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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4217727?pdf=render |
| _version_ | 1818318517054734336 |
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| author | Agota Fodor Vincent Segura Marie Denis Samuel Neuenschwander Alexandre Fournier-Level Philippe Chatelet Félix Abdel Aziz Homa Thierry Lacombe Patrice This Loic Le Cunff |
| author_facet | Agota Fodor Vincent Segura Marie Denis Samuel Neuenschwander Alexandre Fournier-Level Philippe Chatelet Félix Abdel Aziz Homa Thierry Lacombe Patrice This Loic Le Cunff |
| author_sort | Agota Fodor |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-13T09:54:28Z |
| format | Article |
| id | doaj.art-8be8312f8d6945c890655acb2cf95fe9 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T09:54:28Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-8be8312f8d6945c890655acb2cf95fe92022-12-21T23:51:50ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-01911e11043610.1371/journal.pone.0110436Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine.Agota FodorVincent SeguraMarie DenisSamuel NeuenschwanderAlexandre Fournier-LevelPhilippe ChateletFélix Abdel Aziz HomaThierry LacombePatrice ThisLoic Le CunffNowadays, 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.http://europepmc.org/articles/PMC4217727?pdf=render |
| spellingShingle | Agota Fodor Vincent Segura Marie Denis Samuel Neuenschwander Alexandre Fournier-Level Philippe Chatelet Félix Abdel Aziz Homa Thierry Lacombe Patrice This Loic Le Cunff Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine. PLoS ONE |
| 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 |
| url | http://europepmc.org/articles/PMC4217727?pdf=render |
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