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Kobayashi M, Yamaguchi S, Kusano S, Kumagai S, Ito T. Non-thermal atmospheric-pressure plasma exposure as a practical method for improvement of Brassica juncea seed germination. J Biotechnol 2024; 392:103-108. [PMID: 38944385 DOI: 10.1016/j.jbiotec.2024.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Here we report that non-thermal atmospheric-pressure plasma exposure can improve Brassica juncea (leaf mustard) seed germination rate from 50 % to 98 %. The commercially relevant germination rate was achieved by plasma exposure for only 10 minutes and the effect sustains at least for one month under an appropriate storage condition. Improved germination by plasma exposure was also observed for Brassica rapa subsp. pekinensis (Chinese cabbage) seeds. The plasma device used is simple. No pure gas flow system is necessary and it is easy to handle. A large number of seeds can be treated by simply scaling up the device. Plasma exposure can be a practical method for improving seed germination of crop plants important for agriculture.
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Affiliation(s)
- Mime Kobayashi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; Department of Physics, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka 569-8686, Japan.
| | - Sho Yamaguchi
- Takii & Company, Limited, Shimogyo-ku, Kyoto 600-8243, Japan
| | - Shintaro Kusano
- Takii & Company, Limited, Shimogyo-ku, Kyoto 600-8243, Japan
| | - Shinya Kumagai
- Department of Electrical and Electronic Engineering, Meijo University, Tempaku-ku, Nagoya 468-8502, Japan
| | - Toshiro Ito
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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2
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Marchetti F, Distéfano AM, Cainzos M, Setzes N, Cascallares M, López GA, Zabaleta E, Carolina Pagnussat G. Cell death in bryophytes: emerging models to study core regulatory modules and conserved pathways. ANNALS OF BOTANY 2024; 134:367-384. [PMID: 38953500 PMCID: PMC11341678 DOI: 10.1093/aob/mcae081] [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: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024]
Abstract
This review summarizes recent progress in our current understanding of the mechanisms underlying the cell death pathways in bryophytes, focusing on conserved pathways and particularities in comparison to angiosperms. Regulated cell death (RCD) plays key roles during essential processes along the plant life cycle. It is part of specific developmental programmes and maintains homeostasis of the organism in response to unfavourable environments. Bryophytes could provide valuable models to study developmental RCD processes as well as those triggered by biotic and abiotic stresses. Some pathways analogous to those present in angiosperms occur in the gametophytic haploid generation of bryophytes, allowing direct genetic studies. In this review, we focus on such RCD programmes, identifying core conserved mechanisms and raising new key questions to analyse RCD from an evolutionary perspective.
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Affiliation(s)
- Fernanda Marchetti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Ayelén Mariana Distéfano
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Maximiliano Cainzos
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Nicolás Setzes
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Milagros Cascallares
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Gabriel Alejandro López
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
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García P, Singh S, Graciet E. New Insights into the Connections between Flooding/Hypoxia Response and Plant Defenses against Pathogens. PLANTS (BASEL, SWITZERLAND) 2024; 13:2176. [PMID: 39204612 PMCID: PMC11358971 DOI: 10.3390/plants13162176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
The impact of global climate change has highlighted the need for a better understanding of how plants respond to multiple simultaneous or sequential stresses, not only to gain fundamental knowledge of how plants integrate signals and mount a coordinated response to stresses but also for applications to improve crop resilience to environmental stresses. In recent years, there has been a stronger emphasis on understanding how plants integrate stresses and the molecular mechanisms underlying the crosstalk between the signaling pathways and transcriptional programs that underpin plant responses to multiple stresses. The combination of flooding (or resulting hypoxic stress) with pathogen infection is particularly relevant due to the frequent co-occurrence of both stresses in nature. This review focuses on (i) experimental approaches and challenges associated with the study of combined and sequential flooding/hypoxia and pathogen infection, (ii) how flooding (or resulting hypoxic stress) influences plant immunity and defense responses to pathogens, and (iii) how flooding contributes to shaping the soil microbiome and is linked to plants' ability to fight pathogen infection.
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Affiliation(s)
- Pablo García
- Department of Biology, Maynooth University, W23 X021 Maynooth, Co. Kildare, Ireland; (P.G.); (S.S.)
| | - Shreenivas Singh
- Department of Biology, Maynooth University, W23 X021 Maynooth, Co. Kildare, Ireland; (P.G.); (S.S.)
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, W23 X021 Maynooth, Co. Kildare, Ireland; (P.G.); (S.S.)
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 X021 Maynooth, Co. Kildare, Ireland
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Zaman QU, Garg V, Raza A, Nazir MF, Hui L, Khan D, Khokhar AA, Hussain MA, Wang HF, Varshney RK. Unique regulatory network of dragon fruit simultaneously mitigates the effect of vanadium pollutant and environmental factors. PHYSIOLOGIA PLANTARUM 2024; 176:e14416. [PMID: 38952344 DOI: 10.1111/ppl.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 07/03/2024]
Abstract
Under changing climatic conditions, plants are simultaneously facing conflicting stresses in nature. Plants can sense different stresses, induce systematic ROS signals, and regulate transcriptomic, hormonal, and stomatal responses. We performed transcriptome analysis to reveal the integrative stress response regulatory mechanism underlying heavy metal stress alone or in combination with heat and drought conditions in pitaya (dragon fruit). A total of 70 genes were identified from 31,130 transcripts with conserved differential expression. Furthermore, weighted gene co-expression network analysis (WGCNA) identified trait-associated modules. By integrating information from three modules and protein-protein interaction (PPI) networks, we identified 10 interconnected genes associated with the multifaceted defense mechanism employed by pitaya against co-occurring stresses. To further confirm the reliability of the results, we performed a comparative analysis of 350 genes identified by three trait modules and 70 conserved genes exhibiting their dynamic expression under all treatments. Differential expression pattern of genes and comparative analysis, have proven instrumental in identifying ten putative structural genes. These ten genes were annotated as PLAT/LH2, CAT, MLP, HSP, PB1, PLA, NAC, HMA, and CER1 transcription factors involved in antioxidant activity, defense response, MAPK signaling, detoxification of metals and regulating the crosstalk between the complex pathways. Predictive analysis of putative candidate genes, potentially governing single, double, and multifactorial stress response, by several signaling systems and molecular patterns. These findings represent a valuable resource for pitaya breeding programs, offering the potential to develop resilient "super pitaya" plants.
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Affiliation(s)
- Qamar U Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou, China
| | - Vanika Garg
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Mian Faisal Nazir
- Jiangxi Provincial Key Laboratory of ex-situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, JiuJiang, Jiangxi, China
| | - Liu Hui
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou, China
| | - Darya Khan
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou, China
| | - Aamir Ali Khokhar
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou, China
| | - Muhammad Azhar Hussain
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou, China
| | - Hua-Feng Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou, China
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
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Aggarwal B, Karlowski WM, Nuc P, Jarmolowski A, Szweykowska-Kulinska Z, Pietrykowska H. MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha - insights into their expression pattern, gene structures and function. RNA Biol 2024; 21:1-12. [PMID: 38303117 PMCID: PMC10841014 DOI: 10.1080/15476286.2024.2303555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNAs regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that the differential expression of conserved miRNAs among land plants and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.
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Affiliation(s)
- Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Wojciech Maciej Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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Zhou X, Peng T, Zeng Y, Cai Y, Zuo Q, Zhang L, Dong S, Liu Y. Chromosome-level genome assembly of Niphotrichum japonicum provides new insights into heat stress responses in mosses. FRONTIERS IN PLANT SCIENCE 2023; 14:1271357. [PMID: 37920716 PMCID: PMC10619864 DOI: 10.3389/fpls.2023.1271357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/25/2023] [Indexed: 11/04/2023]
Abstract
With a diversity of approximately 22,000 species, bryophytes (hornworts, liverworts, and mosses) represent a major and diverse lineage of land plants. Bryophytes can thrive in many extreme environments as they can endure the stresses of drought, heat, and cold. The moss Niphotrichum japonicum (Grimmiaceae, Grimmiales) can subsist for extended periods under heat and drought conditions, providing a good candidate for studying the genetic basis underlying such high resilience. Here, we de novo assembled the genome of N. japonicum using Nanopore long reads combined with Hi-C scaffolding technology to anchor the 191.61 Mb assembly into 14 pseudochromosomes. The genome structure of N. japonicum's autosomes is mostly conserved and highly syntenic, in contrast to the sparse and disordered genes present in its sex chromosome. Comparative genomic analysis revealed the presence of 10,019 genes exclusively in N. japonicum. These genes may contribute to the species-specific resilience, as demonstrated by the gene ontology (GO) enrichment. Transcriptome analysis showed that 37.44% (including 3,107 unique genes) of the total annotated genes (26,898) exhibited differential expression as a result of heat-induced stress, and the mechanisms that respond to heat stress are generally conserved across plants. These include the upregulation of HSPs, LEAs, and reactive oxygen species (ROS) scavenging genes, and the downregulation of PPR genes. N. japonicum also appears to have distinctive thermal mechanisms, including species-specific expansion and upregulation of the Self-incomp_S1 gene family, functional divergence of duplicated genes, structural clusters of upregulated genes, and expression piggybacking of hub genes. Overall, our study highlights both shared and species-specific heat tolerance strategies in N. japonicum, providing valuable insights into the heat tolerance mechanism and the evolution of resilient plants.
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Affiliation(s)
- Xuping Zhou
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Colleage of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Tao Peng
- Colleage of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yuying Zeng
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuqing Cai
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qin Zuo
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Li Zhang
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Shanshan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
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Gajardo HA, Gómez-Espinoza O, Boscariol Ferreira P, Carrer H, Bravo LA. The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091892. [PMID: 37176948 PMCID: PMC10181257 DOI: 10.3390/plants12091892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Pedro Boscariol Ferreira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
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