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Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle
BACKGROUND: The success of genomic selection depends mainly on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), the number of animals in the training set (TS) and the heritability (h(2)) of the trait. The extent of LD depends on the genetic structure of th...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224120/ https://www.ncbi.nlm.nih.gov/pubmed/21933416 http://dx.doi.org/10.1186/1471-2156-12-80 |
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author | Brito, Fernanda V Neto, José Braccini Sargolzaei, Mehdi Cobuci, Jaime A Schenkel, Flavio S |
author_facet | Brito, Fernanda V Neto, José Braccini Sargolzaei, Mehdi Cobuci, Jaime A Schenkel, Flavio S |
author_sort | Brito, Fernanda V |
collection | PubMed |
description | BACKGROUND: The success of genomic selection depends mainly on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), the number of animals in the training set (TS) and the heritability (h(2)) of the trait. The extent of LD depends on the genetic structure of the population and the density of markers. The aim of this study was to calculate accuracy of direct genomic estimated breeding values (DGEBV) using best linear unbiased genomic prediction (GBLUP) for different marker densities, heritabilities and sizes of the TS in simulated populations that mimicked previously reported extent and pattern of LD in beef cattle. RESULTS: The accuracy of DGEBV increased significantly (p < 0.05) with the increase in the number of bulls in the TS (480, 960 or 1920), trait h(2 )(0.10, 0.25 or 0.40) and marker densities (40 k or 800 k). Increasing the number of animals in the TS by 4-fold and using their phenotypes to estimate marker effects was not sufficient to maintain or increase the accuracy of DGEBV obtained using estimated breeding values (EBVs) when the trait h(2 )was lower than 0.40 for both marker densities. Comparing to expected accuracies of parent average (PA), the gains by using DGEBV would be of 27%, 13% and 10% for trait h(2 )equal to 0.10, 0.25 and 0.40, respectively, considering the scenario with 40 k markers and 1920 bulls in TS. CONCLUSIONS: As reported in dairy cattle, the size of the TS and the extent of LD have major impact on the accuracy of DGEBV. Based on the findings of this simulation study, large TS, as well as dense marker panels, aiming to increase the level of LD between markers and QTL, will likely be needed in beef cattle for successful implementation of genomic selection. |
format | Online Article Text |
id | pubmed-3224120 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32241202011-11-30 Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle Brito, Fernanda V Neto, José Braccini Sargolzaei, Mehdi Cobuci, Jaime A Schenkel, Flavio S BMC Genet Research Article BACKGROUND: The success of genomic selection depends mainly on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), the number of animals in the training set (TS) and the heritability (h(2)) of the trait. The extent of LD depends on the genetic structure of the population and the density of markers. The aim of this study was to calculate accuracy of direct genomic estimated breeding values (DGEBV) using best linear unbiased genomic prediction (GBLUP) for different marker densities, heritabilities and sizes of the TS in simulated populations that mimicked previously reported extent and pattern of LD in beef cattle. RESULTS: The accuracy of DGEBV increased significantly (p < 0.05) with the increase in the number of bulls in the TS (480, 960 or 1920), trait h(2 )(0.10, 0.25 or 0.40) and marker densities (40 k or 800 k). Increasing the number of animals in the TS by 4-fold and using their phenotypes to estimate marker effects was not sufficient to maintain or increase the accuracy of DGEBV obtained using estimated breeding values (EBVs) when the trait h(2 )was lower than 0.40 for both marker densities. Comparing to expected accuracies of parent average (PA), the gains by using DGEBV would be of 27%, 13% and 10% for trait h(2 )equal to 0.10, 0.25 and 0.40, respectively, considering the scenario with 40 k markers and 1920 bulls in TS. CONCLUSIONS: As reported in dairy cattle, the size of the TS and the extent of LD have major impact on the accuracy of DGEBV. Based on the findings of this simulation study, large TS, as well as dense marker panels, aiming to increase the level of LD between markers and QTL, will likely be needed in beef cattle for successful implementation of genomic selection. BioMed Central 2011-09-20 /pmc/articles/PMC3224120/ /pubmed/21933416 http://dx.doi.org/10.1186/1471-2156-12-80 Text en Copyright ©2011 Brito 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 Article Brito, Fernanda V Neto, José Braccini Sargolzaei, Mehdi Cobuci, Jaime A Schenkel, Flavio S Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle |
title | Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle |
title_full | Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle |
title_fullStr | Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle |
title_full_unstemmed | Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle |
title_short | Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle |
title_sort | accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224120/ https://www.ncbi.nlm.nih.gov/pubmed/21933416 http://dx.doi.org/10.1186/1471-2156-12-80 |
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