Survival biomass production and crop yield are heavily constrained by a wide range of environmental stresses. Several phytohormones among which abscisic acid (ABA), ethylene and salicylic acid (SA) ...are known to mediate plant responses to these stresses. By contrast, the role of the plant hormone auxin in stress responses remains so far poorly studied. Auxin controls many aspects of plant growth and development, and Auxin Response Factors play a key role in the transcriptional activation or repression of auxin-responsive genes through direct binding to their promoters. As a mean to gain more insight on auxin involvement in a set of biotic and abiotic stress responses in tomato, the present study uncovers the expression pattern of SlARF genes in tomato plants subjected to biotic and abiotic stresses. In silico mining of the RNAseq data available through the public TomExpress web platform, identified several SlARFs as responsive to various pathogen infections induced by bacteria and viruses. Accordingly, sequence analysis revealed that 5' regulatory regions of these SlARFs are enriched in biotic and abiotic stress-responsive cis-elements. Moreover, quantitative qPCR expression analysis revealed that many SlARFs were differentially expressed in tomato leaves and roots under salt, drought and flooding stress conditions. Further pointing to the putative role of SlARFs in stress responses, quantitative qPCR expression studies identified some miRNA precursors as potentially involved in the regulation of their SlARF target genes in roots exposed to salt and drought stresses. These data suggest an active regulation of SlARFs at the post-transcriptional level under stress conditions. Based on the substantial change in the transcript accumulation of several SlARF genes, the data presented in this work strongly support the involvement of auxin in stress responses thus enabling to identify a set of candidate SlARFs as potential mediators of biotic and abiotic stress responses.
Summary
The TomExpress platform was developed to provide the tomato research community with a browser and integrated web tools for public RNA‐Seq data visualization and data mining. To avoid major ...biases that can result from the use of different mapping and statistical processing methods, RNA‐Seq raw sequence data available in public databases were mapped de novo on a unique tomato reference genome sequence and post‐processed using the same pipeline with accurate parameters. Following the calculation of the number of counts per gene in each RNA‐Seq sample, a communal global normalization method was applied to all expression values. This unifies the whole set of expression data and makes them comparable. A database was designed where each expression value is associated with corresponding experimental annotations. Sample details were manually curated to be easily understandable by biologists. To make the data easily searchable, a user‐friendly web interface was developed that provides versatile data mining web tools via on‐the‐fly generation of output graphics, such as expression bar plots, comprehensive in planta representations and heatmaps of hierarchically clustered expression data. In addition, it allows for the identification of co‐expressed genes and the visualization of correlation networks of co‐regulated gene groups. TomExpress provides one of the most complete free resources of publicly available tomato RNA‐Seq data, and allows for the immediate interrogation of transcriptional programs that regulate vegetative and reproductive development in tomato under diverse conditions. The design of the pipeline developed in this project enables easy updating of the database with newly published RNA‐Seq data, thereby allowing for continuous enrichment of the resource.
Significance Statement
After applying a bioinformatics and statistics pipeline, a unified TomExpress platform was developed to provide the tomato research community with a browser and integrated web tools for public RNA‐Seq data visualization and data mining via on‐the‐fly generation of output graphics such as expression bar plots, comprehensive in planta representations and heatmaps of hierarchically clustered expression data. TomExpress provides one of the most complete free resources of publicly available tomato RNA‐Seq data.
This study aims to assess the level of metal contamination and the ecological risk index at the abandoned Zaida Pb/Zn mining site in eastern Morocco and identify native plant species found on the ...site that can be used in site rehabilitation through phytoremediation strategies. Samples from seven native and abundant plant species at the site, along with their rhizospheric soils, were collected and analyzed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to determine the concentrations of various metal(loid)s, including As, Cu, Ni, Cd, Sb, Zn, and Pb. Indicators of soil pollution and ecological risks were also assessed, including the enrichment factor (EF), pollution index (PI), and ecological risk index (ERI). The Biological Accumulation Coefficient (BAC), Translocation Factor (TF), and Biological Concentration Factor (BCF) of plant samples were calculated. The results reveal polymetallic soil contamination, with notably higher concentrations of Pb, Cu and Zn, reaching respectively 5568 mg kg-1 DW, 152 mg kg-.sup.1 DW, and 148 mg kg-1 DW, indicating a significant potential ecological risk. The enrichment factor (EF) was also assessed for each metal(loid)s, and the results indicated that the metal contamination was of anthropogenic origin and linked to intensive mining activities in Zaida. These findings are supported by the pollution index (PI) ranging from 1.6 to 10.01, which reveals an extremely high metal(loid)s pollution level. None of the plant species exhibited a hyperaccumulation of metal(loid)s. However, Artemisia herba alba demonstrated a strong capacity to accumulate Pb in its aboveground parts, with a concentration of 468 mg kg-.sup.1 DW. Stipa tenacissima, Retama spherocarpa, and Astragalus armatus, showed a significant Pb accumulation in their roots reaching 280, 260, and 256 mg kg-.sup.1 DW.respectively. Based on BAC, TF, and BCF, Stipa tenacissima exhibited potential for Ni and Cd phytostabilization, as well as the ability for Zn phytoextraction. Additionally, Artemisia herba alba displayed the capability to phytoextract Cd and had a high propensity to translocate all the studied metal(loid)s. Astragalus armatus has the potential to be used in the phytostabilization of Zn and Ni, as well as for the phytoextraction of As and Sb. These native species from the Zaida site, although not hyperaccumulators, have the potential to contribute significantly to the phytoextraction or phytostabilization of potentially toxic elements (PTEs). Moreover, they can serve as vegetative cover to mitigate the erosion and dispersion of metal(loid)s.
Zinc is an essential microelement involved in many aspects of plant growth and development. Abnormal zinc amounts, mostly due to human activities, can be toxic to flora, fauna, and humans. In plants, ...excess zinc causes morphological, biochemical, and physiological disorders. Some plants have the ability to resist and even accumulate zinc in their tissues. To date, 28 plant species have been described as zinc hyperaccumulators. These plants display several morphological, physiological, and biochemical adaptations resulting from the activation of molecular Zn hyperaccumulation mechanisms. These adaptations can be varied between species and within populations. In this review, we describe the physiological and biochemical as well as molecular mechanisms involved in zinc hyperaccumulation in plants.
Auxin controls multiple aspects of plant growth and development. However, its role in stress responses remains poorly understood. Auxin acts on the transcriptional regulation of target genes, mainly ...through Auxin Response Factors (
). This study focuses on the involvement of
in tomato tolerance to salinity and osmotic stress. Using a reverse genetic approach, we found that the antisense down-regulation of
promotes root development and density, increases soluble sugars content and maintains chlorophyll content at high levels under stress conditions. Furthermore,
-as displayed higher tolerance to salt and osmotic stress through reduced stomatal conductance coupled with increased leaf relative water content and Abscisic acid (ABA) content under normal and stressful conditions. This increase in ABA content was correlated with the activation of ABA biosynthesis genes and the repression of ABA catabolism genes.
and
genes were up-regulated in
-as plants which can result in a better tolerance to salt and osmotic stress. A CRISPR/Cas9 induced
mutant showed similar growth and stomatal responses as
-as plants, which suggest that
can tolerate salt and osmotic stresses. Our data support the involvement of
as a key factor in tomato tolerance to salt and osmotic stresses and confirm the use of CRISPR technology as an efficient tool for functional reverse genetics studies.
Salinity is one of the most significant environmental factors limiting legumes development and productivity. Salt stress disturbs all developmental stages of legumes and affects their hormonal ...regulation, photosynthesis and biological nitrogen fixation, causing nutritional imbalance, plant growth inhibition and yield losses. At the molecular level, salt stress exposure involves large number of factors that are implicated in stress perception, transduction, and regulation of salt responsive genes’ expression through the intervention of transcription factors. Along with the complex gene network, epigenetic regulation mediated by non-coding RNAs, and DNA methylation events are also involved in legumes’ response to salinity. Different alleviation strategies can increase salt tolerance in legume plants. The most promising ones are Plant Growth Promoting Rhizobia, Arbuscular Mycorrhizal Fungi, seed and plant’s priming. Genetic manipulation offers an effective approach for improving salt tolerance. In this review, we present a detailed overview of the adverse effect of salt stress on legumes and their molecular responses. We also provide an overview of various ameliorative strategies that have been implemented to mitigate/overcome the harmful effects of salt stress on legumes.
Microalgae are widely used in a variety of fields, including agriculture, the environment, medicine, cosmetics, food, and feed. They are used as feedstock for sustainably produced chemicals and ...biofuel. However, the production of microalgal-derived products is economically unprofitable. Integrated biorefinery based on microalgae-derived products is one of the long-term solutions that could be economically and environmentally viable with zero waste. This review emphasizes the integration of wastewater treatment with CO2 biosequestration from industrial flue gas and proposes an integrated biomass valorization strategy based on microalgae biorefineries. A model of integrated biorefinery with a techno-economic analysis and the possible microalgae-derived products that can be valorized after domestic wastewater and flue gas use as low-cost inputs for microalgae culture are also proposed.
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Auxin response factors (
) act as key elements of the auxin-signaling pathway and play important roles in the process of a plant's growth, development, and response to environmental conditions. We ...studied the implication of the
gene in the tomato response to salt (150 mM of NaCl) and drought (15% PEG 20000) stresses. The functional characterization of
knockdown tomato mutants revealed that the downregulation of this gene enhanced primary root length and root branching and reduced plant wilting. At the physiological level, the
mutant line displayed higher chlorophyll, soluble sugars, proline, and relative water contents as well as lower stomatal conductance and a decreased malondialdehyde content. Moreover,
knockdown tomato mutants demonstrated higher activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) under salt and drought stresses than the wild type. Indeed, the stress tolerance of the
mutant was also reflected by the upregulation of stress-related genes involved in ROS scavenging and plant defense, including
,
,
, and
, which can ultimately result in a better resistance to salt and drought stresses. Furthermore, the transcriptional levels of the
(
) gene were upregulated in the
mutant after stress, in correlation with the higher levels of proline. Taken together, our findings reveal that
is implicated in salt and drought tolerance in tomato and provides some considerable elements for improving the abiotic stress tolerance and increasing the crop yields of tomato.
Lentil (
Medikus) is a protein-rich cool-season food legume with an excellent source of protein, prebiotic carbohydrates, minerals, and vitamins. With climate change, heat, and drought stresses have ...become more frequent and intense in lentil growing areas with a strong influence on phenology, grain yield, and nutritional quality. This study aimed to assess the impact of heat and drought stresses on phenology, grain yield, and nutritional quality of lentil. For this purpose, 100 lentil genotypes from the global collection were evaluated under normal, heat, and combined heat-drought conditions. Analysis of variance revealed significant differences (
< 0.001) among lentil genotypes for phenological traits, yield components, and grain quality traits. Under no stress conditions, mineral concentrations among lentil genotypes varied from 48 to 109 mg kg
for iron (Fe) and from 31 to 65 mg kg
for zinc (Zn), while crude protein content ranged from 22.5 to 32.0%. Iron, zinc, and crude protein content were significantly reduced under stress conditions, and the effect of combined heat-drought stress was more severe than heat stress alone. A significant positive correlation was observed between iron and zinc concentrations under both no stress and stress conditions. Based on grain yield, crude protein, and iron and zinc concentrations, lentil genotypes were grouped into three clusters following the hierarchical cluster analysis. Promising lentil genotypes with high micronutrient contents, crude protein, and grain yield with the least effect of heat and drought stress were identified as the potential donors for biofortification in the lentil breeding program.
Increasing global warming has made heat stress a serious threat to crop productivity and global food security in recent years. One of the most promising solutions to address this issue is developing ...heat-stress-tolerant plants. Hence, a thorough understanding of heat stress response mechanisms, particularly molecular ones, is crucial.
Although numerous studies have used microarray expression profiling technology to explore this area, these experiments often face limitations, leading to inconsistent results. To overcome these limitations, a random effects meta-analysis was employed using advanced statistical methods. A meta-analysis of 16 microarray datasets related to heat stress response in
was conducted.
The analysis revealed 1,972 significant differentially expressed genes between control and heat-stressed plants (826 over-expressed and 1,146 down-expressed), including 128 differentially expressed transcription factors from different families. The most significantly enriched biological processes, molecular functions, and KEGG pathways for over-expressed genes included heat response, mRNA splicing via spliceosome pathways, unfolded protein binding, and heat shock protein binding. Conversely, for down-expressed genes, the most significantly enriched categories included cell wall organization or biogenesis, protein phosphorylation, transmembrane transporter activity, ion transmembrane transporter, biosynthesis of secondary metabolites, and metabolic pathways.
Through our comprehensive meta-analysis of heat stress transcriptomics, we have identified pivotal genes integral to the heat stress response, offering profound insights into the molecular mechanisms by which plants counteract such stressors. Our findings elucidate that heat stress influences gene expression both at the transcriptional phase and post-transcriptionally, thereby substantially augmenting our comprehension of plant adaptive strategies to heat stress.
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