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A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values

BACKGROUND: Genomic selection can increase genetic gain within aquaculture breeding programs, but the high costs related to high-density genotyping of a large number of individuals would make the breeding program expensive. In this study, a low-cost method using low-density genotyping of pre-selecte...

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Autores principales: Lillehammer, Marie, Meuwissen, Theo H E, Sonesson, Anna K
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854107/
https://www.ncbi.nlm.nih.gov/pubmed/24127852
http://dx.doi.org/10.1186/1297-9686-45-39
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author Lillehammer, Marie
Meuwissen, Theo H E
Sonesson, Anna K
author_facet Lillehammer, Marie
Meuwissen, Theo H E
Sonesson, Anna K
author_sort Lillehammer, Marie
collection PubMed
description BACKGROUND: Genomic selection can increase genetic gain within aquaculture breeding programs, but the high costs related to high-density genotyping of a large number of individuals would make the breeding program expensive. In this study, a low-cost method using low-density genotyping of pre-selected candidates and their sibs was evaluated by stochastic simulation. METHODS: A breeding scheme with selection for two traits, one measured on candidates and one on sibs was simulated. Genomic breeding values were estimated within families and combined with conventional family breeding values for candidates that were pre-selected based on conventional BLUP breeding values. This strategy was compared with a conventional breeding scheme and a full genomic selection program for which genomic breeding values were estimated across the whole population. The effects of marker density, level of pre-selection and number of sibs tested and genotyped for the sib-trait were studied. RESULTS: Within-family genomic breeding values increased genetic gain by 15% and reduced rate of inbreeding by 15%. Genetic gain was robust to a reduction in marker density, with only moderate reductions, even for very low densities. Pre-selection of candidates down to approximately 10% of the candidates before genotyping also had minor effects on genetic gain, but depended somewhat on marker density. The number of test-individuals, i.e. individuals tested for the sib-trait, affected genetic gain, but the fraction of the test-individuals genotyped only affected the relative contribution of each trait to genetic gain. CONCLUSIONS: A combination of genomic within-family breeding values, based on low-density genotyping, and conventional BLUP family breeding values was shown to be a possible low marker density implementation of genomic selection for species with large full-sib families for which the costs of genotyping must be kept low without compromising the effect of genomic selection on genetic gain.
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spelling pubmed-38541072013-12-16 A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values Lillehammer, Marie Meuwissen, Theo H E Sonesson, Anna K Genet Sel Evol Research BACKGROUND: Genomic selection can increase genetic gain within aquaculture breeding programs, but the high costs related to high-density genotyping of a large number of individuals would make the breeding program expensive. In this study, a low-cost method using low-density genotyping of pre-selected candidates and their sibs was evaluated by stochastic simulation. METHODS: A breeding scheme with selection for two traits, one measured on candidates and one on sibs was simulated. Genomic breeding values were estimated within families and combined with conventional family breeding values for candidates that were pre-selected based on conventional BLUP breeding values. This strategy was compared with a conventional breeding scheme and a full genomic selection program for which genomic breeding values were estimated across the whole population. The effects of marker density, level of pre-selection and number of sibs tested and genotyped for the sib-trait were studied. RESULTS: Within-family genomic breeding values increased genetic gain by 15% and reduced rate of inbreeding by 15%. Genetic gain was robust to a reduction in marker density, with only moderate reductions, even for very low densities. Pre-selection of candidates down to approximately 10% of the candidates before genotyping also had minor effects on genetic gain, but depended somewhat on marker density. The number of test-individuals, i.e. individuals tested for the sib-trait, affected genetic gain, but the fraction of the test-individuals genotyped only affected the relative contribution of each trait to genetic gain. CONCLUSIONS: A combination of genomic within-family breeding values, based on low-density genotyping, and conventional BLUP family breeding values was shown to be a possible low marker density implementation of genomic selection for species with large full-sib families for which the costs of genotyping must be kept low without compromising the effect of genomic selection on genetic gain. BioMed Central 2013-10-15 /pmc/articles/PMC3854107/ /pubmed/24127852 http://dx.doi.org/10.1186/1297-9686-45-39 Text en Copyright © 2013 Lillehammer et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Lillehammer, Marie
Meuwissen, Theo H E
Sonesson, Anna K
A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values
title A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values
title_full A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values
title_fullStr A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values
title_full_unstemmed A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values
title_short A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values
title_sort low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854107/
https://www.ncbi.nlm.nih.gov/pubmed/24127852
http://dx.doi.org/10.1186/1297-9686-45-39
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