate genetic progress in aquaculture breeding programmes, particularly for traits measured on siblings of selection candidates. However, it is not widely implemented in most aquaculture species, and remains expensive due to high genotyping costs. Genotype imputation is a...
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ftfrontimediafig:oai:figshare.com:article/22810124 2024-09-15T17:56:35+00:00 Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf Christina Kriaridou Smaragda Tsairidou Clémence Fraslin Gregor Gorjanc Mark E. Looseley Ian A. Johnston Ross D. Houston Diego Robledo 2023-05-12T06:40:24Z https://doi.org/10.3389/fgene.2023.1194266.s001 https://figshare.com/articles/figure/Image1_Evaluation_of_low-density_SNP_panels_and_imputation_for_cost-effective_genomic_selection_in_four_aquaculture_species_pdf/22810124 unknown doi:10.3389/fgene.2023.1194266.s001 https://figshare.com/articles/figure/Image1_Evaluation_of_low-density_SNP_panels_and_imputation_for_cost-effective_genomic_selection_in_four_aquaculture_species_pdf/22810124 CC BY 4.0 Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy selective breeding imputation genomic prediction aquaculture fish bivalve Image Figure 2023 ftfrontimediafig https://doi.org/10.3389/fgene.2023.1194266.s001 2024-08-19T06:19:56Z Genomic selection can accelerate genetic progress in aquaculture breeding programmes, particularly for traits measured on siblings of selection candidates. However, it is not widely implemented in most aquaculture species, and remains expensive due to high genotyping costs. Genotype imputation is a promising strategy that can reduce genotyping costs and facilitate the broader uptake of genomic selection in aquaculture breeding programmes. Genotype imputation can predict ungenotyped SNPs in populations genotyped at a low-density (LD), using a reference population genotyped at a high-density (HD). In this study, we used datasets of four aquaculture species (Atlantic salmon, turbot, common carp and Pacific oyster), phenotyped for different traits, to investigate the efficacy of genotype imputation for cost-effective genomic selection. The four datasets had been genotyped at HD, and eight LD panels (300–6,000 SNPs) were generated in silico. SNPs were selected to be: i) evenly distributed according to physical position ii) selected to minimise the linkage disequilibrium between adjacent SNPs or iii) randomly selected. Imputation was performed with three different software packages (AlphaImpute2, FImpute v.3 and findhap v.4). The results revealed that FImpute v.3 was faster and achieved higher imputation accuracies. Imputation accuracy increased with increasing panel density for both SNP selection methods, reaching correlations greater than 0.95 in the three fish species and 0.80 in Pacific oyster. In terms of genomic prediction accuracy, the LD and the imputed panels performed similarly, reaching values very close to the HD panels, except in the pacific oyster dataset, where the LD panel performed better than the imputed panel. In the fish species, when LD panels were used for genomic prediction without imputation, selection of markers based on either physical or genetic distance (instead of randomly) resulted in a high prediction accuracy, whereas imputation achieved near maximal prediction accuracy independently of ... Still Image Atlantic salmon Pacific oyster Turbot Frontiers: Figshare |
institution |
Open Polar |
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Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy selective breeding imputation genomic prediction aquaculture fish bivalve |
spellingShingle |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy selective breeding imputation genomic prediction aquaculture fish bivalve Christina Kriaridou Smaragda Tsairidou Clémence Fraslin Gregor Gorjanc Mark E. Looseley Ian A. Johnston Ross D. Houston Diego Robledo Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf |
topic_facet |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy selective breeding imputation genomic prediction aquaculture fish bivalve |
description |
Genomic selection can accelerate genetic progress in aquaculture breeding programmes, particularly for traits measured on siblings of selection candidates. However, it is not widely implemented in most aquaculture species, and remains expensive due to high genotyping costs. Genotype imputation is a promising strategy that can reduce genotyping costs and facilitate the broader uptake of genomic selection in aquaculture breeding programmes. Genotype imputation can predict ungenotyped SNPs in populations genotyped at a low-density (LD), using a reference population genotyped at a high-density (HD). In this study, we used datasets of four aquaculture species (Atlantic salmon, turbot, common carp and Pacific oyster), phenotyped for different traits, to investigate the efficacy of genotype imputation for cost-effective genomic selection. The four datasets had been genotyped at HD, and eight LD panels (300–6,000 SNPs) were generated in silico. SNPs were selected to be: i) evenly distributed according to physical position ii) selected to minimise the linkage disequilibrium between adjacent SNPs or iii) randomly selected. Imputation was performed with three different software packages (AlphaImpute2, FImpute v.3 and findhap v.4). The results revealed that FImpute v.3 was faster and achieved higher imputation accuracies. Imputation accuracy increased with increasing panel density for both SNP selection methods, reaching correlations greater than 0.95 in the three fish species and 0.80 in Pacific oyster. In terms of genomic prediction accuracy, the LD and the imputed panels performed similarly, reaching values very close to the HD panels, except in the pacific oyster dataset, where the LD panel performed better than the imputed panel. In the fish species, when LD panels were used for genomic prediction without imputation, selection of markers based on either physical or genetic distance (instead of randomly) resulted in a high prediction accuracy, whereas imputation achieved near maximal prediction accuracy independently of ... |
format |
Still Image |
author |
Christina Kriaridou Smaragda Tsairidou Clémence Fraslin Gregor Gorjanc Mark E. Looseley Ian A. Johnston Ross D. Houston Diego Robledo |
author_facet |
Christina Kriaridou Smaragda Tsairidou Clémence Fraslin Gregor Gorjanc Mark E. Looseley Ian A. Johnston Ross D. Houston Diego Robledo |
author_sort |
Christina Kriaridou |
title |
Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf |
title_short |
Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf |
title_full |
Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf |
title_fullStr |
Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf |
title_full_unstemmed |
Image1_Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.pdf |
title_sort |
image1_evaluation of low-density snp panels and imputation for cost-effective genomic selection in four aquaculture species.pdf |
publishDate |
2023 |
url |
https://doi.org/10.3389/fgene.2023.1194266.s001 https://figshare.com/articles/figure/Image1_Evaluation_of_low-density_SNP_panels_and_imputation_for_cost-effective_genomic_selection_in_four_aquaculture_species_pdf/22810124 |
genre |
Atlantic salmon Pacific oyster Turbot |
genre_facet |
Atlantic salmon Pacific oyster Turbot |
op_relation |
doi:10.3389/fgene.2023.1194266.s001 https://figshare.com/articles/figure/Image1_Evaluation_of_low-density_SNP_panels_and_imputation_for_cost-effective_genomic_selection_in_four_aquaculture_species_pdf/22810124 |
op_rights |
CC BY 4.0 |
op_doi |
https://doi.org/10.3389/fgene.2023.1194266.s001 |
_version_ |
1810432775068581888 |