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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.)...

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Autores principales: He, Sang, Zhao, Yusheng, Mette, M Florian, Bothe, Reiner, Ebmeyer, Erhard, Sharbel, Timothy F, Reif, Jochen C, Jiang, Yong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
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.
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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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