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Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.)
BACKGROUND: The main goal of our study was to investigate the implementation, prospects, and limits of marker imputation for quantitative genetic studies contrasting map-independent and map-dependent algorithms. We used a diversity panel consisting of 372 European elite wheat (Triticum aestivum L.)...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364688/ https://www.ncbi.nlm.nih.gov/pubmed/25886991 http://dx.doi.org/10.1186/s12864-015-1366-y |
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author | He, Sang Zhao, Yusheng Mette, M Florian Bothe, Reiner Ebmeyer, Erhard Sharbel, Timothy F Reif, Jochen C Jiang, Yong |
author_facet | He, Sang Zhao, Yusheng Mette, M Florian Bothe, Reiner Ebmeyer, Erhard Sharbel, Timothy F Reif, Jochen C Jiang, Yong |
author_sort | He, Sang |
collection | PubMed |
description | BACKGROUND: The main goal of our study was to investigate the implementation, prospects, and limits of marker imputation for quantitative genetic studies contrasting map-independent and map-dependent algorithms. We used a diversity panel consisting of 372 European elite wheat (Triticum aestivum L.) varieties, which had been genotyped with SNP arrays, and performed intensive simulation studies. RESULTS: Our results clearly showed that imputation accuracy was substantially higher for map-dependent compared to map-independent methods. The accuracy of marker imputation depended strongly on the linkage disequilibrium between the markers in the reference panel and the markers to be imputed. For the decay of linkage disequilibrium present in European wheat, we concluded that around 45,000 markers are needed for low cost, low-density marker profiling. This will facilitate high imputation accuracy, also for rare alleles. Genomic selection and diversity studies profited only marginally from imputing missing values. In contrast, the power of association mapping increased substantially when missing values were imputed. CONCLUSIONS: Imputing missing values is especially of interest for an economic implementation of association mapping in breeding populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1366-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4364688 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-43646882015-03-19 Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.) He, Sang Zhao, Yusheng Mette, M Florian Bothe, Reiner Ebmeyer, Erhard Sharbel, Timothy F Reif, Jochen C Jiang, Yong BMC Genomics Research Article BACKGROUND: The main goal of our study was to investigate the implementation, prospects, and limits of marker imputation for quantitative genetic studies contrasting map-independent and map-dependent algorithms. We used a diversity panel consisting of 372 European elite wheat (Triticum aestivum L.) varieties, which had been genotyped with SNP arrays, and performed intensive simulation studies. RESULTS: Our results clearly showed that imputation accuracy was substantially higher for map-dependent compared to map-independent methods. The accuracy of marker imputation depended strongly on the linkage disequilibrium between the markers in the reference panel and the markers to be imputed. For the decay of linkage disequilibrium present in European wheat, we concluded that around 45,000 markers are needed for low cost, low-density marker profiling. This will facilitate high imputation accuracy, also for rare alleles. Genomic selection and diversity studies profited only marginally from imputing missing values. In contrast, the power of association mapping increased substantially when missing values were imputed. CONCLUSIONS: Imputing missing values is especially of interest for an economic implementation of association mapping in breeding populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1366-y) contains supplementary material, which is available to authorized users. BioMed Central 2015-03-11 /pmc/articles/PMC4364688/ /pubmed/25886991 http://dx.doi.org/10.1186/s12864-015-1366-y Text en © He et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article He, Sang Zhao, Yusheng Mette, M Florian Bothe, Reiner Ebmeyer, Erhard Sharbel, Timothy F Reif, Jochen C Jiang, Yong Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.) |
title | Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.) |
title_full | Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.) |
title_fullStr | Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.) |
title_full_unstemmed | Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.) |
title_short | Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.) |
title_sort | prospects and limits of marker imputation in quantitative genetic studies in european elite wheat (triticum aestivum l.) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364688/ https://www.ncbi.nlm.nih.gov/pubmed/25886991 http://dx.doi.org/10.1186/s12864-015-1366-y |
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