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Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine

Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods fo...

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Autores principales: Fodor, Agota, Segura, Vincent, Denis, Marie, Neuenschwander, Samuel, Fournier-Level, Alexandre, Chatelet, Philippe, Homa, Félix Abdel Aziz, Lacombe, Thierry, This, Patrice, Le Cunff, Loic
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217727/
https://www.ncbi.nlm.nih.gov/pubmed/25365338
http://dx.doi.org/10.1371/journal.pone.0110436
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author Fodor, Agota
Segura, Vincent
Denis, Marie
Neuenschwander, Samuel
Fournier-Level, Alexandre
Chatelet, Philippe
Homa, Félix Abdel Aziz
Lacombe, Thierry
This, Patrice
Le Cunff, Loic
author_facet Fodor, Agota
Segura, Vincent
Denis, Marie
Neuenschwander, Samuel
Fournier-Level, Alexandre
Chatelet, Philippe
Homa, Félix Abdel Aziz
Lacombe, Thierry
This, Patrice
Le Cunff, Loic
author_sort Fodor, Agota
collection PubMed
description Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.
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spelling pubmed-42177272014-11-05 Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine Fodor, Agota Segura, Vincent Denis, Marie Neuenschwander, Samuel Fournier-Level, Alexandre Chatelet, Philippe Homa, Félix Abdel Aziz Lacombe, Thierry This, Patrice Le Cunff, Loic PLoS One Research Article Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics. Public Library of Science 2014-11-03 /pmc/articles/PMC4217727/ /pubmed/25365338 http://dx.doi.org/10.1371/journal.pone.0110436 Text en © 2014 Fodor et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Fodor, Agota
Segura, Vincent
Denis, Marie
Neuenschwander, Samuel
Fournier-Level, Alexandre
Chatelet, Philippe
Homa, Félix Abdel Aziz
Lacombe, Thierry
This, Patrice
Le Cunff, Loic
Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine
title Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine
title_full Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine
title_fullStr Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine
title_full_unstemmed Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine
title_short Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine
title_sort genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217727/
https://www.ncbi.nlm.nih.gov/pubmed/25365338
http://dx.doi.org/10.1371/journal.pone.0110436
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