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Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

BACKGROUND: WRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to stresses. Broomcorn millet is one of the most important crops in drought areas wor...

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Autores principales: Yue, Hong, Wang, Meng, Liu, Siyan, Du, Xianghong, Song, Weining, Nie, Xiaojun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862231/
https://www.ncbi.nlm.nih.gov/pubmed/27165545
http://dx.doi.org/10.1186/s12864-016-2677-3
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author Yue, Hong
Wang, Meng
Liu, Siyan
Du, Xianghong
Song, Weining
Nie, Xiaojun
author_facet Yue, Hong
Wang, Meng
Liu, Siyan
Du, Xianghong
Song, Weining
Nie, Xiaojun
author_sort Yue, Hong
collection PubMed
description BACKGROUND: WRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to stresses. Broomcorn millet is one of the most important crops in drought areas worldwide. However, the WRKY gene family in broomcorn millet remains unknown. RESULTS: A total of 32 PmWRKY genes were identified in this study using computational prediction method. Structural analysis found that PmWRKY proteins contained a highly conserved motif WRKYGQK and two common variant motifs, namely WRKYGKK and WRKYGEK. Phylogenetic analysis of PmWRKYs together with the homologous genes from the representative species could classify them into three groups, with the number of 1, 15, and 16, respectively. Finally, the transcriptional profiles of these 32 PmWRKY genes in various tissues or under different abiotic stresses were systematically investigated using qRT-PCR analysis. Results showed that the expression level of 22 PmWRKY genes varied significantly under one or more abiotic stress treatments, which could be defined as abiotic stress-responsive genes. CONCLUSIONS: This was the first study to identify the organization and transcriptional profiles of PmWRKY genes, which not only facilitates the functional analysis of the PmWRKY genes, and also lays the foundation to reveal the molecular mechanism of stress tolerance in this important crop. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2677-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-48622312016-05-11 Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.) Yue, Hong Wang, Meng Liu, Siyan Du, Xianghong Song, Weining Nie, Xiaojun BMC Genomics Research Article BACKGROUND: WRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to stresses. Broomcorn millet is one of the most important crops in drought areas worldwide. However, the WRKY gene family in broomcorn millet remains unknown. RESULTS: A total of 32 PmWRKY genes were identified in this study using computational prediction method. Structural analysis found that PmWRKY proteins contained a highly conserved motif WRKYGQK and two common variant motifs, namely WRKYGKK and WRKYGEK. Phylogenetic analysis of PmWRKYs together with the homologous genes from the representative species could classify them into three groups, with the number of 1, 15, and 16, respectively. Finally, the transcriptional profiles of these 32 PmWRKY genes in various tissues or under different abiotic stresses were systematically investigated using qRT-PCR analysis. Results showed that the expression level of 22 PmWRKY genes varied significantly under one or more abiotic stress treatments, which could be defined as abiotic stress-responsive genes. CONCLUSIONS: This was the first study to identify the organization and transcriptional profiles of PmWRKY genes, which not only facilitates the functional analysis of the PmWRKY genes, and also lays the foundation to reveal the molecular mechanism of stress tolerance in this important crop. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2677-3) contains supplementary material, which is available to authorized users. BioMed Central 2016-05-10 /pmc/articles/PMC4862231/ /pubmed/27165545 http://dx.doi.org/10.1186/s12864-016-2677-3 Text en © Yue et al. 2016 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
Yue, Hong
Wang, Meng
Liu, Siyan
Du, Xianghong
Song, Weining
Nie, Xiaojun
Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)
title Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)
title_full Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)
title_fullStr Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)
title_full_unstemmed Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)
title_short Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)
title_sort transcriptome-wide identification and expression profiles of the wrky transcription factor family in broomcorn millet (panicum miliaceum l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862231/
https://www.ncbi.nlm.nih.gov/pubmed/27165545
http://dx.doi.org/10.1186/s12864-016-2677-3
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