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Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

BACKGROUND: Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying...

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Autores principales: Chen, Rongfa, Fan, Yegeng, Zhou, Huiwen, Mo, Shanping, Zhou, Zhongfeng, Yan, Haifeng, Luo, Ting, Huang, Xing, Weng, Mengling, Lakshmanan, Prakash, Li, Yangrui, Qiu, Lihang, Wu, Jianming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7831198/
https://www.ncbi.nlm.nih.gov/pubmed/33494722
http://dx.doi.org/10.1186/s12864-020-07352-w
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author Chen, Rongfa
Fan, Yegeng
Zhou, Huiwen
Mo, Shanping
Zhou, Zhongfeng
Yan, Haifeng
Luo, Ting
Huang, Xing
Weng, Mengling
Lakshmanan, Prakash
Li, Yangrui
Qiu, Lihang
Wu, Jianming
author_facet Chen, Rongfa
Fan, Yegeng
Zhou, Huiwen
Mo, Shanping
Zhou, Zhongfeng
Yan, Haifeng
Luo, Ting
Huang, Xing
Weng, Mengling
Lakshmanan, Prakash
Li, Yangrui
Qiu, Lihang
Wu, Jianming
author_sort Chen, Rongfa
collection PubMed
description BACKGROUND: Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. RESULTS: In the present study, we first obtained high-quality long transcripts from the internodes of sugarcane using the PacBio Sequel System. A total of 72,671 isoforms, with N50 at 3073, were generated. These long isoforms were used as a reference for the subsequent RNA-seq. Afterwards, short reads generated from the Illumina HiSeq 4000 platform were used to compare the differentially expressed genes in both the DPC and the control groups. Transcriptome profiling showed that most significant gene changes occurred after six days post DPC treatment. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating that DPC affected multiple pathways, in addition to suppressing gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the 36 constructed modules, the top positive correlated module, at the stage of six days post spraying DPC, was sienna3. Notably, Stf0 sulfotransferase, cyclin-like F-box, and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. Furthermore, the qPCR validated the high accuracy of the RNA-seq results. CONCLUSION: Taken together, we have demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07352-w.
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spelling pubmed-78311982021-01-26 Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride Chen, Rongfa Fan, Yegeng Zhou, Huiwen Mo, Shanping Zhou, Zhongfeng Yan, Haifeng Luo, Ting Huang, Xing Weng, Mengling Lakshmanan, Prakash Li, Yangrui Qiu, Lihang Wu, Jianming BMC Genomics Research Article BACKGROUND: Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. RESULTS: In the present study, we first obtained high-quality long transcripts from the internodes of sugarcane using the PacBio Sequel System. A total of 72,671 isoforms, with N50 at 3073, were generated. These long isoforms were used as a reference for the subsequent RNA-seq. Afterwards, short reads generated from the Illumina HiSeq 4000 platform were used to compare the differentially expressed genes in both the DPC and the control groups. Transcriptome profiling showed that most significant gene changes occurred after six days post DPC treatment. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating that DPC affected multiple pathways, in addition to suppressing gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the 36 constructed modules, the top positive correlated module, at the stage of six days post spraying DPC, was sienna3. Notably, Stf0 sulfotransferase, cyclin-like F-box, and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. Furthermore, the qPCR validated the high accuracy of the RNA-seq results. CONCLUSION: Taken together, we have demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07352-w. BioMed Central 2021-01-25 /pmc/articles/PMC7831198/ /pubmed/33494722 http://dx.doi.org/10.1186/s12864-020-07352-w Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.
spellingShingle Research Article
Chen, Rongfa
Fan, Yegeng
Zhou, Huiwen
Mo, Shanping
Zhou, Zhongfeng
Yan, Haifeng
Luo, Ting
Huang, Xing
Weng, Mengling
Lakshmanan, Prakash
Li, Yangrui
Qiu, Lihang
Wu, Jianming
Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
title Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
title_full Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
title_fullStr Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
title_full_unstemmed Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
title_short Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
title_sort global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7831198/
https://www.ncbi.nlm.nih.gov/pubmed/33494722
http://dx.doi.org/10.1186/s12864-020-07352-w
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