Characterization of the cytokinin-responsive transcriptome in rice

BACKGROUND: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of...

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Autores principales: Raines, Tracy, Blakley, Ivory C., Tsai, Yu-Chang, Worthen, Jennifer M., Franco-Zorrilla, José Manuel, Solano, Roberto, Schaller, G. Eric, Loraine, Ann E., Kieber, Joseph J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146874/
https://www.ncbi.nlm.nih.gov/pubmed/27931185
http://dx.doi.org/10.1186/s12870-016-0932-z
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author Raines, Tracy
Blakley, Ivory C.
Tsai, Yu-Chang
Worthen, Jennifer M.
Franco-Zorrilla, José Manuel
Solano, Roberto
Schaller, G. Eric
Loraine, Ann E.
Kieber, Joseph J.
author_facet Raines, Tracy
Blakley, Ivory C.
Tsai, Yu-Chang
Worthen, Jennifer M.
Franco-Zorrilla, José Manuel
Solano, Roberto
Schaller, G. Eric
Loraine, Ann E.
Kieber, Joseph J.
author_sort Raines, Tracy
collection PubMed
description BACKGROUND: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice. RESULTS: We identified over 4,600 and approximately 2,400 genes differentially expressed in response to cytokinin in roots and shoots respectively. There were some similarities in the sets of cytokinin-regulated genes identified in rice and Arabidopsis, including an up-regulation of genes that act to reduce cytokinin function. Consistent with this, we found that the preferred DNA-binding motif of a rice type-B response regulator is similar to those from Arabidopsis. Analysis of the genes regulated by cytokinin in rice revealed a large number of transcription factors, receptor-like kinases, and genes involved in protein degradation, as well as genes involved in development and the response to biotic stress. Consistent with the over-representation of genes involved in biotic stress, there is a substantial overlap in the genes regulated by cytokinin and those differentially expressed in response to pathogen infection, suggesting that cytokinin plays an integral role in the transcriptional response to pathogens in rice, including the induction of a large number of WRKY transcription factors. CONCLUSIONS: These results begin to unravel the complex gene regulation after cytokinin perception in a crop of agricultural importance and provide insight into the processes and responses modulated by cytokinin in monocots. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0932-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-51468742016-12-15 Characterization of the cytokinin-responsive transcriptome in rice Raines, Tracy Blakley, Ivory C. Tsai, Yu-Chang Worthen, Jennifer M. Franco-Zorrilla, José Manuel Solano, Roberto Schaller, G. Eric Loraine, Ann E. Kieber, Joseph J. BMC Plant Biol Research Article BACKGROUND: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice. RESULTS: We identified over 4,600 and approximately 2,400 genes differentially expressed in response to cytokinin in roots and shoots respectively. There were some similarities in the sets of cytokinin-regulated genes identified in rice and Arabidopsis, including an up-regulation of genes that act to reduce cytokinin function. Consistent with this, we found that the preferred DNA-binding motif of a rice type-B response regulator is similar to those from Arabidopsis. Analysis of the genes regulated by cytokinin in rice revealed a large number of transcription factors, receptor-like kinases, and genes involved in protein degradation, as well as genes involved in development and the response to biotic stress. Consistent with the over-representation of genes involved in biotic stress, there is a substantial overlap in the genes regulated by cytokinin and those differentially expressed in response to pathogen infection, suggesting that cytokinin plays an integral role in the transcriptional response to pathogens in rice, including the induction of a large number of WRKY transcription factors. CONCLUSIONS: These results begin to unravel the complex gene regulation after cytokinin perception in a crop of agricultural importance and provide insight into the processes and responses modulated by cytokinin in monocots. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0932-z) contains supplementary material, which is available to authorized users. BioMed Central 2016-12-08 /pmc/articles/PMC5146874/ /pubmed/27931185 http://dx.doi.org/10.1186/s12870-016-0932-z Text en © The Author(s). 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
Raines, Tracy
Blakley, Ivory C.
Tsai, Yu-Chang
Worthen, Jennifer M.
Franco-Zorrilla, José Manuel
Solano, Roberto
Schaller, G. Eric
Loraine, Ann E.
Kieber, Joseph J.
Characterization of the cytokinin-responsive transcriptome in rice
title Characterization of the cytokinin-responsive transcriptome in rice
title_full Characterization of the cytokinin-responsive transcriptome in rice
title_fullStr Characterization of the cytokinin-responsive transcriptome in rice
title_full_unstemmed Characterization of the cytokinin-responsive transcriptome in rice
title_short Characterization of the cytokinin-responsive transcriptome in rice
title_sort characterization of the cytokinin-responsive transcriptome in rice
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146874/
https://www.ncbi.nlm.nih.gov/pubmed/27931185
http://dx.doi.org/10.1186/s12870-016-0932-z
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