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Han X, Zhang Y, Lou Z, Li J, Wang Z, Gao C, Liu Y, Ren Z, Liu W, Li B, Pan W, Zhang H, Sang Q, Wan M, He H, Deng XW. Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings. NATURE PLANTS 2023; 9:2095-2109. [PMID: 37903986 PMCID: PMC10724060 DOI: 10.1038/s41477-023-01544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 09/19/2023] [Indexed: 11/01/2023]
Abstract
Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specific differentiation and the associated transcriptional regulation is still lacking. Here we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes. These results provide information concerning the light signalling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating the molecular mechanism of cell development and differentiation in response to light.
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Affiliation(s)
- Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zhiying Lou
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Zheng Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Chunlei Gao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Yi Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zizheng Ren
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Weimin Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Wenbo Pan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Huawei Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Qing Sang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Miaomiao Wan
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
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2
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Stafen CF, Kleine-Vehn J, Maraschin FDS. Signaling events for photomorphogenic root development. TRENDS IN PLANT SCIENCE 2022; 27:1266-1282. [PMID: 36057533 DOI: 10.1016/j.tplants.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.
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Affiliation(s)
- Cássia Fernanda Stafen
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Jürgen Kleine-Vehn
- Institute of Biology II, Chair of Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Felipe Dos Santos Maraschin
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Botânica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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3
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de Almeida RMC, Thomas GL, Glazier JA. Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. NAR Genom Bioinform 2022; 4:lqac020. [PMID: 35300459 PMCID: PMC8923009 DOI: 10.1093/nargab/lqac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 in vitro infection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression. Without knowing in advance which genes are relevant, classical analyses detect every gene with statistically-significant differential expression, leaving us with too many genes and hypotheses to be useful. Using a Transcriptogram-based top-down approach, we identified three major, differentially-expressed gene sets comprising 219 mainly immune-response-related genes. We identified timescales for alterations in mitochondrial activity, signaling and transcription regulation of the innate and adaptive immune systems and their relationship to viral titer. The methods can be applied to RNA data sets for SARS-CoV-2 to investigate the origin of differential responses in different tissue types, or due to immune or preexisting conditions or to compare cell culture, organoid culture, animal models and human-derived samples.
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Affiliation(s)
- Rita M C de Almeida
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Instituto Nacional de Ciência e Tecnologia: Sistemas Complexos, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Gilberto L Thomas
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - James A Glazier
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
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4
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Halat LS, Bali B, Wasteneys G. Cytoplasmic Linker Protein-Associating Protein at the Nexus of Hormone Signaling, Microtubule Organization, and the Transition From Division to Differentiation in Primary Roots. FRONTIERS IN PLANT SCIENCE 2022; 13:883363. [PMID: 35574108 PMCID: PMC9096829 DOI: 10.3389/fpls.2022.883363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 05/13/2023]
Abstract
The transition from cell division to differentiation in primary roots is dependent on precise gradients of phytohormones, including auxin, cytokinins and brassinosteroids. The reorganization of microtubules also plays a key role in determining whether a cell will enter another round of mitosis or begin to rapidly elongate as the first step in terminal differentiation. In the last few years, progress has been made to establish connections between signaling pathways at distinct locations within the root. This review focuses on the different factors that influence whether a root cell remains in the division zone or transitions to elongation and differentiation using Arabidopsis thaliana as a model system. We highlight the role of the microtubule-associated protein CLASP as an intermediary between sustaining hormone signaling and controlling microtubule organization. We discuss new, innovative tools and methods, such as hormone sensors and computer modeling, that are allowing researchers to more accurately visualize the belowground growth dynamics of plants.
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5
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Zhai S, Cai W, Xiang ZX, Chen CY, Lu YT, Yuan TT. PIN3-mediated auxin transport contributes to blue light-induced adventitious root formation in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111044. [PMID: 34620442 DOI: 10.1016/j.plantsci.2021.111044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Adventitious rooting is a heritable quantitative trait that is influenced by multiple endogenous and exogenous factors in plants, and one important environmental factor required for efficient adventitious root formation is light signaling. However, the physiological significance and molecular mechanism of light underlying adventitious root formation are still largely unexplored. Here, we report that blue light-induced adventitious root formation is regulated by PIN-FORMED3 (PIN3)-mediated auxin transport in Arabidopsis. Adventitious root formation is significantly impaired in the loss-of-function mutants of the blue light receptors, PHOTOROPIN1 (PHOT1) and PHOTOROPIN2 (PHOT2), as well as the phototropic transducer, NON-PHOTOTROPIC HYPOCOTYL3 (NPH3). In addition, blue light enhanced the auxin content in the adventitious root, and the pin3 loss-of-function mutant had a reduced adventitious rooting response under blue light compared to the wild type. The PIN3 protein level was higher in plants treated with blue light than in those in darkness, especially in the hypocotyl pericycle, while PIN3-GFP failed to accumulate in nph3 PIN3::PIN3-GFP. Furthermore, the results showed that PIN3 physically interacted with NPH3, a key transducer in phototropic signaling. Taken together, our study demonstrates that blue light induces adventitious root formation through the phototropic signal transducer, NPH3, which regulates adventitious root formation by affecting PIN3-mediated auxin transport.
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Affiliation(s)
- Shuang Zhai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wei Cai
- Institute of Crop Science of Wuhan Academy of Agriculture Science, Wuhan, 430345, China
| | - Zhi-Xin Xiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Cai-Yan Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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6
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Riegler S, Servi L, Scarpin MR, Godoy Herz MA, Kubaczka MG, Venhuizen P, Meyer C, Brunkard JO, Kalyna M, Barta A, Petrillo E. Light regulates alternative splicing outcomes via the TOR kinase pathway. Cell Rep 2021; 36:109676. [PMID: 34496244 PMCID: PMC8547716 DOI: 10.1016/j.celrep.2021.109676] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022] Open
Abstract
For plants, light is the source of energy and the most relevant regulator of growth and adaptations to the environment by inducing changes in gene expression at various levels, including alternative splicing. Light-triggered chloroplast retrograde signals control alternative splicing in Arabidopsis thaliana. Here, we provide evidence that light regulates the expression of a core set of splicing-related factors in roots. Alternative splicing responses in roots are not directly caused by light but are instead most likely triggered by photo-synthesized sugars. The target of rapamycin (TOR) kinase plays a key role in this shoot-to-root signaling pathway. Knocking down TOR expression or pharmacologically inhibiting TOR activity disrupts the alternative splicing responses to light and exogenous sugars in roots. Consistently, splicing decisions are modulated by mitochondrial activity in roots. In conclusion, by activating the TOR pathway, sugars act as mobile signals to coordinate alternative splicing responses to light throughout the whole plant. Riegler et al. reveal a central role for TOR kinase paired with retrograde signaling in alternative splicing regulation by light in roots and, to a certain extent, in leaves. Activating the TOR pathway, sugars act as mobile signals to coordinate alternative splicing responses to light throughout the whole plant.
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Affiliation(s)
- Stefan Riegler
- Department of Applied Genetics and Cell Biology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Lucas Servi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina
| | - M Regina Scarpin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710, USA
| | - Micaela A Godoy Herz
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina
| | - María G Kubaczka
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina
| | - Peter Venhuizen
- Department of Applied Genetics and Cell Biology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710, USA; Laboratory of Genetics, University of Wisconsin, Madison, Madison, WI 53706, USA
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Andrea Barta
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus, 1030 Vienna, Austria
| | - Ezequiel Petrillo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina.
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7
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de Almeida RMC, Thomas GL, Glazier JA. Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 32587961 PMCID: PMC7310616 DOI: 10.1101/2020.06.16.155267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 in vitro infection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression. Without knowing in advance which genes are relevant, classical analyses detect every gene with statistically-significant differential expression, leaving us with too many genes and hypotheses to be useful. Using a Transcriptogram-based top-down approach, we identified three major, differentially-expressed gene sets comprising 219 mainly immune-response-related genes. We identified timescales for alterations in mitochondrial activity, signaling and transcription regulation of the innate and adaptive immune systems and their relationship to viral titer. At the individual-gene level, EGR3 was significantly upregulated in infected cells. Similar activation in T-cells and fibroblasts in infected lung could explain the T-cell anergy and eventual fibrosis seen in SARS-CoV-1 infection. The methods can be applied to RNA data sets for SARS-CoV-2 to investigate the origin of differential responses in different tissue types, or due to immune or preexisting conditions or to compare cell culture, organoid culture, animal models, and human-derived samples.
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Affiliation(s)
- Rita M C de Almeida
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Instituto Nacional de Ciência e Tecnologia: Sistemas Complexos, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Gilberto L Thomas
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - James A Glazier
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
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8
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Miotto YE, da Costa CT, Offringa R, Kleine-Vehn J, Maraschin FDS. Effects of Light Intensity on Root Development in a D-Root Growth System. FRONTIERS IN PLANT SCIENCE 2021; 12:778382. [PMID: 34975962 PMCID: PMC8715079 DOI: 10.3389/fpls.2021.778382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/08/2021] [Indexed: 05/10/2023]
Abstract
Plant development is highly affected by light quality, direction, and intensity. Under natural growth conditions, shoots are directly exposed to light whereas roots develop underground shielded from direct illumination. The photomorphogenic development strongly represses shoot elongation whereas promotes root growth. Over the years, several studies helped the elucidation of signaling elements that coordinate light perception and underlying developmental outputs. Light exposure of the shoots has diverse effects on main root growth and lateral root (LR) formation. In this study, we evaluated the phenotypic root responses of wild-type Arabidopsis plants, as well as several mutants, grown in a D-Root system. We observed that sucrose and light act synergistically to promote root growth and that sucrose alone cannot overcome the light requirement for root growth. We also have shown that roots respond to the light intensity applied to the shoot by changes in primary and LR development. Loss-of-function mutants for several root light-response genes display varying phenotypes according to the light intensity to which shoots are exposed. Low light intensity strongly impaired LR development for most genotypes. Only vid-27 and pils4 mutants showed higher LR density at 40 μmol m-2 s-1 than at 80 μmol m-2 s-1 whereas yuc3 and shy2-2 presented no LR development in any light condition, reinforcing the importance of auxin signaling in light-dependent root development. Our results support the use of D-Root systems to avoid the effects of direct root illumination that might lead to artifacts and unnatural phenotypic outputs.
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Affiliation(s)
- Yohanna Evelyn Miotto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cibele Tesser da Costa
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Molecular Plant Physiology, Institute of Biology, University of Freiburg, Freiburg, Germany
- Center for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Felipe dos Santos Maraschin
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Felipe dos Santos Maraschin,
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9
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Cadavid IC, Guzman F, de Oliveira-Busatto L, de Almeida RMC, Margis R. Transcriptional analyses of two soybean cultivars under salt stress. Mol Biol Rep 2020; 47:2871-2888. [PMID: 32227253 DOI: 10.1007/s11033-020-05398-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/25/2020] [Indexed: 01/12/2023]
Abstract
Soybean is an economically important plant, and its production is affected in soils with high salinity levels. It is important to understand the adaptive mechanisms through which plants overcome this kind of stress and to identify potential genes for improving abiotic stress tolerance. RNA-Seq data of two Glycine max cultivars, a drought-sensitive (C08) and a tolerant (Conquista), subjected to different periods of salt stress were analyzed. The transcript expression profile was obtained using a transcriptogram approach, comparing both cultivars and different times of treatment. After 4 h of salt stress, Conquista cultivar had 1400 differentially expressed genes, 647 induced and 753 repressed. Comparative expression revealed that 719 genes share the same pattern of induction or repression between both cultivars. Among them, 393 genes were up- and 326 down-regulated. Salt stress also modified the expression of 54 isoforms of miRNAs in Conquista, by the maturation of 39 different pre-miRNAs. The predicted targets for 12 of those mature miRNAs also have matches with 15 differentially expressed genes from our analyses. We found genes involved in important pathways related to stress adaptation. Genes from both ABA and BR signaling pathways were modulated, with possible crosstalk between them, and with a likely post-transcriptional regulation by miRNAs. Genes related to ethylene biosynthesis, DNA repair, and plastid translation process were those that could be regulated by miRNA.
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Affiliation(s)
- Isabel Cristina Cadavid
- Progama de Pos-gradação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Frank Guzman
- Progama de Pos-gradação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Av. La Molina, 1981, Lima 12, Perú
| | - Luisa de Oliveira-Busatto
- Progama de Pos-gradação em Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rita M C de Almeida
- Instituto de Física, Sistemas Complexos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Nacional de Ciência E Tecnologia: Sistemas Complexos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós Graduação Em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Rogerio Margis
- Progama de Pos-gradação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
- Progama de Pos-gradação em Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
- Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas (LGPP), Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves, 9500 - Prédio 43422, Laboratório 206, Porto Alegre, Brazil.
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