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Li S, Wang S, Ye W, Yao Y, Sun F, Zhang C, Liu S, Xi Y. Effect of Mowing on Wheat Growth at Seeding Stage. Int J Mol Sci 2023; 24:15353. [PMID: 37895031 PMCID: PMC10607078 DOI: 10.3390/ijms242015353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/09/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Winter wheat is used as forage at the tillering stage in many countries; however, the regrowth pattern of wheat after mowing remains unclear. In this study, the growth patterns of wheat were revealed through cytological and physiological assessments as well as transcriptome sequencing. The results of agronomic traits and paraffin sections showed that the shoot growth rate increased, but root growth was inhibited after mowing. The submicroscopic structure revealed a decrease in heterochromatin in the tillering node cell and a change in mitochondrial shape in the tillering node and secondary root. Analysis of the transcriptome showed the number of differentially expressed genes (DEGs) involved in biological processes, cellular components, and molecular functions; 2492 upregulated DEGs and 1534 downregulated DEGs were identified. The results of the experimental study showed that mowing induced expression of DEGs in the phenylpropanoid biosynthesis pathway and increased the activity of PAL and 4CL. The upregulated DEGs in the starch and sucrose metabolism pathways and related enzyme activity alterations indicated that the sugar degradation rate increased. The DEGs in the nitrogen metabolism pathway biosynthesis of the amino acids, phenylpropanoid biosynthesis metabolism, and in the TCA pathway also changed after mowing. Hormone content and related gene expression was also altered in the tillering and secondary roots after mowing. When jasmonic acid and ethylene were used to treat the wheat after mowing, the regeneration rate increased, whereas abscisic acid inhibited regrowth. This study revealed the wheat growth patterns after mowing, which could lead to a better understanding of the development of dual-purpose wheat.
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Affiliation(s)
| | | | | | | | | | | | | | - Yajun Xi
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (S.L.); (S.W.); (W.Y.); (Y.Y.); (F.S.); (C.Z.); (S.L.)
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Liu W, Zhang Y, Fang X, Tran S, Zhai N, Yang Z, Guo F, Chen L, Yu J, Ison MS, Zhang T, Sun L, Bian H, Zhang Y, Yang L, Xu L. Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses. PLANT COMMUNICATIONS 2022; 3:100306. [PMID: 35605192 PMCID: PMC9284295 DOI: 10.1016/j.xplc.2022.100306] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Detached Arabidopsis thaliana leaves can regenerate adventitious roots, providing a platform for studying de novo root regeneration (DNRR). However, the comprehensive transcriptional framework of DNRR remains elusive. Here, we provide a high-resolution landscape of transcriptome reprogramming from wound response to root organogenesis in DNRR and show key factors involved in DNRR. Time-lapse RNA sequencing (RNA-seq) of the entire leaf within 12 h of leaf detachment revealed rapid activation of jasmonate, ethylene, and reactive oxygen species (ROS) pathways in response to wounding. Genetic analyses confirmed that ethylene and ROS may serve as wound signals to promote DNRR. Next, time-lapse RNA-seq within 5 d of leaf detachment revealed the activation of genes involved in organogenesis, wound-induced regeneration, and resource allocation in the wounded region of detached leaves during adventitious rooting. Genetic studies showed that BLADE-ON-PETIOLE1/2, which control aboveground organs, PLETHORA3/5/7, which control root organogenesis, and ETHYLENE RESPONSE FACTOR115, which controls wound-induced regeneration, are involved in DNRR. Furthermore, single-cell RNA-seq data revealed gene expression patterns in the wounded region of detached leaves during adventitious rooting. Overall, our study not only provides transcriptome tools but also reveals key factors involved in DNRR from detached Arabidopsis leaves.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Xing Fang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Sorrel Tran
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Zhengfei Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Fu Guo
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
| | - Lyuqin Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Jie Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Madalene S Ison
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Teng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Li Yang
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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Pan X, Yang Z, Xu L. Dual roles of jasmonate in adventitious rooting. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6808-6810. [PMID: 34698862 PMCID: PMC8547146 DOI: 10.1093/jxb/erab378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This article comments on: Dob A, Lakehal A, Novak O, Bellini C. 2021. Jasmonate inhibits adventitious root initiation through repression of CKX1 and activation of RAP2.6L transcription factor in Arabidopsis. Journal of Experimental Botany 72, 7107–7118.
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Affiliation(s)
- Xuan Pan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Zhengfei Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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Tu M, Wang W, Yao N, Cai C, Liu Y, Lin C, Zuo Z, Zhu Q. The transcriptional dynamics during de novo shoot organogenesis of Ma bamboo (Dendrocalamus latiflorus Munro): implication of the contributions of the abiotic stress response in this process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1513-1532. [PMID: 34181801 DOI: 10.1111/tpj.15398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 06/08/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
De novo shoot organogenesis is an important biotechnological tool for fundamental studies in plant. However, it is difficult in most bamboo species, and the genetic control of this highly dynamic and complicated regeneration process remains unclear. In this study, based on an in-depth analysis at the cellular level, the shoot organogenesis from calli of Ma bamboo (Dendrocalamus latiflorus Munro) was divided into five stages. Subsequently, single-molecule long-read isoform sequencing of tissue samples pooled from all five stages was performed to generate a full-length transcript landscape. A total of 83 971 transcripts, including 73 209 high-quality full-length transcripts, were captured, which served as an annotation reference for the subsequent RNA sequencing analysis. Time-course transcriptome analysis of samples at the abovementioned five stages was conducted to investigate the global gene expression atlas showing genome-wide expression of transcripts during the course of bamboo shoot organogenesis. K-means clustering analysis and stage-specific transcript identification revealed important dynamically expressed transcription regulators that function in bamboo shoot organogenesis. The majority of abiotic stress-responsive genes altered their expression levels during this process, and further experiments demonstrated that exogenous application of moderate but not severe abiotic stress increased the shoot regeneration efficiency. In summary, our study provides an overview of the genetic flow dynamics during bamboo shoot organogenesis. Full-length cDNA sequences generated in this study can serve as a valuable resource for fundamental and applied research in bamboo in the future.
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Affiliation(s)
- Min Tu
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenjia Wang
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Nan Yao
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Changyang Cai
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yuanyuan Liu
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Zecheng Zuo
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
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Ikeuchi M, Rymen B, Sugimoto K. How do plants transduce wound signals to induce tissue repair and organ regeneration? CURRENT OPINION IN PLANT BIOLOGY 2020; 57:72-77. [PMID: 32738736 DOI: 10.1016/j.pbi.2020.06.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 05/27/2023]
Abstract
Wounding is a primary trigger for tissue repair and organ regeneration, yet the exact regulatory role of local wound signals remained elusive for many years. Recent studies demonstrated that a key signaling molecule of wound response, jasmonic acid (JA), plays pivotal roles in root regeneration. JA signaling induces cell proliferation and restores root meristem by ectopically inducing an AP2/ERF transcription factor ETHYLENE RESPONSE FACTOR 115 (ERF115) which in normal development, replenishes quiescent center cells. During shoot regeneration, another wound-inducible AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) promotes callus formation and shoot regeneration via direct induction of a shoot meristem regulator. Discovery of these regulatory mechanisms highlights the direct link between stress signaling and ectopic activation of developmental programs. Given that genes encoding key developmental regulators are often under epigenetic regulation, transcriptional activation of these genes likely entails changes in their chromatin status. Recent efforts indeed began to reveal massive changes in histone modification status during cellular reprogramming after wounding.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata, Japan.
| | - Bart Rymen
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
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Coleman D, Kawamura A, Ikeuchi M, Favero DS, Lambolez A, Rymen B, Iwase A, Suzuki T, Sugimoto K. The SUMO E3 Ligase SIZ1 Negatively Regulates Shoot Regeneration. PLANT PHYSIOLOGY 2020; 184:330-344. [PMID: 32611787 PMCID: PMC7479894 DOI: 10.1104/pp.20.00626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/23/2020] [Indexed: 05/20/2023]
Abstract
Plants form calluses and regenerate new organs when incubated on phytohormone-containing media. While accumulating evidence suggests that these regenerative processes are governed by transcriptional networks orchestrating wound response and developmental transitions, it remains unknown if posttranslational regulatory mechanisms are involved in this process. In this study, we demonstrate that SAP AND MIZ1 DOMAIN- CONTAINING LIGASE1 (SIZ1), an E3 ligase-catalyzing attachment of the SMALL UBIQUITIN-LIKE MODIFIER (SUMO) to proteins, regulates wound-induced signal transduction and organ regeneration in Arabidopsis (Arabidopsis thaliana). We show that loss-of-function mutants for SIZ1 exhibit overproduction of shoot meristems under in vitro tissue culture conditions, while this defect is rescued in a complementation line expressing pSIZ1::SIZ1 RNA sequencing analysis revealed that siz1-2 mutants exhibit enhanced transcriptional responses to wound stress, resulting in the hyper-induction of over 400 genes immediately after wounding. Among them, we show that elevated levels of WOUND INDUCED DEDIFFERENTIATION1 (WIND1) and WIND2 contribute to the enhanced shoot regeneration observed in siz1 mutants, as expression of the dominant-negative chimeric protein WIND1-SRDX (SUPERMAN repression domain) in siz1-3 mutants partly rescues this phenotype. Although compromised SIZ1 function does not modify the transcription of genes implicated in auxin-induced callus formation and/or pluripotency acquisition, it does lead to enhanced induction of cytokinin-induced shoot meristem regulators such as WUSCHEL, promoting the formation of WUSCHEL-expressing foci in explants. This study thus suggests that SIZ1 negatively regulates shoot regeneration in part by repressing wound-induced developmental reprogramming.
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Affiliation(s)
- Duncan Coleman
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biology, Faculty of Science, Niigata University, Nishi-ku, Niigata 950-2181, Japan
| | - David S Favero
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Alice Lambolez
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Bart Rymen
- Institut de Biologie Moléculaire des Plantes, 67084 Strasboug cedex, France
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
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