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      Transcriptomic profiling provides molecular insights into hydrogen peroxide-induced adventitious rooting in mung bean seedlings

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          Abstract

          Background

          Hydrogen peroxide (H 2O 2) has been known to function as a signalling molecule involved in the modulation of various physiological processes in plants. H 2O 2 has been shown to act as a promoter during adventitious root formation in hypocotyl cuttings. In this study, RNA-Seq was performed to reveal the molecular mechanisms underlying H 2O 2-induced adventitious rooting.

          Results

          RNA-Seq data revealed that H 2O 2 treatment greatly increased the numbers of clean reads and expressed genes and abundance of gene expression relative to the water treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that a profound change in gene function occurred in the 6-h H 2O 2 treatment and that H 2O 2 mainly enhanced gene expression levels at the 6-h time point but reduced gene expression levels at the 24-h time point compared with the water treatment. In total, 4579 differentially expressed (2-fold change > 2) unigenes (DEGs), of which 78.3% were up-regulated and 21.7% were down-regulated; 3525 DEGs, of which 64.0% were up-regulated and 36.0% were down-regulated; and 7383 DEGs, of which 40.8% were up-regulated and 59.2% were down-regulated were selected in the 6-h, 24-h, and from 6- to 24-h treatments, respectively. The number of DEGs in the 6-h treatment was 29.9% higher than that in the 24-h treatment. The functions of the most highly regulated genes were associated with stress response, cell redox homeostasis and oxidative stress response, cell wall loosening and modification, metabolic processes, and transcription factors (TFs), as well as plant hormone signalling, including auxin, ethylene, cytokinin, gibberellin, and abscisic acid pathways. Notably, a large number of genes encoding for heat shock proteins (HSPs) and heat shock transcription factors (HSFs) were significantly up-regulated during H 2O 2 treatments. Furthermore, real-time quantitative PCR (qRT-PCR) results showed that, during H 2O 2 treatments, the expression levels of ARFs, IAAs, AUXs, NACs, RD22, AHKs, MYBs, PIN1, AUX15A, LBD29, LBD41, ADH1b, and QORL were significantly up-regulated at the 6- and/or 24-h time points. In contrast, PER1 and PER2 were significantly down-regulated by H 2O 2 treatment. These qRT-PCR results strongly correlated with the RNA-Seq data.

          Conclusions

          Using RNA-Seq and qRT-PCR techniques, we analysed the global changes in gene expression and functional profiling during H 2O 2-induced adventitious rooting in mung bean seedlings. These results strengthen the current understanding of H 2O 2-induced adventitious rooting and the molecular traits of H 2O 2 priming in plants.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12864-017-3576-y) contains supplementary material, which is available to authorized users.

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          Most cited references64

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Cytokinin oxidase regulates rice grain production.

            Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.
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              Reactive oxygen species produced by NADPH oxidase regulate plant cell growth.

              Cell expansion is a central process in plant morphogenesis, and the elongation of roots and root hairs is essential for uptake of minerals and water from the soil. Ca2+ influx from the extracellular store is required for (and sets the rates of) cell elongation in roots. Arabidopsis thaliana rhd2 mutants are defective in Ca2+ uptake and consequently cell expansion is compromised--rhd2 mutants have short root hairs and stunted roots. To determine the regulation of Ca2+ acquisition in growing root cells we show here that RHD2 is an NADPH oxidase, a protein that transfers electrons from NADPH to an electron acceptor leading to the formation of reactive oxygen species (ROS). We show that ROS accumulate in growing wild-type (WT) root hairs but their levels are markedly decreased in rhd2 mutants. Blocking the activity of the NADPH oxidase with diphenylene iodonium (DPI) inhibits ROS formation and phenocopies Rhd2-. Treatment of rhd2 roots with ROS partly suppresses the mutant phenotype and stimulates the activity of plasma membrane hyperpolarization-activated Ca2+ channels, the predominant root Ca2+ acquisition system. This indicates that NADPH oxidases control development by making ROS that regulate plant cell expansion through the activation of Ca2+ channels.
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                Author and article information

                Contributors
                +86 931 4938097 , lishweng@mail.lzjtu.cn
                lengyan_cool@126.com
                02130564@stu.lzjtu
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                17 February 2017
                17 February 2017
                2017
                : 18
                : 188
                Affiliations
                ISNI 0000 0000 9533 0029, GRID grid.411290.f, School of Environmental and Municipal Engineering, Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, , Lanzhou Jiaotong University, ; 88 West Anning Road, Lanzhou, 730070 People’s Republic of China
                Article
                3576
                10.1186/s12864-017-3576-y
                5316208
                28212614
                acff1422-0352-4c7d-94c5-f541b9a3f716
                © 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.

                History
                : 2 June 2016
                : 9 February 2017
                Funding
                Funded by: the National Natural Science Foundation of China
                Award ID: 31560121 and 31260090
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Genetics
                vigna radiata (l.) r. wilczek,adventitious roots,gene expression,hydrogen peroxide (h2o2),transcriptome,rna-seq

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