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Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout

Salmonid rickettsial syndrome (SRS), caused by the intracellular bacterium Piscirickettsia salmonis, is one of the main diseases affecting rainbow trout (Oncorhynchus mykiss) farming. To accelerate genetic progress, genomic selection methods can be used as an effective approach to control the diseas...

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Autores principales: Yoshida, Grazyella M., Bangera, Rama, Carvalheiro, Roberto, Correa, Katharina, Figueroa, René, Lhorente, Jean P., Yáñez, José M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5919750/
https://www.ncbi.nlm.nih.gov/pubmed/29255117
http://dx.doi.org/10.1534/g3.117.300499
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author Yoshida, Grazyella M.
Bangera, Rama
Carvalheiro, Roberto
Correa, Katharina
Figueroa, René
Lhorente, Jean P.
Yáñez, José M.
author_facet Yoshida, Grazyella M.
Bangera, Rama
Carvalheiro, Roberto
Correa, Katharina
Figueroa, René
Lhorente, Jean P.
Yáñez, José M.
author_sort Yoshida, Grazyella M.
collection PubMed
description Salmonid rickettsial syndrome (SRS), caused by the intracellular bacterium Piscirickettsia salmonis, is one of the main diseases affecting rainbow trout (Oncorhynchus mykiss) farming. To accelerate genetic progress, genomic selection methods can be used as an effective approach to control the disease. The aims of this study were: (i) to compare the accuracy of estimated breeding values using pedigree-based best linear unbiased prediction (PBLUP) with genomic BLUP (GBLUP), single-step GBLUP (ssGBLUP), Bayes C, and Bayesian Lasso (LASSO); and (ii) to test the accuracy of genomic prediction and PBLUP using different marker densities (0.5, 3, 10, 20, and 27 K) for resistance against P. salmonis in rainbow trout. Phenotypes were recorded as number of days to death (DD) and binary survival (BS) from 2416 fish challenged with P. salmonis. A total of 1934 fish were genotyped using a 57 K single-nucleotide polymorphism (SNP) array. All genomic prediction methods achieved higher accuracies than PBLUP. The relative increase in accuracy for different genomic models ranged from 28 to 41% for both DD and BS at 27 K SNP. Between different genomic models, the highest relative increase in accuracy was obtained with Bayes C (∼40%), where 3 K SNP was enough to achieve a similar accuracy to that of the 27 K SNP for both traits. For resistance against P. salmonis in rainbow trout, we showed that genomic predictions using GBLUP, ssGBLUP, Bayes C, and LASSO can increase accuracy compared with PBLUP. Moreover, it is possible to use relatively low-density SNP panels for genomic prediction without compromising accuracy predictions for resistance against P. salmonis in rainbow trout.
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spelling pubmed-59197502018-04-27 Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout Yoshida, Grazyella M. Bangera, Rama Carvalheiro, Roberto Correa, Katharina Figueroa, René Lhorente, Jean P. Yáñez, José M. G3 (Bethesda) Genomic Selection Salmonid rickettsial syndrome (SRS), caused by the intracellular bacterium Piscirickettsia salmonis, is one of the main diseases affecting rainbow trout (Oncorhynchus mykiss) farming. To accelerate genetic progress, genomic selection methods can be used as an effective approach to control the disease. The aims of this study were: (i) to compare the accuracy of estimated breeding values using pedigree-based best linear unbiased prediction (PBLUP) with genomic BLUP (GBLUP), single-step GBLUP (ssGBLUP), Bayes C, and Bayesian Lasso (LASSO); and (ii) to test the accuracy of genomic prediction and PBLUP using different marker densities (0.5, 3, 10, 20, and 27 K) for resistance against P. salmonis in rainbow trout. Phenotypes were recorded as number of days to death (DD) and binary survival (BS) from 2416 fish challenged with P. salmonis. A total of 1934 fish were genotyped using a 57 K single-nucleotide polymorphism (SNP) array. All genomic prediction methods achieved higher accuracies than PBLUP. The relative increase in accuracy for different genomic models ranged from 28 to 41% for both DD and BS at 27 K SNP. Between different genomic models, the highest relative increase in accuracy was obtained with Bayes C (∼40%), where 3 K SNP was enough to achieve a similar accuracy to that of the 27 K SNP for both traits. For resistance against P. salmonis in rainbow trout, we showed that genomic predictions using GBLUP, ssGBLUP, Bayes C, and LASSO can increase accuracy compared with PBLUP. Moreover, it is possible to use relatively low-density SNP panels for genomic prediction without compromising accuracy predictions for resistance against P. salmonis in rainbow trout. Genetics Society of America 2017-12-18 /pmc/articles/PMC5919750/ /pubmed/29255117 http://dx.doi.org/10.1534/g3.117.300499 Text en Copyright © 2018 Yoshida et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genomic Selection
Yoshida, Grazyella M.
Bangera, Rama
Carvalheiro, Roberto
Correa, Katharina
Figueroa, René
Lhorente, Jean P.
Yáñez, José M.
Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout
title Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout
title_full Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout
title_fullStr Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout
title_full_unstemmed Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout
title_short Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout
title_sort genomic prediction accuracy for resistance against piscirickettsia salmonis in farmed rainbow trout
topic Genomic Selection
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5919750/
https://www.ncbi.nlm.nih.gov/pubmed/29255117
http://dx.doi.org/10.1534/g3.117.300499
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