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Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat

BACKGROUND: Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes. Understanding these mechanisms is important for breeding cold-resistant wheat cultivars. In this study, we combined three...

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Autores principales: Tchagang, Alain B., Fauteux, François, Tulpan, Dan, Pan, Youlian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356398/
https://www.ncbi.nlm.nih.gov/pubmed/28302069
http://dx.doi.org/10.1186/s12859-017-1596-x
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author Tchagang, Alain B.
Fauteux, François
Tulpan, Dan
Pan, Youlian
author_facet Tchagang, Alain B.
Fauteux, François
Tulpan, Dan
Pan, Youlian
author_sort Tchagang, Alain B.
collection PubMed
description BACKGROUND: Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes. Understanding these mechanisms is important for breeding cold-resistant wheat cultivars. In this study, we combined three computational techniques for the analysis of gene expression data from spring and winter wheat cultivars subjected to low temperature treatments. Our main objective was to construct a comprehensive network of cold response transcriptional events in wheat, and to identify novel cold tolerance candidate genes in wheat. RESULTS: We assigned novel cold stress-related roles to 35 wheat genes, uncovered novel transcription (TF)-gene interactions, and identified 127 genes representing known and novel candidate targets associated with cold tolerance in wheat. Our results also show that delays in terms of activation or repression of the same genes across wheat cultivars play key roles in phenotypic differences among winter and spring wheat cultivars, and adaptation to low temperature stress, cold shock and cold acclimation. CONCLUSIONS: Using three computational approaches, we identified novel putative cold-response genes and TF-gene interactions. These results provide new insights into the complex mechanisms regulating the expression of cold-responsive genes in wheat. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1596-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-53563982017-03-22 Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat Tchagang, Alain B. Fauteux, François Tulpan, Dan Pan, Youlian BMC Bioinformatics Research Article BACKGROUND: Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes. Understanding these mechanisms is important for breeding cold-resistant wheat cultivars. In this study, we combined three computational techniques for the analysis of gene expression data from spring and winter wheat cultivars subjected to low temperature treatments. Our main objective was to construct a comprehensive network of cold response transcriptional events in wheat, and to identify novel cold tolerance candidate genes in wheat. RESULTS: We assigned novel cold stress-related roles to 35 wheat genes, uncovered novel transcription (TF)-gene interactions, and identified 127 genes representing known and novel candidate targets associated with cold tolerance in wheat. Our results also show that delays in terms of activation or repression of the same genes across wheat cultivars play key roles in phenotypic differences among winter and spring wheat cultivars, and adaptation to low temperature stress, cold shock and cold acclimation. CONCLUSIONS: Using three computational approaches, we identified novel putative cold-response genes and TF-gene interactions. These results provide new insights into the complex mechanisms regulating the expression of cold-responsive genes in wheat. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1596-x) contains supplementary material, which is available to authorized users. BioMed Central 2017-03-16 /pmc/articles/PMC5356398/ /pubmed/28302069 http://dx.doi.org/10.1186/s12859-017-1596-x Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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
Tchagang, Alain B.
Fauteux, François
Tulpan, Dan
Pan, Youlian
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
title Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
title_full Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
title_fullStr Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
title_full_unstemmed Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
title_short Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
title_sort bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356398/
https://www.ncbi.nlm.nih.gov/pubmed/28302069
http://dx.doi.org/10.1186/s12859-017-1596-x
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