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Xue Z, Ferrand M, Gilbault E, Zurfluh O, Clément G, Marmagne A, Huguet S, Jiménez-Gómez JM, Krapp A, Meyer C, Loudet O. Natural variation in response to combined water and nitrogen deficiencies in Arabidopsis. THE PLANT CELL 2024; 36:3378-3398. [PMID: 38916908 PMCID: PMC11371182 DOI: 10.1093/plcell/koae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 01/24/2024] [Accepted: 06/08/2024] [Indexed: 06/26/2024]
Abstract
Understanding plant responses to individual stresses does not mean that we understand real-world situations, where stresses usually combine and interact. These interactions arise at different levels, from stress exposure to the molecular networks of the stress response. Here, we built an in-depth multiomic description of plant responses to mild water (W) and nitrogen (N) limitations, either individually or combined, among 5 genetically different Arabidopsis (Arabidopsis thaliana) accessions. We highlight the different dynamics in stress response through integrative traits such as rosette growth and the physiological status of the plants. We also used transcriptomic and metabolomic profiling during a stage when the plant response was stabilized to determine the wide diversity in stress-induced changes among accessions, highlighting the limited reality of a "universal" stress response. The main effect of the W × N interaction was an attenuation of the N-deficiency syndrome when combined with mild drought, but to a variable extent depending on the accession. Other traits subject to W × N interactions are often accession specific. Multiomic analyses identified a subset of transcript-metabolite clusters that are critical to stress responses but essentially variable according to the genotype factor. Including intraspecific diversity in our descriptions of plant stress response places our findings in perspective.
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Affiliation(s)
- Zeyun Xue
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Marina Ferrand
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Elodie Gilbault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Olivier Zurfluh
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Anne Marmagne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
| | - José M Jiménez-Gómez
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Anne Krapp
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Christian Meyer
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
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2
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Cong J, Zhang S, Zhang Q, Yu X, Huang J, Wei X, Huang X, Qiu J, Zhou X. Conserved features and diversity attributes of chimeric RNAs across accessions in four plants. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39087631 DOI: 10.1111/pbi.14437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 06/17/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
As a non-collinear expression form of genetic information, chimeric RNAs increase the complexity of transcriptome in diverse organisms. Although chimeric RNAs have been identified in plants, few common features have been revealed. Here, we systemically explored the landscape of chimeric RNAs across multi-accession and multi-tissue using pan-genome and transcriptome data of four plants: rice, maize, soybean, and Arabidopsis. Among the four species, conserved characteristics of breakpoints and parental genes were discovered. In each species, chimeric RNAs displayed a high level of diversity among accessions, and the clustering of accessions using chimeric events was generally concordant with clustering based on genomic variants, implying a general relationship between genetic variations and chimeric RNAs. Through mass spectrometry, we confirmed a fusion protein OsNDC1-OsGID1L2 and observed its subcellular localization, which differed from the original proteins. Phenotypic cues in transgenic rice suggest the potential functions of OsNDC1-OsGID1L2. Moreover, an intriguing chimeric event Os01g0216500-Os01g0216900, generated by a large deletion in basmati rice, also exists in another accession without the deletion, demonstrating its convergence in evolution. Our results illuminate the characteristics and hint at the evolutionary implications of plant chimeric RNAs, which serve as a supplement to genetic variations, thus expanding our understanding of genetic diversity.
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Affiliation(s)
- Jia Cong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Sinan Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiting Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jiazhi Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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Díez AR, Szakonyi D, Lozano-Juste J, Duque P. Alternative splicing as a driver of natural variation in abscisic acid response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:9-27. [PMID: 38659400 DOI: 10.1111/tpj.16773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Abscisic acid (ABA) is a crucial player in plant responses to the environment. It accumulates under stress, activating downstream signaling to implement molecular responses that restore homeostasis. Natural variance in ABA sensitivity remains barely understood, and the ABA pathway has been mainly studied at the transcriptional level, despite evidence that posttranscriptional regulation, namely, via alternative splicing, contributes to plant stress tolerance. Here, we identified the Arabidopsis accession Kn-0 as less sensitive to ABA than the reference Col-0, as shown by reduced effects of the hormone on seedling establishment, root branching, and stomatal closure, as well as by decreased induction of ABA marker genes. An in-depth comparative transcriptome analysis of the ABA response in the two variants revealed lower expression changes and fewer genes affected for the least ABA-sensitive ecotype. Notably, Kn-0 exhibited reduced levels of the ABA-signaling SnRK2 protein kinases and lower basal expression of ABA-reactivation genes, consistent with our finding that Kn-0 contains less endogenous ABA than Col-0. ABA also markedly affected alternative splicing, primarily intron retention, with Kn-0 being less responsive regarding both the number and magnitude of alternative splicing events, particularly exon skipping. We find that alternative splicing introduces a more ecotype-specific layer of ABA regulation and identify ABA-responsive splicing changes in key ABA pathway regulators that provide a functional and mechanistic link to the differential sensitivity of the two ecotypes. Our results offer new insight into the natural variation of ABA responses and corroborate a key role for alternative splicing in implementing ABA-mediated stress responses.
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Affiliation(s)
- Alba R Díez
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Dóra Szakonyi
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), 46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
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Dos Reis CHG, da Silva PN, de Castro EM, Pereira FJ. Tolerance to mild shading levels in cattail as related to increased photosynthesis and changes in its leaf area and anatomy. JOURNAL OF PLANT RESEARCH 2024; 137:627-640. [PMID: 38517654 DOI: 10.1007/s10265-024-01538-z] [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: 10/10/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024]
Abstract
Shading is an environmental factor that has been little investigated regarding its effects on emergent aquatic plants. Typha domingensis Pers. is an emergent macrophyte that demonstrates some plasticity for self-shading, and as it can shade other species in the same area, the effect of shading on its traits deserves further investigation. The objective of the present study was to evaluate the gas exchange, leaf anatomy, and growth of T. domingensis cultivated under increasing shading intensities. The plants were collected and propagated in a greenhouse, and the clones were subjected to four shading intensities: 0% (unshaded), 35%, 73%, and 83% shading created by black nets. Growth traits, clonal production, photosynthesis, transpiration, and leaf anatomy were evaluated. The 73% and 83% shading promoted the death of all plants, but all plants survived in the 35% and unshaded treatments. Compared with the unshaded treatment, the 35% shading treatment promoted a higher photosynthetic rate and greater transpiration, supporting increased growth and production of clones. The increase in the photosynthetic rate in the 35% shading was related to the increase in leaf area which increased the photosynthesis of the whole plant. The 73% and 83% treatments inhibited the development of photosynthetic parenchyma and stomata in T. domingensis, leading to a drastic reduction in photosynthesis and energy depletion. Therefore, T. domingensis does not tolerate intense shading, but its photosynthetic characteristics and growth are favored by mild shading, a factor that may be of great importance for its competitiveness and invasive behavior.
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Affiliation(s)
| | - Poliana Noemia da Silva
- Instituto de Ciências Naturais (ICN), Universidade Federal de Lavras, Campus Universitário, Lavras, MG, 37200-900, Brazil
| | - Evaristo Mauro de Castro
- Instituto de Ciências Naturais (ICN), Universidade Federal de Lavras, Campus Universitário, Lavras, MG, 37200-900, Brazil
| | - Fabricio José Pereira
- Instituto de Ciências da Natureza (ICN), Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700, Centro, Alfenas, MG, 37130- 001, Brazil.
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Yoshida T, Mergner J, Yang Z, Liu J, Kuster B, Fernie AR, Grill E. Integrating multi-omics data reveals energy and stress signaling activated by abscisic acid in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1112-1133. [PMID: 38613775 DOI: 10.1111/tpj.16765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 03/24/2024] [Accepted: 03/31/2024] [Indexed: 04/15/2024]
Abstract
Phytohormones are essential signaling molecules regulating various processes in growth, development, and stress responses. Genetic and molecular studies, especially using Arabidopsis thaliana (Arabidopsis), have discovered many important players involved in hormone perception, signal transduction, transport, and metabolism. Phytohormone signaling pathways are extensively interconnected with other endogenous and environmental stimuli. However, our knowledge of the huge and complex molecular network governed by a hormone remains limited. Here we report a global overview of downstream events of an abscisic acid (ABA) receptor, REGULATORY COMPONENTS OF ABA RECEPTOR (RCAR) 6 (also known as PYRABACTIN RESISTANCE 1 [PYR1]-LIKE [PYL] 12), by integrating phosphoproteomic, proteomic and metabolite profiles. Our data suggest that the RCAR6 overexpression constitutively decreases the protein levels of its coreceptors, namely clade A protein phosphatases of type 2C, and activates sucrose non-fermenting-1 (SNF1)-related protein kinase 1 (SnRK1) and SnRK2, the central regulators of energy and ABA signaling pathways. Furthermore, several enzymes in sugar metabolism were differentially phosphorylated and expressed in the RCAR6 line, and the metabolite profile revealed altered accumulations of several organic acids and amino acids. These results indicate that energy- and water-saving mechanisms mediated by the SnRK1 and SnRK2 kinases, respectively, are under the control of the ABA receptor-coreceptor complexes.
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Affiliation(s)
- Takuya Yoshida
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
| | - Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Zhenyu Yang
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Jinghui Liu
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
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Song Q, Kong L, Yang J, Lin M, Zhang Y, Yang X, Wang X, Zhao Z, Zhang M, Pan J, Zhu S, Jiao B, Xu C, Luo K. The transcription factor PtoMYB142 enhances drought tolerance in Populus tomentosa by regulating gibberellin catabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:42-57. [PMID: 38112614 DOI: 10.1111/tpj.16588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/20/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
Drought stress caused by global warming has resulted in significant tree mortality, driving the evolution of water conservation strategies in trees. Although phytohormones have been implicated in morphological adaptations to water deficits, the molecular mechanisms underlying these processes in woody plants remain unclear. Here, we report that overexpression of PtoMYB142 in Populus tomentosa results in a dwarfism phenotype with reduced leaf cell size, vessel lumen area, and vessel density in the stem xylem, leading to significantly enhanced drought resistance. We found that PtoMYB142 modulates gibberellin catabolism in response to drought stress by binding directly to the promoter of PtoGA2ox4, a GA2-oxidase gene induced under drought stress. Conversely, knockout of PtoMYB142 by the CRISPR/Cas9 system reduced drought resistance. Our results show that the reduced leaf size and vessel area, as well as the increased vessel density, improve leaf relative water content and stem water potential under drought stress. Furthermore, exogenous GA3 application rescued GA-deficient phenotypes in PtoMYB142-overexpressing plants and reversed their drought resistance. By suppressing the expression of PtoGA2ox4, the manifestation of GA-deficient characteristics, as well as the conferred resistance to drought in PtoMYB142-overexpressing poplars, was impeded. Our study provides insights into the molecular mechanisms underlying tree drought resistance, potentially offering novel transgenic strategies to enhance tree resistance to drought.
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Affiliation(s)
- Qin Song
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Lingfei Kong
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jiarui Yang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Minghui Lin
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yuqian Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xuerui Yang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaojing Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zhengjie Zhao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Meng Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jiarui Pan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shunqin Zhu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Bo Jiao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Plant Genetic Engineering Center of Heibei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
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Yim C, Bellis ES, DeLeo VL, Gamba D, Muscarella R, Lasky JR. Climate biogeography of Arabidopsis thaliana: linking distribution models and individual variation. JOURNAL OF BIOGEOGRAPHY 2024; 51:560-574. [PMID: 38596256 PMCID: PMC11000247 DOI: 10.1111/jbi.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/19/2023] [Indexed: 04/11/2024]
Abstract
AIM Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATION Global. TAXON Arabidopsis thaliana ("Arabidopsis"). METHODS We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on ~900 natural accessions. RESULTS The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONS Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
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Affiliation(s)
- Christina Yim
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Emily S. Bellis
- Department of Biology, Pennsylvania State University, University Park, USA
- Department of Computer Science, Arkansas State University, Jonesboro, USA
| | - Victoria L. DeLeo
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Robert Muscarella
- Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, USA
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Zhang X, Xu H, She Y, Hu C, Zhu T, Wang L, Wu L, You C, Ke J, Zhang Q, He H. Improving the prediction performance of leaf water content by coupling multi-source data with machine learning in rice (Oryza sativa L.). PLANT METHODS 2024; 20:48. [PMID: 38521920 PMCID: PMC10960999 DOI: 10.1186/s13007-024-01168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/28/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Leaf water content (LWC) significantly affects rice growth and development. Real-time monitoring of rice leaf water status is essential to obtain high yield and water use efficiency of rice plants with precise irrigation regimes in rice fields. Hyperspectral remote sensing technology is widely used in monitoring crop water status because of its rapid, nondestructive, and real-time characteristics. Recently, multi-source data have been attempted to integrate into a monitored model of crop water status based on spectral indices. However, there are fewer studies using spectral index model coupled with multi-source data for monitoring LWC in rice plants. Therefore, 2-year field experiments were conducted with three irrigation regimes using four rice cultivars in this study. The multi-source data, including canopy ecological factors and physiological parameters, were incorporated into the vegetation index to accurately predict LWC in rice plants. RESULTS The results presented that the model accuracy of rice LWC estimation after combining data from multiple sources improved by 6-44% compared to the accuracy of a single spectral index normalized difference index (ND). Additionally, the optimal prediction accuracy of rice LWC was produced using a machine algorithm of gradient boosted decision tree (GBDT) based on the combination of ND(1287,1673) and crop water stress index (CWSI) (R2 = 0.86, RMSE = 0.01). CONCLUSIONS The machine learning estimation model constructed based on multi-source data fully utilizes the spectral information and considers the environmental changes in the crop canopy after introducing multi-source data parameters, thus improving the performance of spectral technology for monitoring rice LWC. The findings may be helpful to the water status diagnosis and accurate irrigation management of rice plants.
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Affiliation(s)
- Xuenan Zhang
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Haocong Xu
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Yehong She
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Chao Hu
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Tiezhong Zhu
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Lele Wang
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Liquan Wu
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China.
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing, 210095, Jiangsu, People's Republic of China.
| | - Cuicui You
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
- Yingshang Agricultural Green Development Promotion Center, Fuyang, 236200, Anhui, People's Republic of China
| | - Jian Ke
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
- Yingshang Agricultural Green Development Promotion Center, Fuyang, 236200, Anhui, People's Republic of China
| | - Qiangqiang Zhang
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Haibing He
- Agricultural College, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China.
- Yingshang Agricultural Green Development Promotion Center, Fuyang, 236200, Anhui, People's Republic of China.
- Germplasm Creation and Application Laboratory of Grain and Oil Crops in Wanjiang Plain, Enterprise Key Laboratory of Ministry of Agriculture and Rural Affairs, Tongling, 244002, China.
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VanBuren R, Nguyen A, Marks RA, Mercado C, Pardo A, Pardo J, Schuster J, Aubin BS, Wilson ML, Rhee SY. Variability in drought gene expression datasets highlight the need for community standardization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578814. [PMID: 38370805 PMCID: PMC10871248 DOI: 10.1101/2024.02.04.578814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Physiologically relevant drought stress is difficult to apply consistently, and the heterogeneity in experimental design, growth conditions, and sampling schemes make it challenging to compare water deficit studies in plants. Here, we re-analyzed hundreds of drought gene expression experiments across diverse model and crop species and quantified the variability across studies. We found that drought studies are surprisingly uncomparable, even when accounting for differences in genotype, environment, drought severity, and method of drying. Many studies, including most Arabidopsis work, lack high-quality phenotypic and physiological datasets to accompany gene expression, making it impossible to assess the severity or in some cases the occurrence of water deficit stress events. From these datasets, we developed supervised learning classifiers that can accurately predict if RNA-seq samples have experienced a physiologically relevant drought stress, and suggest this can be used as a quality control for future studies. Together, our analyses highlight the need for more community standardization, and the importance of paired physiology data to quantify stress severity for reproducibility and future data analyses.
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10
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Licaj I, Germinario C, Di Meo MC, Varricchio E, Rocco M. The physiology and anatomy study in leaves of Saragolla and Svevo wheat cultivars under polyethylene glycol-simulated drought stress. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23151. [PMID: 38326232 DOI: 10.1071/fp23151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
Drought stress is increasing in frequency and severity with the progression of global climate change, thereby becoming a major concern for the growth and yield of crop plants, including wheat. The current challenge is to explore different ways of developing wheat genotypes with increased tolerance to drought. Therefore, we renewed interest in 'ancient' varieties expected to be more tolerant to environmental stress than the few elite varieties nowadays cultivated. This study aimed to perform comparative analysis of the effect of drought-simulating polyethylene glycol (PEG-6000) treatment on morpho-anatomical and physiological foliar traits of two durum wheat seedlings cultivars, Saragolla and Svevo, as these can reflect the adaptability of the plant to the environment to a certain extent. Results demonstrated that drought-stressed Saragolla leaves exhibited a greater reduction of stomatal density, a minor reduction of stomatal pore width, a wider xylem vessel mean area, greater compactness of mesophyll cells, a minor loss of chlorophyll content, as well as better photosynthetic and growth performance compared to the other variety. From such behaviours, we consider the Saragolla cultivar more drought tolerant than Svevo and therefore probably very promising for cultivation in dry areas.
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Affiliation(s)
- Ilva Licaj
- Department of Science and Technology, University of Sannio, Benevento 82100, Italy
| | - Chiara Germinario
- Department of Science and Technology, University of Sannio, Benevento 82100, Italy
| | - Maria Chiara Di Meo
- Department of Science and Technology, University of Sannio, Benevento 82100, Italy
| | - Ettore Varricchio
- Department of Science and Technology, University of Sannio, Benevento 82100, Italy
| | - Mariapina Rocco
- Department of Science and Technology, University of Sannio, Benevento 82100, Italy
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11
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Lainé CMS, AbdElgawad H, Beemster GTS. Cellular dynamics in the maize leaf growth zone during recovery from chilling depends on the leaf developmental stage. PLANT CELL REPORTS 2024; 43:38. [PMID: 38200224 DOI: 10.1007/s00299-023-03116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/16/2023] [Indexed: 01/12/2024]
Abstract
KEY MESSAGE A novel non-steady-state kinematic analysis shows differences in cell division and expansion determining a better recovery from a 3-day cold spell in emerged compared to non-emerged maize leaves. Zea mays is highly sensitive to chilling which frequently occurs during its seedling stage. Although the direct effect of chilling is well studied, the mechanisms determining the subsequent recovery are still unknown. Our goal is to determine the cellular basis of the leaf growth response to chilling and during recovery of leaves exposed before or after their emergence. We first studied the effect of a 3-day cold spell on leaf growth at the plant level. Then, we performed a kinematic analysis to analyse the dynamics of cell division and elongation during recovery of the 4th leaf after exposure to cold before or after emergence. Our results demonstrated cold more strongly reduced the final length of non-emerged than emerged leaves (- 13 vs. - 18%). This was not related to growth differences during cold, but a faster and more complete recovery of the growth of emerged leaves. This difference was due to a higher cell division rate on the 1st and a higher cell elongation rate on the 2nd day of recovery, respectively. The dynamics of cell division and expansion during recovery determines developmental stage-specific differences in cold tolerance of maize leaves.
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Affiliation(s)
- Cindy M S Lainé
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, Antwerp University, Groenenborgerlaan 171, 2020, Antwerp, Belgium.
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, Antwerp University, Groenenborgerlaan 171, 2020, Antwerp, Belgium
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, Antwerp University, Groenenborgerlaan 171, 2020, Antwerp, Belgium.
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12
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Bollier N, Micol-Ponce R, Dakdaki A, Maza E, Zouine M, Djari A, Bouzayen M, Chevalier C, Delmas F, Gonzalez N, Hernould M. Various tomato cultivars display contrasting morphological and molecular responses to a chronic heat stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1278608. [PMID: 37965003 PMCID: PMC10642206 DOI: 10.3389/fpls.2023.1278608] [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: 08/16/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023]
Abstract
Climate change is one of the biggest threats that human society currently needs to face. Heat waves associated with global warming negatively affect plant growth and development and will increase in intensity and frequency in the coming years. Tomato is one of the most produced and consumed fruit in the world but remarkable yield losses occur every year due to the sensitivity of many cultivars to heat stress (HS). New insights into how tomato plants are responding to HS will contribute to the development of cultivars with high yields under harsh temperature conditions. In this study, the analysis of microsporogenesis and pollen germination rate of eleven tomato cultivars after exposure to a chronic HS revealed differences between genotypes. Pollen development was either delayed and/or desynchronized by HS depending on the cultivar considered. In addition, except for two, pollen germination was abolished by HS in all cultivars. The transcriptome of floral buds at two developmental stages (tetrad and pollen floral buds) of five cultivars revealed common and specific molecular responses implemented by tomato cultivars to cope with chronic HS. These data provide valuable insights into the diversity of the genetic response of floral buds from different cultivars to HS and may contribute to the development of future climate resilient tomato varieties.
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Affiliation(s)
- N. Bollier
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | | | - A. Dakdaki
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - E. Maza
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - M. Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - A. Djari
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - M. Bouzayen
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - C. Chevalier
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - F. Delmas
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - N. Gonzalez
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - M. Hernould
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
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13
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da Cunha Cruz Y, Scarpa ALM, Díaz AS, Pereira MP, de Castro EM, Pereira FJ. Influence of seasonal variation to the population growth and ecophysiology of Typha domingensis (Typhaceae). JOURNAL OF PLANT RESEARCH 2023; 136:665-678. [PMID: 37219754 DOI: 10.1007/s10265-023-01468-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Precipitation is an important climatic element that defines the hydrological regime, and its seasonal variation produces annual dry and wet periods in some areas. This seasonality changes wetland environments and leverages the growth dynamics of macrophytes present, including Typha domingensis Pers. This study aimed to evaluate the influence of seasonal variation on the growth, anatomy and ecophysiology of T. domingensis in a natural wetland. Biometric, anatomical and ecophysiological traits of T. domingensis were evaluated over one year at four-month intervals. Reductions in photosynthesis were evidenced at the end of the wet periods and during the dry periods, and these reductions were associated with thinner palisade parenchymas. Increased stomatal indexes and densities as well as thinner epidermis observed at the beginning dry periods can be associated with higher transpiration rates during this period. The plants maintained their water contents during the dry periods, which may be related to the storage of water in leaf trabecular parenchyma, as this is the first time that results indicate the function of this tissue as a seasonal aquiferous parenchyma. In addition, increasing proportions of aerenchymas were evident during the wet periods, which may be related to a compensation mechanism for soil waterlogging. Therefore, the growth, anatomy and ecophysiology of T. domingensis plants change throughout the year to adjust to both the dry and wet periods, providing conditions for the survival of the plants and modulating population growth.
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Affiliation(s)
| | | | | | | | | | - Fabricio José Pereira
- Instituto de Ciências da Natureza, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, nº700, Centro, Alfenas, MG, CEP: 37130-001, Brasil.
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14
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Dadras A, Fürst-Jansen JMR, Darienko T, Krone D, Scholz P, Sun S, Herrfurth C, Rieseberg TP, Irisarri I, Steinkamp R, Hansen M, Buschmann H, Valerius O, Braus GH, Hoecker U, Feussner I, Mutwil M, Ischebeck T, de Vries S, Lorenz M, de Vries J. Environmental gradients reveal stress hubs pre-dating plant terrestrialization. NATURE PLANTS 2023; 9:1419-1438. [PMID: 37640935 PMCID: PMC10505561 DOI: 10.1038/s41477-023-01491-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unravelled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum. Here we used fine-combed RNA sequencing in tandem with a photophysiological assessment on Mesotaenium exposed to a continuous range of temperature and light cues. Our data establish a grid of 42 different conditions, resulting in 128 transcriptomes and ~1.5 Tbp (~9.9 billion reads) of data to study the combinatory effects of stress response using clustering along gradients. Mesotaenium shares with land plants major hubs in genetic networks underpinning stress response and acclimation. Our data suggest that lipid droplet formation and plastid and cell wall-derived signals have denominated molecular programmes since more than 600 million years of streptophyte evolution-before plants made their first steps on land.
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Affiliation(s)
- Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Denis Krone
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Patricia Scholz
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
| | - Siqi Sun
- Institute of Plant Biology and Biotechnology, Green Biotechnology, University of Münster, Münster, Germany
| | - Cornelia Herrfurth
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Rasmus Steinkamp
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maike Hansen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences, Biocenter, University of Cologne, Cologne, Germany
| | - Henrik Buschmann
- Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Oliver Valerius
- Institute of Microbiology and Genetics and Göttingen Center for Molecular Biosciences and Service Unit LCMS Protein Analytics, Department of Molecular Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Gerhard H Braus
- Institute of Microbiology and Genetics and Göttingen Center for Molecular Biosciences and Service Unit LCMS Protein Analytics, Department of Molecular Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences, Biocenter, University of Cologne, Cologne, Germany
| | - Ivo Feussner
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Till Ischebeck
- Institute of Plant Biology and Biotechnology, Green Biotechnology, University of Münster, Münster, Germany
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maike Lorenz
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Experimental Phycology and SAG Culture Collection of Algae, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- Goettingen Center for Molecular Biosciences, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
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15
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Xu X, Fonseca de Lima CF, Vu LD, De Smet I. When drought meets heat - a plant omics perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1250878. [PMID: 37674736 PMCID: PMC10478009 DOI: 10.3389/fpls.2023.1250878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Changes in weather patterns with emerging drought risks and rising global temperature are widespread and negatively affect crop growth and productivity. In nature, plants are simultaneously exposed to multiple biotic and abiotic stresses, but most studies focus on individual stress conditions. However, the simultaneous occurrence of different stresses impacts plant growth and development differently than a single stress. Plants sense the different stress combinations in the same or in different tissues, which could induce specific systemic signalling and acclimation responses; impacting different stress-responsive transcripts, protein abundance and modifications, and metabolites. This mini-review focuses on the combination of drought and heat, two abiotic stress conditions that often occur together. Recent omics studies indicate common or independent regulators involved in heat or drought stress responses. Here, we summarize the current research results, highlight gaps in our knowledge, and flag potential future focus areas.
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Affiliation(s)
- Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cassio Flavio Fonseca de Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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16
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Han J, Liu Y, Shen Y, Li W. A Surprising Diversity of Xyloglucan Endotransglucosylase/Hydrolase in Wheat: New in Sight to the Roles in Drought Tolerance. Int J Mol Sci 2023; 24:9886. [PMID: 37373033 DOI: 10.3390/ijms24129886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Drought has become a major limiting factor for wheat productivity, and its negative impact on crop growth is anticipated to increase with climate deterioration in arid areas. Xyloglucan endoglycosylases/hydrolases (XTHs) are involved in constructing and remodeling cell wall structures and play an essential role in regulating cell wall extensibility and stress responses. However, there are no systematic studies on the wheat XTH gene family. In this study, 71 wheat XTH genes (TaXTHs) were characterized and classified into three subgroups through phylogenetic analysis. Genomic replication promoted the expansion of TaXTHs. We found a catalytically active motif and a potential N-linked glycosylation domain in all TaXTHs. Further expression analysis revealed that many TaXTHs in the roots and shoots were significantly associated with drought stress. The wheat TaXTH12.5a gene was transferred into Arabidopsis to verify a possible role of TaXTHs in stress response. The transgenic plants possessed higher seed germination rates and longer roots and exhibited improved tolerance to drought. In conclusion, bioinformatics and gene expression pattern analysis indicated that the TaXTH genes played a role in regulating drought response in wheat. The expression of TaXTH12.5a enhanced drought tolerance in Arabidopsis and supported the XTH genes' role in regulating drought stress response in plants.
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Affiliation(s)
- Junjie Han
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
| | - Yichen Liu
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
| | - Yiting Shen
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
| | - Weihua Li
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
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17
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Driesen E, De Proft M, Saeys W. Drought stress triggers alterations of adaxial and abaxial stomatal development in basil leaves increasing water-use efficiency. HORTICULTURE RESEARCH 2023; 10:uhad075. [PMID: 37303614 PMCID: PMC10251137 DOI: 10.1093/hr/uhad075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
The physiological control of stomatal opening by which plants adjust for water availability has been extensively researched. However, the impact of water availability on stomatal development has not received as much attention, especially for amphistomatic plants. Therefore, the acclimation of stomatal development in basil (Ocimum basilicum L.) leaves was investigated. Our results show that leaves developed under water-deficit conditions possess higher stomatal densities and decreased stomatal length for both the adaxial and abaxial leaf sides. Although the stomatal developmental reaction to water deficit was similar for the two leaf surfaces, it was proven that adaxial stomata are more sensitive to water stress than abaxial stomata, with more closed adaxial stomata under water-deficit conditions. Furthermore, plants with leaves containing smaller stomata at higher densities possessed a higher water use efficiency. Our findings highlight the importance of stomatal development as a tool for long-term acclimation to limit water loss, with minimal reduction in biomass production. This highlights the central role that stomata play in both the short (opening) and long-term (development) reaction of plants to water availability, making them key tools for efficient resource use and anticipation of future environmental changes.
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Affiliation(s)
| | - Maurice De Proft
- Department of Biosystems, KU Leuven, Willem De Croylaan 42, 3001 Leuven, Belgium
| | - Wouter Saeys
- Department of Biosystems, KU Leuven, Willem De Croylaan 42, 3001 Leuven, Belgium
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18
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Li J, Mintgen MAC, D'Haeyer S, Helfer A, Nelissen H, Inzé D, Dhondt S. PhenoWell®-A novel screening system for soil-grown plants. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:55-69. [PMID: 37288161 PMCID: PMC10243540 DOI: 10.1002/pei3.10098] [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: 06/14/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 06/09/2023]
Abstract
As agricultural production is reaching its limits regarding outputs and land use, the need to further improve crop yield is greater than ever. The limited translatability from in vitro lab results into more natural growth conditions in soil remains problematic. Although considerable progress has been made in developing soil-growth assays to tackle this bottleneck, the majority of these assays use pots or whole trays, making them not only space- and resource-intensive, but also hampering the individual treatment of plants. Therefore, we developed a flexible and compact screening system named PhenoWell® in which individual seedlings are grown in wells filled with soil allowing single-plant treatments. The system makes use of an automated image-analysis pipeline that extracts multiple growth parameters from individual seedlings over time, including projected rosette area, relative growth rate, compactness, and stockiness. Macronutrient, hormone, salt, osmotic, and drought stress treatments were tested in the PhenoWell® system. The system is also optimized for maize with results that are consistent with Arabidopsis while different in amplitude. We conclude that the PhenoWell® system enables a high-throughput, precise, and uniform application of a small amount of solution to individually soil-grown plants, which increases the replicability and reduces variability and compound usage.
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Affiliation(s)
- Ji Li
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems BiologyVIBGhentBelgium
| | - Michael A. C. Mintgen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems BiologyVIBGhentBelgium
| | - Sam D'Haeyer
- Discovery SciencesVIBGhentBelgium
- Screening CoreVIBGhentBelgium
| | | | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems BiologyVIBGhentBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems BiologyVIBGhentBelgium
| | - Stijn Dhondt
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems BiologyVIBGhentBelgium
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19
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Jiang Y, Su S, Chen H, Li S, Shan X, Li H, Liu H, Dong H, Yuan Y. Transcriptome analysis of drought-responsive and drought-tolerant mechanisms in maize leaves under drought stress. PHYSIOLOGIA PLANTARUM 2023; 175:e13875. [PMID: 36775906 DOI: 10.1111/ppl.13875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/18/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Maize is a major crop essential for food and feed, but its production is threatened by various biotic and abiotic stresses. Drought is one of the most common abiotic stresses, causing severe crop yield reduction. Although several studies have been devoted to selecting drought-tolerant maize lines and detecting the drought-responsive mechanism of maize, the transcriptomic differences between drought-tolerant and drought-susceptible maize lines are still largely unknown. In our study, RNA-seq was performed on leaves of the drought-tolerant line W9706 and the drought-susceptible line B73 after drought treatment. We identified 3147 differentially expressed genes (DEGs) between these two lines. The upregulated DEGs in W9706 were enriched in specific processes, including ABA signaling, wax biosynthesis, CHO metabolism, signal transduction and brassinosteroid biosynthesis-related processes, while the downregulated DEGs were enriched in specific processes, such as stomatal movement. Altogether, transcriptomic analysis suggests that the different drought resistances were correlated with the differential expression of genes, while the drought tolerance of W9706 is due to the more rapid response to stimulus, higher water retention capacity and stable cellular environment under water deficit conditions.
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Affiliation(s)
- Yuan Jiang
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Shengzhong Su
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Hao Chen
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Shipeng Li
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Xiaohui Shan
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - He Li
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Hongkui Liu
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Haixiao Dong
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Yaping Yuan
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
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20
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Thirumalaikumar VP, Fernie AR, Skirycz A. Untargeted Proteomics and Metabolomics Analysis of Plant Organ Development. Methods Mol Biol 2023; 2698:75-85. [PMID: 37682470 DOI: 10.1007/978-1-0716-3354-0_6] [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] [Indexed: 09/09/2023]
Abstract
Our understanding of major developmental transitions in plants and animals has been transformed by the emergence of omics technologies. The majority of leaf growth research has been conducted at the transcriptional level. Although historically understudied, alterations at the protein and metabolite levels have begun to gain traction in recent years. Here, we present a protocol for metabolite and protein extraction followed by untargeted metabolomics and proteomics analysis of the growing leaves.
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Affiliation(s)
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
| | - Aleksandra Skirycz
- Boyce Thompson Institute, Ithaca, NY, USA.
- Cornell University, Ithaca, NY, USA.
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21
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Rauschendorfer J, Rooney R, Külheim C. Strategies to mitigate shifts in red oak (Quercus sect. Lobatae) distribution under a changing climate. TREE PHYSIOLOGY 2022; 42:2383-2400. [PMID: 35867476 DOI: 10.1093/treephys/tpac090] [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: 11/24/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Red oaks (Quercus sect. Lobatae) are a taxonomic group of hardwood trees, which occur in swamp forests, subtropical chaparral and savannahs from Columbia to Canada. They cover a wide range of ecological niches, and many species are thought to be able to cope with current trends in climate change. Genus Quercus encompasses ca. 500 species, of which ca. 80 make up sect. Lobatae. Species diversity is greatest within the southeastern USA and within the northern and eastern regions of Mexico. This review discusses the weak reproductive barriers between species of red oaks and the effects this has on speciation and niche range. Distribution and diversity have been shaped by drought adaptations common to the species of sect. Lobatae, which enable them to fill various xeric niches across the continent. Drought adaptive traits of this taxonomic group include deciduousness, deep tap roots, ring-porous xylem, regenerative stump sprouting, greater leaf thickness and smaller stomata. The complex interplay between these anatomical and morphological traits has given red oaks features of drought tolerance and avoidance. Here, we discuss physiological and genetic components of these adaptations to address how many species of sect. Lobatae reside within xeric sites and/or sustain normal metabolic function during drought. Although extensive drought adaptation appears to give sect. Lobatae a resilience to climate change, aging tree stands, oak life history traits and the current genetic structures place many red oak species at risk. Furthermore, oak decline, a complex interaction between abiotic and biotic agents, has severe effects on red oaks and is likely to accelerate species decline and fragmentation. We suggest that assisted migration can be used to avoid species fragmentation and increase climate change resilience of sect. Lobatae.
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Affiliation(s)
- James Rauschendorfer
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rebecca Rooney
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Carsten Külheim
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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22
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Yu K, Wei L, Yuan H, Zhang W, Zeng X, Wang B, Wang Y. Genetic architecture of inducible and constitutive metabolic profile related to drought resistance in qingke (Tibetan hulless barley). FRONTIERS IN PLANT SCIENCE 2022; 13:1076000. [PMID: 36561451 PMCID: PMC9763626 DOI: 10.3389/fpls.2022.1076000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Qingke (Tibetan hulless barley, Hordeum vulgare L. var. nudum) is the primary food crop on the Tibet Plateau, the long-term drought and other harsh environments makes qingke an important resource for the study of abiotic resistance. Here, we evaluated the drought sensitivity of 246 qingke varieties. Genome-wide association studies (GWAS) found that root-specific expressed gene CYP84 may be involved in the regulation of drought resistance. Based on widely targeted metabolic profiling, we identified 2,769 metabolites in qingke leaves, of which 302 were significantly changed in response to drought stress, including 4-aminobutyric acid (GABA), proline, sucrose and raffinose. Unexpectedly, these drought-induced metabolites changed more violently in drought-sensitive qingkes, while the constitutive metabolites that had little response to drought stress, such as C-glycosylflavonoids and some amino acids, accumulated excessively in drought-resistant qingkes. Combined with metabolite-based genome-wide association study (mGWAS), a total of 1,006 metabolites under optimal condition and 1,031 metabolites under mild drought stress had significant associated loci. As a marker metabolite induced by drought stress, raffinose was significantly associated with two conservatively adjacent α-galactosidase genes, qRT-PCR suggests that these two genes may jointly regulate the raffinose content in qingke. Besides, as constituent metabolites with stable differences between drought-sensitive and drought-resistant qingkes, a class of C-glycosylflavonoids are simultaneously regulated by a UDP-glucosyltransferase gene. Overall, we performed GWAS for sensitivity and widely targeted metabolites during drought stress in qingke for the first time, which provides new insights into the response mechanism of plant drought stress and drought resistance breeding.
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Affiliation(s)
- Kuohai Yu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Lingling Wei
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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23
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Savvides AM, Velez‐Ramirez AI, Fotopoulos V. Challenging the water stress index concept: Thermographic assessment of Arabidopsis transpiration. PHYSIOLOGIA PLANTARUM 2022; 174:e13762. [PMID: 36281841 PMCID: PMC9542539 DOI: 10.1111/ppl.13762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 05/31/2023]
Abstract
Water stress may greatly limit plant functionality and growth. Stomatal closure and consequently reduced transpiration are considered as early and sensitive plant responses to drought and salinity stress. An important consequence of stomatal closure under water stress is the rise of leaf temperature (Tleaf ), yet Tleaf is not only fluctuating with stomatal closure. It is regulated by several plant parameters and environmental factors. Thermal imaging and different stress indices, incorporating actual leaf/crop temperature and reference temperatures, were developed in previous studies toward normalizing for effects unassociated to water stress on Tleaf , aiming at a more efficient water stress assessment. The concept of stress indices has not been extensively studied on the model plant Arabidopsis thaliana. Therefore, the aim of this study was to examine the different indices employed in previous studies in assessing rosette transpiration rate (E) in Arabidopsis plants grown under two different light environments and subjected to salinity. After salinity imposition, E was gravimetrically quantified, and thermal imaging was employed to quantify rosette (Trosette ) and artificial reference temperature (Twet, Tdry ). Trosette and several water stress indices were tested for their relation to E. Among the microclimatic growth conditions tested, RWSI1 ([Trosette - Twet ]/[Tdry - Twet ]) and RWSI2 ([Tdry - Trosette ]/[Tdry - Twet ]) were well linearly-related to E, irrespective of the light environment, while the sole use of either Twet or Tdry in different combinations with Trosette returned less accurate results. This study provides evidence that selected combinations of Trosette , Tdry , and Twet can be utilized to assess E under water stress irrespective of the light environment.
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Affiliation(s)
- Andreas M. Savvides
- Department of Agricultural Sciences, Biotechnology and Food ScienceCyprus University of TechnologyLimassolCyprus
| | - Aaron I. Velez‐Ramirez
- Laboratorio de Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad LeónUniversidad Nacional Autónoma de MéxicoLeónMexico
- Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad LeónUniversidad Nacional Autónoma de MéxicoLeónMexico
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food ScienceCyprus University of TechnologyLimassolCyprus
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Bajpai PK, Harel A, Shafir S, Barazani O. Whole genome sequencing reveals footprints of adaptive genetic variation in populations of Eruca sativa. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.938981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Populations of Eruca sativa (Brassicaceae) derived from arid and Mediterranean habitats exhibit ecotypic differentiation. Here, pooled DNA sequencing was used to assess adaptive genome differentiation in the two ecotypes. Differentiated SNP loci were scanned with the empirical FST outlier method and by correlating allele frequencies with environmental parameters. Genetic diversity values were relatively higher in the pooled arid genome, whereas the pooled Mediterranean genome exhibited stronger directional selection, indicating the impact of climatic conditions on genetic diversity. GO enrichment analysis categorized the annotated differentiated loci according to biological processes, revealing a large set of candidate genes related to abiotic and biotic stress responses. Allelic variation was detected in regulatory elements and coding regions (synonymous and non-synonymous mutations) of genes belonging to different transcription factors and phytohormone signaling, suggesting adaptation to both abiotic and biotic conditions. Furthermore, SNP mutations were also found in genic regions belonging to the synthesis of secondary metabolites, including aliphatic glucosinolates and their hydrolyzed bioactive compounds, among others. The results of this eco-genomic study demonstrate the role of divergent abiotic and biotic selection factors in evolutionary processes leading to adaptive ecotypic differentiation.
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25
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de Oliveira JPV, Duarte VP, de Castro EM, Magalhães PC, Pereira FJ. Stomatal cavity modulates the gas exchange of Sorghum bicolor (L.) Moench. grown under different water levels. PROTOPLASMA 2022; 259:1081-1097. [PMID: 34755230 DOI: 10.1007/s00709-021-01722-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/01/2021] [Indexed: 05/12/2023]
Abstract
This work aimed to evaluate the effects of lower water levels on leaf intercellular spaces and to assess their relations with the gas exchange, anatomy, and growth of Sorghum bicolor. Experiments were conducted in a greenhouse, in which plants were subjected to three water conditions (ten replicates, n = 30): well-irrigated, decreased irrigation, and limited irrigation. Lower water levels had no significant effect on the growth of S. bicolor but increased the biomass of the roots. Moreover, the number of leaves, leaf area, and leaf size as well as the chlorophyll content were not affected by lower water levels, and no significant changes were detected for whole plant photosynthesis, transpiration, or stomatal conductance. The water content of the plants and the water potential remained unchanged. However, compared with other treatments, the decreased irrigation decreased water loss and increased the water retention. Lower water levels increased the intercellular CO2 percentage, mesophyll area, and proportion of stomatal cavities and promoted minor changes in leaf tissue and stomatal traits. The increased stomatal cavities provided higher CO2 uptake and prevented excessive water loss. Thus, modifications to the intercellular spaces promoted conditions to avoid excessive water loss while concurrently improving CO2 uptake, which are important traits for drought-tolerant plants.
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Affiliation(s)
| | | | | | | | - Fabricio José Pereira
- Instituto de Ciências da Natureza (ICN), Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700, Centro, Alfenas, MG, 37130-001, Brazil.
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Kherfi-Nacer A, Yan Z, Bouherama A, Schmitz L, Amrane SO, Franken C, Schneijderberg M, Cheng X, Amrani S, Geurts R, Bisseling T. High Salt Levels Reduced Dissimilarities in Root-Associated Microbiomes of Two Barley Genotypes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:592-603. [PMID: 35316093 DOI: 10.1094/mpmi-12-21-0294-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plants harbor in and at their roots bacterial microbiomes that contribute to their health and fitness. The microbiome composition is controlled by the environment and plant genotype. Previously, it was shown that the plant genotype-dependent dissimilarity of root microbiome composition of different species becomes smaller under drought stress. However, it remains unknown whether this reduced plant genotype-dependent effect is a specific response to drought stress or a more generic response to abiotic stress. To test this, we studied the effect of salt stress on two distinct barley (Hordeum vulgare L.) genotypes: the reference cultivar Golden Promise and the Algerian landrace AB. As inoculum, we used soil from salinized and degraded farmland on which barley was cultivated. Controlled laboratory experiments showed that plants inoculated with this soil displayed growth stimulation under high salt stress (200 mM) in a plant genotype-independent manner, whereas the landrace AB also showed significant growth stimulation at low salt concentrations. Subsequent analysis of the root microbiomes revealed a reduced dissimilarity of the bacterial communities of the two barley genotypes in response to high salt, especially in the endophytic compartment. High salt level did not reduce α-diversity (richness) in the endophytic compartment of both plant genotypes but was associated with an increased number of shared strains that respond positively to high salt. Among these, Pseudomonas spp. were most abundant. These findings suggest that the plant genotype-dependent microbiome composition is altered generically by abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Asma Kherfi-Nacer
- Laboratory of Biology and Physiology of Organisms (LBPO), Biological Sciences Faculty, Houari Boumediène Sciences and Technology University (USTHB), BP 32, El-Alia, Bab Ezzouar, Algiers 16111, Algeria
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Zhichun Yan
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Amina Bouherama
- Laboratory of Biology and Physiology of Organisms (LBPO), Biological Sciences Faculty, Houari Boumediène Sciences and Technology University (USTHB), BP 32, El-Alia, Bab Ezzouar, Algiers 16111, Algeria
- Sciences Faculty, Yahia Farès University, Médéa 26000, Algeria
| | - Lucas Schmitz
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Saadia Ouled Amrane
- Laboratory of Biology and Physiology of Organisms (LBPO), Biological Sciences Faculty, Houari Boumediène Sciences and Technology University (USTHB), BP 32, El-Alia, Bab Ezzouar, Algiers 16111, Algeria
- Research Experimental Field Station, Belbachir, El-Meniaa, Ghardaïa 47001, Algeria
| | - Carolien Franken
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Martinus Schneijderberg
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Xu Cheng
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Said Amrani
- Laboratory of Biology and Physiology of Organisms (LBPO), Biological Sciences Faculty, Houari Boumediène Sciences and Technology University (USTHB), BP 32, El-Alia, Bab Ezzouar, Algiers 16111, Algeria
| | - Rene Geurts
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Science Group, Wageningen University and Research (WUR), Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
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27
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Fradera-Soler M, Grace OM, Jørgensen B, Mravec J. Elastic and collapsible: current understanding of cell walls in succulent plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2290-2307. [PMID: 35167681 PMCID: PMC9015807 DOI: 10.1093/jxb/erac054] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/11/2022] [Indexed: 05/11/2023]
Abstract
Succulent plants represent a large functional group of drought-resistant plants that store water in specialized tissues. Several co-adaptive traits accompany this water-storage capacity to constitute the succulent syndrome. A widely reported anatomical adaptation of cell walls in succulent tissues allows them to fold in a regular fashion during extended drought, thus preventing irreversible damage and permitting reversible volume changes. Although ongoing research on crop and model species continuously reports the importance of cell walls and their dynamics in drought resistance, the cell walls of succulent plants have received relatively little attention to date, despite the potential of succulents as natural capital to mitigate the effects of climate change. In this review, we summarize current knowledge of cell walls in drought-avoiding succulents and their effects on tissue biomechanics, water relations, and photosynthesis. We also highlight the existing knowledge gaps and propose a hypothetical model for regulated cell wall folding in succulent tissues upon dehydration. Future perspectives of methodological development in succulent cell wall characterization, including the latest technological advances in molecular and imaging techniques, are also presented.
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Affiliation(s)
- Marc Fradera-Soler
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Correspondence: or
| | | | | | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Correspondence: or
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28
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Terletskaya NV, Seitimova GA, Kudrina NO, Meduntseva ND, Ashimuly K. The Reactions of Photosynthetic Capacity and Plant Metabolites of Sedum hybridum L. in Response to Mild and Moderate Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060828. [PMID: 35336710 PMCID: PMC8955115 DOI: 10.3390/plants11060828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/26/2022] [Accepted: 03/06/2022] [Indexed: 05/17/2023]
Abstract
In this article, for the first time, an experimental study of the effect of mild and moderate osmotic stress, NaCl content and the effect of low positive temperature on photosynthetic activity and composition of metabolites of immature plants Sedum hybridum L. is reported. In this representative of the genus Sedum adapted to arid conditions and having the properties of a succulent, a change in photosynthetic activity and an increase in the level of protective metabolites in the shoots were revealed when exposed to mild and moderate stress factors. The results of this study can be used in work on the adaptation of succulent plants to arid conditions, environmental monitoring and work on the directed induction of valuable secondary metabolites in succulents to obtain new herbal medicines.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
- Correspondence: (N.V.T.); (N.O.K.); Tel.: +7-(777)-2993-335 (N.V.T.); +7-(705)-1811-440 (N.O.K.)
| | - Gulnaz A. Seitimova
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
| | - Nataliya O. Kudrina
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
- Correspondence: (N.V.T.); (N.O.K.); Tel.: +7-(777)-2993-335 (N.V.T.); +7-(705)-1811-440 (N.O.K.)
| | - Nataliya D. Meduntseva
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
| | - Kazhybek Ashimuly
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
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29
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Tanabata T, Kodama K, Hashiguchi T, Inomata D, Tanaka H, Isobe S. Development of a plant conveyance system using an AGV and a self-designed plant-handling device: A case study of DIY plant phenotyping. BREEDING SCIENCE 2022; 72:85-95. [PMID: 36045895 PMCID: PMC8987848 DOI: 10.1270/jsbbs.21070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/19/2022] [Indexed: 06/15/2023]
Abstract
Plant phenotyping technology has been actively developed in recent years, but the introduction of these technologies into the field of agronomic research has not progressed as expected, in part due to the need for flexibility and low cost. "DIY" (Do It Yourself) methodologies are an efficient way to overcome such obstacles. Devices with modular functionality are critical to DIY experimentation, allowing researchers flexibility of design. In this study, we developed a plant conveyance system using a commercial AGV (Automated Guided Vehicle) as a case study of DIY plant phenotyping. The convey module consists of two devices, a running device and a plant-handling device. The running device was developed based on a commercial AGV Kit. The plant-handling device, plant stands, and pot attachments were originally designed and fabricated by us and our associates. Software was also developed for connecting the devices and operating the system. The run route was set with magnetic tape, which can be easily changed or rerouted. Our plant delivery system was developed with low cost and having high flexibility, as a unit that can contribute to others' DIY' plant research efforts as well as our own. It is expected that the developed devices will contribute to diverse phenotype observations of plants in the greenhouse as well as to other important functions in plant breeding and agricultural production.
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Affiliation(s)
- Takanari Tanabata
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kunihiro Kodama
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takuyu Hashiguchi
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan
| | | | - Hidenori Tanaka
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
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30
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Nieto-Garibay A, Barraza A, Caamal-Chan G, Murillo-Amador B, Troyo-Diéguez E, Burgoa-Cruz CA, Jaramillo-Limón JN, Loera-Muro A. Habanero pepper ( Capsicum chinense) adaptation to water-deficit stress in a protected agricultural system. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:295-306. [PMID: 35130477 DOI: 10.1071/fp20394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Drought is one of the major factors limiting global crop yield. In Mexico, agriculture is expected to be severely affected by drought. The Capsicum genus has several crop species of agricultural importance. In this work, we analysed the Capsicum chinense plant physiological responses and differentially expressed genes under water stress mainly focused on the responses elicited following recovery through repetitive stress. Plants were cultivated in an experimental block. Each block consisted of plants under water deficit and a control group without deficit. Morphometric and functional parameters, and the expression of genes related to resistance to abiotic stresses were measured. Morphological differences were observed. Plants subjected to water deficit showed impaired growth. Nonetheless, in the physiological parameters, no differences were observed between treatments. We selected abiotic stress-related genes that include heat-shock proteins (HSPs), heat-shock factors (HSFs), transcription factors related to abiotic stress (MYB, ETR1 , and WRKY ), and those associated with biotic and abiotic stress responses (Jar1 and Lox2 ). HSF, HSP, MYB72, ETR1, Jar1, WRKYa , and Lox2 genes were involved in the response to water-deficit stress in C. chinense plants. In conclusion, our work may improve our understanding of the morphological, physiological, and molecular mechanisms underlying hydric stress response in C. chinense .
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Affiliation(s)
- Alejandra Nieto-Garibay
- Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, Baja California Sur, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
| | - Goretty Caamal-Chan
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
| | - Bernardo Murillo-Amador
- Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, Baja California Sur, Mexico
| | - Enrique Troyo-Diéguez
- Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, Baja California Sur, Mexico
| | - Carlos Alexis Burgoa-Cruz
- Instituto Tecnológico de La Paz, Boulevard Forjadores de Baja California Sur 4720, 8 de Octubre 2da Secc, La Paz, Baja California Sur, C.P. 23080, Mexico
| | - Jhesy Nury Jaramillo-Limón
- Universidad de Occidente, Unidad los Mochis Boulevard Macario Gaxiola SN Col. Las Malvinas, C.P. 81216, Los Mochis, Sinaloa, Mexico
| | - Abraham Loera-Muro
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
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31
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Kuromori T, Fujita M, Takahashi F, Yamaguchi‐Shinozaki K, Shinozaki K. Inter-tissue and inter-organ signaling in drought stress response and phenotyping of drought tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:342-358. [PMID: 34863007 PMCID: PMC9300012 DOI: 10.1111/tpj.15619] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 05/10/2023]
Abstract
Plant response to drought stress includes systems for intracellular regulation of gene expression and signaling, as well as inter-tissue and inter-organ signaling, which helps entire plants acquire stress resistance. Plants sense water-deficit conditions both via the stomata of leaves and roots, and transfer water-deficit signals from roots to shoots via inter-organ signaling. Abscisic acid is an important phytohormone involved in the drought stress response and adaptation, and is synthesized mainly in vascular tissues and guard cells of leaves. In leaves, stress-induced abscisic acid is distributed to various tissues by transporters, which activates stomatal closure and expression of stress-related genes to acquire drought stress resistance. Moreover, the stepwise stress response at the whole-plant level is important for proper understanding of the physiological response to drought conditions. Drought stress is sensed by multiple types of sensors as molecular patterns of abiotic stress signals, which are transmitted via separate parallel signaling networks to induce downstream responses, including stomatal closure and synthesis of stress-related proteins and metabolites. Peptide molecules play important roles in the inter-organ signaling of dehydration from roots to shoots, as well as signaling of osmotic changes and reactive oxygen species/Ca2+ . In this review, we have summarized recent advances in research on complex plant drought stress responses, focusing on inter-tissue signaling in leaves and inter-organ signaling from roots to shoots. We have discussed the mechanisms via which drought stress adaptations and resistance are acquired at the whole-plant level, and have proposed the importance of quantitative phenotyping for measuring plant growth under drought conditions.
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Affiliation(s)
- Takashi Kuromori
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science2‐1 HirosawaWakoSaitama351‐0198Japan
| | - Miki Fujita
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
| | - Fuminori Takahashi
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
- Department of Biological Science and TechnologyGraduate School of Advanced EngineeringTokyo University of Science6‐3‐1 Niijyuku, Katsushika‐kuTokyo125‐8585Japan
| | - Kazuko Yamaguchi‐Shinozaki
- Laboratory of Plant Molecular PhysiologyGraduate School of Agricultural and Life SciencesThe University of Tokyo1‐1‐1 Yayoi, Bunkyo‐kuTokyo113‐8657Japan
- Research Institute for Agricultural and Life SciencesTokyo University of Agriculture1‐1‐1 Sakuragaoka, Setagaya‐kuTokyo156‐8502Japan
| | - Kazuo Shinozaki
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science2‐1 HirosawaWakoSaitama351‐0198Japan
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
- Biotechonology CenterNational Chung Hsing University (NCHU)Taichung402Taiwan
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Chen H, Bullock DA, Alonso JM, Stepanova AN. To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010033. [PMID: 35009037 PMCID: PMC8747122 DOI: 10.3390/plants11010033] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 05/04/2023]
Abstract
Plants often live in adverse environmental conditions and are exposed to various stresses, such as heat, cold, heavy metals, salt, radiation, poor lighting, nutrient deficiency, drought, or flooding. To adapt to unfavorable environments, plants have evolved specialized molecular mechanisms that serve to balance the trade-off between abiotic stress responses and growth. These mechanisms enable plants to continue to develop and reproduce even under adverse conditions. Ethylene, as a key growth regulator, is leveraged by plants to mitigate the negative effects of some of these stresses on plant development and growth. By cooperating with other hormones, such as jasmonic acid (JA), abscisic acid (ABA), brassinosteroids (BR), auxin, gibberellic acid (GA), salicylic acid (SA), and cytokinin (CK), ethylene triggers defense and survival mechanisms thereby coordinating plant growth and development in response to abiotic stresses. This review describes the crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses.
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Geldhof B, Pattyn J, Eyland D, Carpentier S, Van de Poel B. A digital sensor to measure real-time leaf movements and detect abiotic stress in plants. PLANT PHYSIOLOGY 2021; 187:1131-1148. [PMID: 34618089 PMCID: PMC8566216 DOI: 10.1093/plphys/kiab407] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/02/2021] [Indexed: 05/31/2023]
Abstract
Plant and plant organ movements are the result of a complex integration of endogenous growth and developmental responses, partially controlled by the circadian clock, and external environmental cues. Monitoring of plant motion is typically done by image-based phenotyping techniques with the aid of computer vision algorithms. Here we present a method to measure leaf movements using a digital inertial measurement unit (IMU) sensor. The lightweight sensor is easily attachable to a leaf or plant organ and records angular traits in real-time for two dimensions (pitch and roll) with high resolution (measured sensor oscillations of 0.36 ± 0.53° for pitch and 0.50 ± 0.65° for roll). We were able to record simple movements such as petiole bending, as well as complex lamina motions, in several crops, ranging from tomato to banana. We also assessed growth responses in terms of lettuce rosette expansion and maize seedling stem movements. The IMU sensors are capable of detecting small changes of nutations (i.e. bending movements) in leaves of different ages and in different plant species. In addition, the sensor system can also monitor stress-induced leaf movements. We observed that unfavorable environmental conditions evoke certain leaf movements, such as drastic epinastic responses, as well as subtle fading of the amplitude of nutations. In summary, the presented digital sensor system enables continuous detection of a variety of leaf motions with high precision, and is a low-cost tool in the field of plant phenotyping, with potential applications in early stress detection.
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Affiliation(s)
- Batist Geldhof
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - Jolien Pattyn
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - David Eyland
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
| | - Sebastien Carpentier
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
- Bioversity International, Leuven, 3001, Belgium
| | - Bram Van de Poel
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
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D'Ippólito S, Rey-Burusco MF, Feingold SE, Guevara MG. Role of proteases in the response of plants to drought. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:1-9. [PMID: 34607206 DOI: 10.1016/j.plaphy.2021.09.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/02/2021] [Accepted: 09/28/2021] [Indexed: 05/25/2023]
Abstract
Plants are sessile organisms that, to survive they develop response mechanisms under water deficit conditions. Plant proteases play an essential role in a diversity of biological processes, among them tolerance to drought stress. Proteolysis is a critical regulator of stomatal development. Plant proteases are involved in the crosstalk among phytohormones and adjustment of stomatal aperture. Plant proteases are also related to the increment in reactive oxygen species (ROS) production detected in the plant biochemical response to drought. Plant proteases mitigate this process by degrading damaged, denatured, and aggregated proteins, remobilizing amino acids, and generating molecules involved in signal transductions. Although many roles for proteases have been proposed, molecular bases that regulate these mechanisms remain unknown. In this review, we summarize the current knowledge on the participation of proteases in the signaling pathways of plants in response to water deficit and their relationship with plant stress tolerance.
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Affiliation(s)
- Sebastián D'Ippólito
- Biological Research Institute, National Council of Scientific and Technique Research (CONICET), University of Mar del Plata, Mar del Plata (UNMDP), Argentina
| | - María Florencia Rey-Burusco
- Agrobiotechnology Laboratory, National Institute of Agrotechnology (INTA) EEA - Balcarce, Route 226, Km 73.5. DC 276, (7620), Balcarce, Argentina
| | - Sergio Enrique Feingold
- Agrobiotechnology Laboratory, National Institute of Agrotechnology (INTA) EEA - Balcarce, Route 226, Km 73.5. DC 276, (7620), Balcarce, Argentina
| | - María Gabriela Guevara
- Biological Research Institute, National Council of Scientific and Technique Research (CONICET), University of Mar del Plata, Mar del Plata (UNMDP), Argentina.
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Tiika RJ, Wei J, Cui G, Ma Y, Yang H, Duan H. Transcriptome-wide characterization and functional analysis of Xyloglucan endo-transglycosylase/hydrolase (XTH) gene family of Salicornia europaea L. under salinity and drought stress. BMC PLANT BIOLOGY 2021; 21:491. [PMID: 34696719 PMCID: PMC8547092 DOI: 10.1186/s12870-021-03269-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 10/11/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Salicornia europaea is a halophyte that has a very pronounced salt tolerance. As a cell wall manipulating enzyme, xyloglucan endotransglycosylase/hydrolase (XTH) plays an important role in plant resistance to abiotic stress. However, no systematic study of the XTH gene family in S. europaea is well known. PacBio Iso-Seq transcriptome sequence data were used for bioinformatics and gene expression analysis using real-time quantitative polymerase chain reaction (RT-qPCR). RESULTS Transcriptome sequencing (PacBio Iso-Seq system) generated 16,465,671 sub-reads and after quality control of Iso-Seq, 29,520 isoforms were obtained with an average length of 2112 bp. A total of 24,869 unigenes, with 98% of which were obtained using coding sequences (CDSs), and 6398 possible transcription factors (TFs) were identified. Thirty-five (35) non-redundant potential SeXTH proteins were identified in S. europaea and categorized into group I/II and group III based on their genetic relatedness. Prediction of the conserved motif revealed that the DE(I/L/F/V)DF(I)EFLG domain was conserved in the S. europaea proteins and a potential N-linked glycosylation domain N(T)V(R/L/T/I)T(S/K/R/F/P)G was also located near the catalytic residues. All SeXTH genes exhibited discrete expression patterns in different tissues, at different times, and under different stresses. For example, 27 and 15 SeXTH genes were positively expressed under salt stress in shoots and roots at 200 mM NaCl in 24 h, and 34 SeXTH genes were also positively regulated under 48 h of drought stress in shoots and roots. This indicates their function in adaptation to salt and drought stress. CONCLUSION The present study discovered SeXTH gene family traits that are potential stress resistance regulators in S. europaea, and this provides a basis for future functional diversity research.
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Affiliation(s)
- Richard John Tiika
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Jia Wei
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Guangxin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yanjun Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Hongshan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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Xiang L, Nolan TM, Bao Y, Elmore M, Tuel T, Gai J, Shah D, Wang P, Huser NM, Hurd AM, McLaughlin SA, Howell SH, Walley JW, Yin Y, Tang L. Robotic Assay for Drought (RoAD): an automated phenotyping system for brassinosteroid and drought responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1837-1853. [PMID: 34216161 DOI: 10.1111/tpj.15401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Brassinosteroids (BRs) are a group of plant steroid hormones involved in regulating growth, development, and stress responses. Many components of the BR pathway have previously been identified and characterized. However, BR phenotyping experiments are typically performed in a low-throughput manner, such as on Petri plates. Additionally, the BR pathway affects drought responses, but drought experiments are time consuming and difficult to control. To mitigate these issues and increase throughput, we developed the Robotic Assay for Drought (RoAD) system to perform BR and drought response experiments in soil-grown Arabidopsis plants. RoAD is equipped with a robotic arm, a rover, a bench scale, a precisely controlled watering system, an RGB camera, and a laser profilometer. It performs daily weighing, watering, and imaging tasks and is capable of administering BR response assays by watering plants with Propiconazole (PCZ), a BR biosynthesis inhibitor. We developed image processing algorithms for both plant segmentation and phenotypic trait extraction to accurately measure traits including plant area, plant volume, leaf length, and leaf width. We then applied machine learning algorithms that utilize the extracted phenotypic parameters to identify image-derived traits that can distinguish control, drought-treated, and PCZ-treated plants. We carried out PCZ and drought experiments on a set of BR mutants and Arabidopsis accessions with altered BR responses. Finally, we extended the RoAD assays to perform BR response assays using PCZ in Zea mays (maize) plants. This study establishes an automated and non-invasive robotic imaging system as a tool to accurately measure morphological and growth-related traits of Arabidopsis and maize plants in 3D, providing insights into the BR-mediated control of plant growth and stress responses.
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Affiliation(s)
- Lirong Xiang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Trevor M Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
| | - Yin Bao
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Mitch Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Taylor Tuel
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Jingyao Gai
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Dylan Shah
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Nicole M Huser
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ashley M Hurd
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sean A McLaughlin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Stephen H Howell
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
| | - Justin W Walley
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
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Das A, Prakash A, Dedon N, Doty A, Siddiqui M, Preston JC. Variation in climatic tolerance, but not stomatal traits, partially explains Pooideae grass species distributions. ANNALS OF BOTANY 2021; 128:83-95. [PMID: 33772589 PMCID: PMC8318108 DOI: 10.1093/aob/mcab046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Grasses in subfamily Pooideae live in some of the world's harshest terrestrial environments, from frigid boreal zones to the arid windswept steppe. It is hypothesized that the climate distribution of species within this group is driven by differences in climatic tolerance, and that tolerance can be partially explained by variation in stomatal traits. METHODS We determined the aridity index (AI) and minimum temperature of the coldest month (MTCM) for 22 diverse Pooideae accessions and one outgroup, and used comparative methods to assess predicted relationships for climate traits versus fitness traits, stomatal diffusive conductance to water (gw) and speed of stomatal closure following drought and/or cold. KEY RESULTS Results demonstrate that AI and MTCM predict variation in survival/regreening following drought/cold, and gw under drought/cold is positively correlated with δ 13C-measured water use efficiency (WUE). However, the relationship between climate traits and fitness under drought/cold was not explained by gw or speed of stomatal closure. CONCLUSIONS These findings suggest that Pooideae distributions are at least partly determined by tolerance to aridity and above-freezing cold, but that variation in tolerance is not uniformly explained by variation in stomatal traits.
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Affiliation(s)
- Aayudh Das
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Anoob Prakash
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Natalie Dedon
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Alex Doty
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Muniba Siddiqui
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Jill C Preston
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
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Leaf Age-Dependent Photosystem II Photochemistry and Oxidative Stress Responses to Drought Stress in Arabidopsis thaliana Are Modulated by Flavonoid Accumulation. Molecules 2021; 26:molecules26144157. [PMID: 34299433 PMCID: PMC8307756 DOI: 10.3390/molecules26144157] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
We investigated flavonoid accumulation and lipid peroxidation in young leaves (YL) and mature leaves (ML) of Arabidopsis thaliana plants, whose watering stopped 24 h before sampling, characterized as onset of drought stress (OnDS), six days before sampling, characterized as mild drought stress (MiDS), and ten days before sampling, characterized as moderate drought stress (MoDS). The response to drought stress (DS) of photosystem II (PSII) photochemistry, in both leaf types, was evaluated by estimating the allocation of absorbed light to photochemistry (ΦPSII), to heat dissipation by regulated non-photochemical energy loss (ΦNPQ) and to non-regulated energy dissipated in PSII (ΦNO). Young leaves were better protected at MoDS than ML leaves, by having higher concentration of flavonoids that promote acclimation of YL PSII photochemistry to MoDS, showing lower lipid peroxidation and excitation pressure (1 - qp). Young leaves at MoDS possessed lower 1 - qp values and lower excess excitation energy (EXC), not only compared to MoDS ML, but even to MiDS YL. They also possessed a higher capacity to maintain low ΦNO, suggesting a lower singlet oxygen (1O2) generation. Our results highlight that leaves of different developmental stage may display different responses to DS, due to differential accumulation of metabolites, and imply that PSII photochemistry in Arabidopsis thaliana may not show a dose dependent DS response.
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De Caroli M, Manno E, Piro G, Lenucci MS. Ride to cell wall: Arabidopsis XTH11, XTH29 and XTH33 exhibit different secretion pathways and responses to heat and drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:448-466. [PMID: 33932060 PMCID: PMC8453972 DOI: 10.1111/tpj.15301] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 05/09/2023]
Abstract
The xyloglucan endotransglucosylase/hydrolases (XTHs) are enzymes involved in cell wall assembly and growth regulation, cleaving and re-joining hemicellulose chains in the xyloglucan-cellulose network. Here, in a homologous system, we compare the secretion patterns of XTH11, XTH33 and XTH29, three members of the Arabidopsis thaliana XTH family, selected for the presence (XTH11 and XTH33) or absence (XTH29) of a signal peptide, and the presence of a transmembrane domain (XTH33). We show that XTH11 and XTH33 reached, respectively, the cell wall and plasma membrane through a conventional protein secretion (CPS) pathway, whereas XTH29 moves towards the apoplast following an unconventional protein secretion (UPS) mediated by exocyst-positive organelles (EXPOs). All XTHs share a common C-terminal functional domain (XET-C) that, for XTH29 and a restricted number of other XTHs (27, 28 and 30), continues with an extraterminal region (ETR) of 45 amino acids. We suggest that this region is necessary for the correct cell wall targeting of XTH29, as the ETR-truncated protein never reaches its final destination and is not recruited by EXPOs. Furthermore, quantitative real-time polymerase chain reaction analyses performed on 4-week-old Arabidopsis seedlings exposed to drought and heat stress suggest a different involvement of the three XTHs in cell wall remodeling under abiotic stress, evidencing stress-, organ- and time-dependent variations in the expression levels. Significantly, XTH29, codifying the only XTH that follows a UPS pathway, is highly upregulated with respect to XTH11 and XTH33, which code for CPS-secreted proteins.
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Affiliation(s)
- Monica De Caroli
- Dipartimento di Scienze e Tecnologie Biologiche e AmbientaliUniversità del SalentoLecce73100Italy
| | - Elisa Manno
- Dipartimento di Scienze e Tecnologie Biologiche e AmbientaliUniversità del SalentoLecce73100Italy
| | - Gabriella Piro
- Dipartimento di Scienze e Tecnologie Biologiche e AmbientaliUniversità del SalentoLecce73100Italy
| | - Marcello S. Lenucci
- Dipartimento di Scienze e Tecnologie Biologiche e AmbientaliUniversità del SalentoLecce73100Italy
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Chen Y, Dubois M, Vermeersch M, Inzé D, Vanhaeren H. Distinct cellular strategies determine sensitivity to mild drought of Arabidopsis natural accessions. PLANT PHYSIOLOGY 2021; 186:1171-1185. [PMID: 33693949 PMCID: PMC8195540 DOI: 10.1093/plphys/kiab115] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/14/2021] [Indexed: 05/18/2023]
Abstract
The worldwide distribution of Arabidopsis (Arabidopsis thaliana) accessions imposes different types of evolutionary pressures, which contributes to various responses of these accessions to environmental stresses. Responses to drought stress have mostly been studied in the Columbia accession, which is predominantly used in plant research. However, the reactions to drought stress are complex and our understanding of the responses that contribute to maintaining plant growth during mild drought (MD) is very limited. Here, we studied the mechanisms with which natural accessions react to MD at a physiological and molecular level during early leaf development. We documented variations in MD responses among natural accessions and used transcriptome sequencing of a drought-sensitive accession, ICE163, and a drought-insensitive accession, Yeg-1, to gain insights into the mechanisms underlying this discrepancy. This revealed that ICE163 preferentially induces jasmonate- and anthocyanin-related pathways, which are beneficial in biotic stress defense, whereas Yeg-1 has a more pronounced activation of abscisic acid signaling, the classical abiotic stress response. Related physiological traits, including the content of proline, anthocyanins, and reactive oxygen species, stomatal closure, and cellular leaf parameters, were investigated and linked to the transcriptional responses. We can conclude that most of these processes constitute general drought response mechanisms that are regulated similarly in drought-insensitive and -sensitive accessions. However, the capacity to close stomata and maintain cell expansion under MD appeared to be major factors that allow to better sustain leaf growth under MD.
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Affiliation(s)
- Ying Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Address for communication:
| | - Hannes Vanhaeren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
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Combining Thermal and RGB Imaging Indices with Multivariate and Data-Driven Modeling to Estimate the Growth, Water Status, and Yield of Potato under Different Drip Irrigation Regimes. REMOTE SENSING 2021. [DOI: 10.3390/rs13091679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in proximal hyperspectral sensing tools, chemometric techniques, and data-driven modeling have enhanced precision irrigation management by facilitating the monitoring of several plant traits. This study investigated the performance of remote sensing indices derived from thermal and red-green-blue (RGB) images combined with stepwise multiple linear regression (SMLR) and an integrated adaptive neuro-fuzzy inference system with a genetic algorithm (ANFIS-GA) for monitoring the biomass fresh weight (BFW), biomass dry weight (BDW), biomass water content (BWC), and total tuber yield (TTY) of two potato varieties under 100%, 75%, and 50% of the estimated crop evapotranspiration (ETc). Results showed that the plant traits and indices varied significantly between the three irrigation regimes. Furthermore, all of the indices exhibited strong relationships with BFW, CWC, and TTY (R2 = 0.80–0.92) and moderate to weak relationships with BDW (R2 = 0.25–0.65) when considered for each variety across the irrigation regimes, for each season across the varieties and irrigation regimes, and across all data combined, but none of the indices successfully assessed any of the plant traits when considered for each irrigation regime across the two varieties. The SMLR and ANFIS-GA models gave the best predictions for the four plant traits in the calibration and testing stages, with the exception of the SMLR testing model for BDW. Thus, the use of thermal and RGB imaging indices with ANFIS-GA models could be a practical tool for managing the growth and production of potato crops under deficit irrigation regimes.
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Jangra S, Chaudhary V, Yadav RC, Yadav NR. High-Throughput Phenotyping: A Platform to Accelerate Crop Improvement. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:31-53. [PMID: 36939738 PMCID: PMC9590473 DOI: 10.1007/s43657-020-00007-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of high-throughput phenotyping technologies has progressed considerably in the last 10 years. These technologies provide precise measurements of desired traits among thousands of field-grown plants under diversified environments; this is a critical step towards selection of better performing lines as to yield, disease resistance, and stress tolerance to accelerate crop improvement programs. High-throughput phenotyping techniques and platforms help unraveling the genetic basis of complex traits associated with plant growth and development and targeted traits. This review focuses on the advancements in technologies involved in high-throughput, field-based, aerial, and unmanned platforms. Development of user-friendly data management tools and softwares to better understand phenotyping will increase the use of field-based high-throughput techniques, which have potential to revolutionize breeding strategies and meet the future needs of stakeholders.
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Affiliation(s)
- Sumit Jangra
- Department of Molecular Biology, Biotechnology, and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Vrantika Chaudhary
- Department of Molecular Biology, Biotechnology, and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Ram C. Yadav
- Department of Molecular Biology, Biotechnology, and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Neelam R. Yadav
- Department of Molecular Biology, Biotechnology, and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
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Metabolomic Variation Aligns with Two Geographically Distinct Subpopulations of Brachypodium Distachyon before and after Drought Stress. Cells 2021; 10:cells10030683. [PMID: 33808796 PMCID: PMC8003576 DOI: 10.3390/cells10030683] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
Brachypodium distachyon (Brachypodium) is a non-domesticated model grass that has been used to assess population level genomic variation. We have previously established a collection of 55 Brachypodium accessions that were sampled to reflect five different climatic regions of Turkey; designated 1a, 1c, 2, 3 and 4. Genomic and methylomic variation differentiated the collection into two subpopulations designated as coastal and central (respectively from regions 1a, 1c and the other from 2, 3 and 4) which were linked to environmental variables such as relative precipitation. Here, we assessed how far genomic variation would be reflected in the metabolomes and if this could be linked to an adaptive trait. Metabolites were extracted from eight-week-old seedlings from each accession and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Principal Component Analysis (PCA) of the derived metabolomes differentiated between samples from coastal and central subpopulations. The major sources of variation between seedling from the coastal and central subpopulations were identified. The central subpopulation was typified by significant increases in alanine, aspartate and glutamate metabolism and the tricarboxylic acid (TCA) cycle. Coastal subpopulation exhibited elevated levels of the auxin, indolacetic acid and rhamnose. The metabolomes of the seedling were also determined following the imposition of drought stress for seven days. The central subpopulation exhibited a metabolomic shift in response to drought, but no significant changes were seen in the coastal one. The drought responses in the central subpopulation were typified by changes in amino acids, increasing the glutamine that could be functioning as a stress signal. There were also changes in sugars that were likely to be an osmotic counter to drought, and changes in bioenergetic metabolism. These data indicate that genomic variation in our Turkish Brachypodium collection is largely reflected as distinctive metabolomes (“metabolotypes”) through which drought tolerance might be mediated.
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Prasetyaningrum P, Mariotti L, Valeri MC, Novi G, Dhondt S, Inzé D, Perata P, van Veen H. Nocturnal gibberellin biosynthesis is carbon dependent and adjusts leaf expansion rates to variable conditions. PLANT PHYSIOLOGY 2021; 185:228-239. [PMID: 33631808 PMCID: PMC8133661 DOI: 10.1093/plphys/kiaa019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/27/2020] [Indexed: 05/02/2023]
Abstract
Optimal plant growth performance requires that the presence and action of growth signals, such as gibberellins (GAs), are coordinated with the availability of photo-assimilates. Here, we studied the links between GA biosynthesis and carbon availability, and the subsequent effects on growth. We established that carbon availability, light and dark cues, and the circadian clock ensure the timing and magnitude of GA biosynthesis and that disruption of these factors results in reduced GA levels and expression of downstream genes. Carbon-dependent nighttime induction of gibberellin 3-beta-dioxygenase 1 (GA3ox1) was severely hampered when preceded by reduced daytime light availability, leading specifically to reduced bioactive GA4 levels, and coinciding with a decline in leaf expansion rate during the night. We attributed this decline in leaf expansion mostly to reduced photo-assimilates. However, plants in which GA limitation was alleviated had significantly improved leaf expansion, demonstrating the relevance of GAs in growth control under varying carbon availability. Carbon-dependent expression of upstream GA biosynthesis genes (Kaurene synthase and gibberellin 20 oxidase 1, GA20ox1) was not translated into metabolite changes within this short timeframe. We propose a model in which the extent of nighttime biosynthesis of bioactive GA4 by GA3ox1 is determined by nighttime consumption of starch reserves, thus providing day-to-day adjustments of GA responses.
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Affiliation(s)
| | - Lorenzo Mariotti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa 56124, Italy
| | | | - Giacomo Novi
- PLANTLAB, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy
| | - Stijn Dhondt
- Center for Plant Systems Biology, Ghent University, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Center for Plant Systems Biology, Ghent University, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pierdomenico Perata
- PLANTLAB, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy
| | - Hans van Veen
- PLANTLAB, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy
- Department of Plantecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, Netherlands
- Author for communication:
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Spyroglou I, Skalák J, Balakhonova V, Benedikty Z, Rigas AG, Hejátko J. Mixed Models as a Tool for Comparing Groups of Time Series in Plant Sciences. PLANTS 2021; 10:plants10020362. [PMID: 33668650 PMCID: PMC7918370 DOI: 10.3390/plants10020362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/22/2021] [Accepted: 02/10/2021] [Indexed: 11/16/2022]
Abstract
Plants adapt to continual changes in environmental conditions throughout their life spans. High-throughput phenotyping methods have been developed to noninvasively monitor the physiological responses to abiotic/biotic stresses on a scale spanning a long time, covering most of the vegetative and reproductive stages. However, some of the physiological events comprise almost immediate and very fast responses towards the changing environment which might be overlooked in long-term observations. Additionally, there are certain technical difficulties and restrictions in analyzing phenotyping data, especially when dealing with repeated measurements. In this study, a method for comparing means at different time points using generalized linear mixed models combined with classical time series models is presented. As an example, we use multiple chlorophyll time series measurements from different genotypes. The use of additional time series models as random effects is essential as the residuals of the initial mixed model may contain autocorrelations that bias the result. The nature of mixed models offers a viable solution as these can incorporate time series models for residuals as random effects. The results from analyzing chlorophyll content time series show that the autocorrelation is successfully eliminated from the residuals and incorporated into the final model. This allows the use of statistical inference.
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Affiliation(s)
- Ioannis Spyroglou
- Plant Sciences Core Facility, CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- Correspondence:
| | - Jan Skalák
- Functional Genomics & Proteomics of Plants, CEITEC—Central European Institute of Technology and National Centre for Biotechnology Research, Faculty of Science, Kamenice 5, 62500 Brno, Czech Republic; (J.S.); (V.B.); (J.H.)
| | - Veronika Balakhonova
- Functional Genomics & Proteomics of Plants, CEITEC—Central European Institute of Technology and National Centre for Biotechnology Research, Faculty of Science, Kamenice 5, 62500 Brno, Czech Republic; (J.S.); (V.B.); (J.H.)
| | - Zuzana Benedikty
- Photon Systems Instruments, (PSI, spol. sr.o.), 66424 Drásov, Czech Republic;
| | - Alexandros G. Rigas
- Department of Electrical and Computer Engineering, Democritus University of Thrace, 67100 Xanthi, Greece;
| | - Jan Hejátko
- Functional Genomics & Proteomics of Plants, CEITEC—Central European Institute of Technology and National Centre for Biotechnology Research, Faculty of Science, Kamenice 5, 62500 Brno, Czech Republic; (J.S.); (V.B.); (J.H.)
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Berni R, Charton S, Planchon S, Legay S, Romi M, Cantini C, Cai G, Hausman JF, Renaut J, Guerriero G. Molecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics. HORTICULTURE RESEARCH 2021; 8:12. [PMID: 33384418 PMCID: PMC7775447 DOI: 10.1038/s41438-020-00445-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 06/12/2023]
Abstract
Sweet cherry (Prunus avium L.) is a stone fruit widely consumed and appreciated for its organoleptic properties, as well as its nutraceutical potential. We here investigated the characteristics of six non-commercial Tuscan varieties of sweet cherry maintained at the Regional Germplasm Bank of the CNR-IBE in Follonica (Italy) and sampled ca. 60 days post-anthesis over three consecutive years (2016-2017-2018). We adopted an approach merging genotyping and targeted gene expression profiling with metabolomics. To complement the data, a study of the soluble proteomes was also performed on two varieties showing the highest content of flavonoids. Metabolomics identified the presence of flavanols and proanthocyanidins in highest abundance in the varieties Morellona and Crognola, while gene expression revealed that some differences were present in genes involved in the phenylpropanoid pathway during the 3 years and among the varieties. Finally, proteomics on Morellona and Crognola showed variations in proteins involved in stress response, primary metabolism and cell wall expansion. To the best of our knowledge, this is the first multi-pronged study focused on Tuscan sweet cherry varieties providing insights into the differential abundance of genes, proteins and metabolites.
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Affiliation(s)
- Roberto Berni
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, I-53100, Siena, Italy
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Sophie Charton
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41, Rue du Brill, L-4422, Belvaux, Luxembourg
| | - Sébastien Planchon
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41, Rue du Brill, L-4422, Belvaux, Luxembourg
| | - Sylvain Legay
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940, Hautcharage, Luxembourg
| | - Marco Romi
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, I-53100, Siena, Italy
| | - Claudio Cantini
- Istituto per la BioEconomia (IBE CNR), Dipartimento di Scienze BioAgroAlimentari, via Aurelia 49, 58022, Follonica, Italy
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, I-53100, Siena, Italy
| | - Jean-Francois Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940, Hautcharage, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41, Rue du Brill, L-4422, Belvaux, Luxembourg.
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940, Hautcharage, Luxembourg.
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Balti I, Benny J, Perrone A, Caruso T, Abdallah D, Salhi-Hannachi A, Martinelli F. Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 48:54-71. [PMID: 32727652 DOI: 10.1071/fp20028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.
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Affiliation(s)
- Imen Balti
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy; and Department of Biology, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Jubina Benny
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy
| | - Anna Perrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, 90128, Italy
| | - Tiziano Caruso
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy
| | - Donia Abdallah
- Department of Biology, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Amel Salhi-Hannachi
- Department of Biology, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, 50019, Italy; and Corresponding author.
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Harnessing High-throughput Phenotyping and Genotyping for Enhanced Drought Tolerance in Crop Plants. J Biotechnol 2020; 324:248-260. [PMID: 33186658 DOI: 10.1016/j.jbiotec.2020.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/28/2020] [Accepted: 11/08/2020] [Indexed: 12/17/2022]
Abstract
Development of drought-tolerant cultivars is one of the challenging tasks for the plant breeders due to its complex inheritance and polygenic regulation. Evaluating genetic material for drought tolerance is a complex process due to its spatiotemporal interactions with environmental factors. The conventional breeding approaches are costly, lengthy, and inefficient to achieve the expected gain in drought tolerance. In this regard, genomics-assisted breeding (GAB) offers promise to develop cultivars with improved drought tolerance in a more efficient, quicker, and cost-effective manner. The success of GAB depends upon the precision in marker-trait association and estimation of genomic estimated breeding values (GEBVs), which mostly depends on coverage and precision of genotyping and phenotyping. A wide gap between the discovery and practical use of quantitative trait loci (QTL) for crop improvement has been observed for many important agronomical traits. Such a limitation could be due to the low accuracy in QTL detection, mainly resulting from low marker density and manually collected phenotypes of complex agronomic traits. Increasing marker density using the high-throughput genotyping (HTG), and accurate and precise phenotyping using high-throughput digital phenotyping (HTP) platforms can improve the precision and power of QTL detection. Therefore, both HTG and HTP can enhance the practical utility of GAB along with a faster characterization of germplasm and breeding material. In the present review, we discussed how the recent innovations in HTG and HTP would assist in the breeding of improved drought-tolerant varieties. We have also discussed strategies, tools, and analytical advances made on the HTG and HTP along with their pros and cons.
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Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu LD, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite JM, Rigal A, Ramans Harborough S, Persiau G, Vanneste S, Kirschner GK, Vandermarliere E, Martens L, Stahl Y, Audenaert D, Friml J, Felix G, Simon R, Bennett MJ, Bishopp A, De Jaeger G, Ljung K, Kepinski S, Robert S, Nemhauser J, Hwang I, Gevaert K, Beeckman T, De Smet I. The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis. Mol Cell Proteomics 2020; 19:1248-1262. [PMID: 32404488 PMCID: PMC8011570 DOI: 10.1074/mcp.ra119.001826] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/02/2020] [Indexed: 01/20/2023] Open
Abstract
Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-TERMINALLY ENCODED PEPTIDE 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical, and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.
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Affiliation(s)
- Stephanie Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Shanshuo Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lisa Joos
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ianto Roberts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Natalia Nikonorova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Antoine Larrieu
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Wei Xuan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Benjamin Goodall
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Brigitte van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jessic Marie Waite
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Adeline Rigal
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sigurd Ramans Harborough
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Gwendolyn K Kirschner
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Elien Vandermarliere
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Dominique Audenaert
- Screening Core, Gent, Belgium; Expertise Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Jirí Friml
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University (MU), Brno, Czech Republic; Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Georg Felix
- Zentrum für Molekularbiologie der Pflanzen, Plant Biochemistry, University Tübingen, Tübingen, Germany
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Malcolm J Bennett
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom; Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Stephanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom; Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom.
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50
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Mochida K, Nishii R, Hirayama T. Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits. PLANT & CELL PHYSIOLOGY 2020; 61:1408-1418. [PMID: 32392328 PMCID: PMC7434589 DOI: 10.1093/pcp/pcaa064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/26/2020] [Indexed: 05/16/2023]
Abstract
To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants' later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant-environment interactions by elucidating plants' temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant-environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Corresponding author: E-mail, ; Fax, +81-45-503-9609
| | - Ryuei Nishii
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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