Plant Hormone Signaling Crosstalks between Biotic and Abiotic Stress Responses

Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq

Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.

ERF Transcription Factor OsBIERF3 Positively Contributes to Immunity against Fungal and Bacterial Diseases but Negatively Regulates Cold Tolerance in Rice

We previously showed that overexpression of the rice ERF transcription factor gene OsBIERF3 in tobacco increased resistance against different pathogens. Here, we report the function of OsBIERF3 in rice immunity and abiotic stress tolerance. Expression of OsBIERF3 was induced by Xanthomonas oryzae pv. oryzae, hormones (e.g., salicylic acid, methyl jasmonate, 1-aminocyclopropane-1-carboxylic acid, and abscisic acid), and abiotic stress (e.g., drought, salt and cold stress). OsBIERF3 has transcriptional activation activity that depends on its C-terminal region. The OsBIERF3-overexpressing (OsBIERF3-OE) plants exhibited increased resistance while OsBIERF3-suppressed (OsBIERF3-Ri) plants displayed decreased resistance to Magnaporthe oryzae and X. oryzae pv. oryzae. A set of genes including those for PRs and MAPK kinases were up-regulated in OsBIERF3-OE plants. Cell wall biosynthetic enzyme genes were up-regulated in OsBIERF3-OE plants but down-regulated in OsBIERF3-Ri plants; accordingly, cell walls became thicker in OsBIERF3-OE plants but thinner in OsBIERF3-Ri plants than WT plants. The OsBIERF3-OE plants attenuated while OsBIERF3-Ri plants enhanced cold tolerance, accompanied by altered expression of cold-responsive genes and proline accumulation. Exogenous abscisic acid and 1-aminocyclopropane-1-carboxylic acid, a precursor of ethylene biosynthesis, restored the attenuated cold tolerance in OsBIERF3-OE plants while exogenous AgNO₃, an inhibitor of ethylene action, significantly suppressed the enhanced cold tolerance in OsBIERF3-Ri plants. These data demonstrate that OsBIERF3 positively contributes to immunity against M. oryzae and X. oryzae pv. oryzae but negatively regulates cold stress tolerance in rice.

Plant salt response: Perception, signaling, and tolerance

Salt stress is one of the significant environmental stressors that severely affects plant growth and development. Plant responses to salt stress involve a series of biological mechanisms, including osmoregulation, redox and ionic homeostasis regulation, as well as hormone or light signaling-mediated growth adjustment, which are regulated by different functional components. Unraveling these adaptive mechanisms and identifying the critical genes involved in salt response and adaption are crucial for developing salt-tolerant cultivars. This review summarizes the current research progress in the regulatory networks for plant salt tolerance, highlighting the mechanisms of salt stress perception, signaling, and tolerance response. Finally, we also discuss the possible contribution of microbiota and nanobiotechnology to plant salt tolerance.

Peroxisomal Proteome Mining of Sweet Pepper (Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis

Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.

To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses

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.

Stress-regulated elements in Lotus spp., as a possible starting point to understand signalling networks and stress adaptation in legumes

Although legumes are of primary economic importance for human and livestock consumption, the information regarding signalling networks during plant stress response in this group is very scarce. Lotus japonicus is a major experimental model within the Leguminosae family, whereas L. corniculatus and L. tenuis are frequent components of natural and agricultural ecosystems worldwide. These species display differences in their perception and response to diverse stresses, even at the genotype level, whereby they have been used in many studies aimed at achieving a better understanding of the plant stress-response mechanisms. However, we are far from the identification of key components of their stress-response signalling network, a previous step for implementing transgenic and editing tools to develop legume stress-resilient genotypes, with higher crop yield and quality. In this review we scope a body of literature, highlighting what is currently known on the stress-regulated signalling elements so far reported in Lotus spp. Our work includes a comprehensive review of transcription factors chaperones, redox signals and proteins of unknown function. In addition, we revised strigolactones and genes regulating phytochelatins and hormone metabolism, due to their involvement as intermediates in several physiological signalling networks. This work was intended for a broad readership in the fields of physiology, metabolism, plant nutrition, genetics and signal transduction. Our results suggest that Lotus species provide a valuable information platform for the study of specific protein-protein (PPI) interactions, as a starting point to unravel signalling networks underlying plant acclimatation to bacterial and abiotic stressors in legumes. Furthermore, some Lotus species may be a source of genes whose regulation improves stress tolerance and growth when introduced ectopically in other plant species.

English plantain deploys stress tolerance mechanisms at various organization levels across an altitudinal gradient in the Pyrenees

High-mountain plants must withstand high solar irradiation and low temperatures during winter. Furthermore, climate change is increasing drought events, which pose an additional threat to plants. Here, we studied the stress tolerance mechanisms at various levels of biological organization in English plantain (Plantago lanceolata L.), focusing on photoprotective and antioxidant responses. The response of populations from three different altitudes in the Eastern Pyrenees (1030, 1380, and 1660 m. a.s.l.) was compared during both autumn and winter. Results showed that plants not only suffered from photoinhibition due to very low temperatures at the highest elevation during winter, but also from mild drought stress at the lowest altitude during autumn. Individuals growing at the highest elevation showed reductions in the maximum photochemical efficiency of PSII (F_v /F_m ratio), which might be caused by the lack of an increased induction of tolerance mechanisms at the highest elevation compared to the intermediate one. Although most leaves died at the highest elevation, plants could withstand stress at the organism level by generating new leaves once the stress ceased. Drought at the lowest elevation during autumn caused mild stress with small decreases in the F_v /F_m ratio, along with an increase in abscisic acid and jasmonic acid content. This study underlines the great capacity of English plantain to adapt to high elevation by activating not only photo- and antioxidant protection mechanisms and adjustments in stress-related phytohormones, but also by fully regenerating its aboveground biomass through renewed growth once the stress has ceased.

Perception and First Defense Responses Against Pseudomonas syringae pv. phaseolicola in Phaseolus vulgaris: Identification of Wall-Associated Kinase Receptors

Common bean (Phaseolus vulgaris) is attacked by several pathogens such as the biotrophic gamma-proteobacterium Pseudomonas syringae pv. phaseolicola. To study the P. syringae pv. phaseolicola-bean interaction during the first stages of infection, leaf discs of a susceptible bean cultivar Riñón were infected with pathogenic P. syringae pv. phaseolicola. Using this experimental system, we tested six new putative wall-associated kinase (WAK) receptors, previously identified in silico. These six P. vulgaris WAKs (PvWAKs) showed high protein sequence homology to the well-described Arabidopsis thaliana WAK1 (AtWAK1) receptor and, by phylogenetic analysis, clustered together with AtWAKs. The expression of PvWAK1 increased at very early stages after the P. syringae pv. phaseolicola infection. Time course experiments were performed to evaluate the accumulation of apoplastic H₂O₂, Ca²⁺ influx, total H₂O₂, antioxidant enzymatic activities, lipid peroxidation, and the concentrations of abscisic acid and salicylic acid (SA), as well as the expression of six defense-related genes: MEKK-1, MAPKK, WRKY33, RIN4, PR1, and NPR1. The results showed that overexpression of PR1 occurred 2 h after P. syringae pv. phaseolicola infection without a concomitant increase in SA levels. Although apoplastic H₂O₂ increased after infection, the oxidative burst was neither intense nor rapid, and an efficient antioxidant response did not occur, suggesting that the observed cellular damage was caused by the initial increase in total H₂O₂ early after infection. In conclusion, Riñón can perceive the presence of P. syringae pv. phaseolicola, but this recognition results in only a modest and slow activation of host defenses, leading to high susceptibility to P. syringae pv. phaseolicola.

Identification and function analysis of bHLH genes in response to cold stress in sweetpotato

Basic/helix-loop-helix (bHLH) transcription factors are involved in various metabolic and physiological processes in plants. Sweetpotato (Ipomoea batatas (L.) Lam.) is an important crop in China but is highly susceptible to cold stress. However, little information on the bHLH gene family is available, and the function of this family in response to cold stress has not been revealed in sweetpotato. Here, 110 IbbHLHs were identified and classified into 17 categories based on phylogenetic relationships, conserved motifs and gene structure analyses. Except for 5 IbbHLHs, 90 IbbHLHs were putative E-box-binding proteins including 70 IbbHLHs belonging to G-box, whereas 15 IbbHLHs were putative non-E box-binding proteins based on DNA-binding analysis. In total, 37 pairs of segmental duplicated genes and 5 pairs of tandem duplication genes were identified within the IbbHLH gene family. The transcript level of 20 IbbHLHs was regulated by cold stress based on RNA-seq data, and 8 genes were selected for further quantitative real-time PCR (qRT-PCR) analysis. IbHLH8 and IbHLH92 are involved in network interaction with several genes related to abiotic and biotic stresses under cold treatment. IbbHLH79, an ICE1-like gene, was isolated and overexpressed in sweetpotato. The IbbHLH79 protein can activate the CBF (C-repeat Binding Factor) pathway, and IbbHLH79-overexpressing transgenic plants display enhanced cold tolerance. Taken together, these results provide valuable information on the IbbHLH gene family; in addition, several IbbHLHs may regulate cold stress, and the results suggest IbbHLH79 will be useful for molecular breeding of enhanced cold tolerance in sweetpotato.

Arabidopsis MADS-box factor AGL16 is a negative regulator of plant response to salt stress by downregulating salt-responsive genes

Sessile plants constantly experience environmental stresses in nature. They must have evolved effective mechanisms to balance growth with stress response. Here we report the MADS-box transcription factor AGL16 acting as a negative regulator in stress response in Arabidopsis. Loss-of-AGL16 confers resistance to salt stress in seed germination, root elongation and soil-grown plants, while elevated AGL16 expression confers the opposite phenotypes compared with wild-type. However, the sensitivity to abscisic acid (ABA) in seed germination is inversely correlated with AGL16 expression levels. Transcriptomic comparison revealed that the improved salt resistance of agl16 mutants was largely attributed to enhanced expression of stress-responsive transcriptional factors and the genes involved in ABA signalling and ion homeostasis. We further demonstrated that AGL16 directly binds to the CArG motifs in the promoter of HKT1;1, HsfA6a and MYB102 and represses their expression. Genetic analyses with double mutants also support that HsfA6a and MYB102 are target genes of AGL16. Taken together, our results show that AGL16 acts as a negative regulator transcriptionally suppressing key components in the stress response and may play a role in balancing stress response with growth.

The NF-Y-PYR module integrates the abscisic acid signal pathway to regulate plant stress tolerance

Drought and salt stresses impose major constraints on soybean production worldwide. However, improving agronomically valuable soybean traits under drought conditions can be challenging due to trait complexity and multiple factors that influence yield. Here, we identified a nuclear factor Y C subunit (NF-YC) family transcription factor member, GmNF-YC14, which formed a heterotrimer with GmNF-YA16 and GmNF-YB2 to activate the GmPYR1-mediated abscisic acid (ABA) signalling pathway to regulate stress tolerance in soybean. Notably, we found that CRISPR/Cas9-generated GmNF-YC14 knockout mutants were more sensitive to drought than wild-type soybean plants. Furthermore, field trials showed that overexpression of GmNF-YC14 or GmPYR1 could increase yield per plant, grain plumpness, and stem base circumference, thus indicating improved adaptation of soybean plants to drought conditions. Taken together, our findings expand the known functional scope of the NF-Y transcription factor functions and raise important questions about the integration of ABA signalling pathways in plants. Moreover, GmNF-YC14 and GmPYR1 have potential for application in the improvement of drought tolerance in soybean plants.

Tomato Ve-resistance locus: resilience in the face of adversity?

The Ve-resistance locus in tomato acts as a resilience gene by affecting both the stress/defense cascade and growth, constituting a signaling intercept with a competitive regulatory mechanism. For decades, the tomato Ve-gene has been recognized as a classical resistance R-gene, inherited as a dominant Mendelian trait and encoding a receptor protein that binds with a fungal effector to provide defense against Verticillium dahliae and V. albo-atrum. However, recent molecular studies suggest that the function and role(s) of the Ve-locus and the two proteins that it encodes are more complex than previously understood. This review summarizes both the background and recent molecular evidence and provides a reinterpretation of the function and role(s) of the Ve1- and Ve2-genes and proteins that better accommodates existing data. It is proposed that these two plasma membrane proteins interact to form a signaling intercept that directly links defense and growth. The induction of Ve1 by infection or wounding promotes growth but also downregulates Ve2 signaling, resulting in a decreased biosynthesis of PR proteins. In this context, the Ve1 R-gene acts as a Resilience gene rather than a Resistance gene, promoting taller more robust tomato plants with reduced symptoms (biotic and abiotic) and Verticillium concentration.

Expression Analysis of AUX/IAA Family Genes in Apple Under Salt Stress

Members of the auxin/indoleacetic acid (Aux/IAA) gene family in plants are primary auxin-responsive genes that play important roles in many aspects of plant development and in responses to abiotic stress. Recently, 33 Aux/IAA have been identified in the apple genome. The biological responses of MdIAAs to salt stress are still unknown. In this study, Malus zumi, Malus baccata, and Malus × domestica 'Fuji' plantlets were subjected to salt stress by supplementing hydroponic media with NaCl at various concentrations. M. zumi showed the strongest salt resistance, followed by 'Fuji', and M. baccata was the most sensitive to salt stress. Tissue-specific expression profiles of MdIAAs were determined by quantitative real-time polymerase chain reaction. When apple plantlets were subjected to salt stress, most of salt-responsive MdIAAs were up-regulated by 1 h, 3 h, and 6 h in roots, shoot tips, and leaves, respectively. Highly expressed MdIAAs in roots, especially for M. zumi, consisted with the salt tolerance of apple rootstocks. Transgenic apple calli were tolerant to salt stress when over-expressed salt-responsive genes, MdIAA8, -9, and -25. These results provide clues about salt resistance in these three Malus species, which helps apple breeding of salt tolerance by genetic transformation.

Molecular Evolution of Calcium Signaling and Transport in Plant Adaptation to Abiotic Stress

Adaptation to unfavorable abiotic stresses is one of the key processes in the evolution of plants. Calcium (Ca2+) signaling is characterized by the spatiotemporal pattern of Ca2+ distribution and the activities of multi-domain proteins in integrating environmental stimuli and cellular responses, which are crucial early events in abiotic stress responses in plants. However, a comprehensive summary and explanation for evolutionary and functional synergies in Ca2+ signaling remains elusive in green plants. We review mechanisms of Ca2+ membrane transporters and intracellular Ca2+ sensors with evolutionary imprinting and structural clues. These may provide molecular and bioinformatics insights for the functional analysis of some non-model species in the evolutionarily important green plant lineages. We summarize the chronological order, spatial location, and characteristics of Ca2+ functional proteins. Furthermore, we highlight the integral functions of calcium-signaling components in various nodes of the Ca2+ signaling pathway through conserved or variant evolutionary processes. These ultimately bridge the Ca2+ cascade reactions into regulatory networks, particularly in the hormonal signaling pathways. In summary, this review provides new perspectives towards a better understanding of the evolution, interaction and integration of Ca2+ signaling components in green plants, which is likely to benefit future research in agriculture, evolutionary biology, ecology and the environment.

Gibberellin regulates UV-B-induced hypocotyl growth inhibition in Arabidopsis thaliana

Plant response to light is a complex and diverse phenomenon. Several studies have elucidated the mechanisms via which light and hormones regulate hypocotyl growth. However, the hormone-dependent ultraviolet-B (UV-B) response in plants remains obscure. Involvement of gibberellins (GAs) in UV-B-induced hypocotyl inhibition and its mechanisms in Arabidopsis thaliana were investigated in the present research. UV-B exposure remarkably decreased the endogenous GA₃ content through the UV RESISTANCE LOCUS 8 (UVR8) receptor pathway, and exogenous GA₃ partially restored the hypocotyl growth. UV-B irradiation affected the expression levels of GA metabolism-related genes (GA20ox1, GA2ox1 and GA3ox1) in the hy5-215 mutant, resulting in increased GA content.ELONGATED HYPOCOTYL 5 (HY5) promoted the accumulation of DELLA proteins under UV-B radiation; HY5 appeared to regulate the abundance of DELLAs at the transcriptional level under UV-B. As a result, the GA₃ content decreased, which eventually led to the shortening of the hypocotyl. To conclude, the present study provides new insight into the regulation of plant photomorphogenesis under UV-B.

Crosstalk among plant growth regulators and signaling molecules during biotic and abiotic stresses: molecular responses and signaling pathways

Plant stress responses are extremely sophisticated which implicate changes at the cellular, physiological and transcriptome levels by activating specific gene expression related to the challenges faced by plants.

Silica Nanoparticles as a Probable Anti-Oomycete Compound Against Downy Mildew, and Yield and Quality Enhancer in Grapevines: Field Evaluation, Molecular, Physiological, Ultrastructural, and Toxicity Investigations

Downy mildew is the most destructive disease of grapevines in the regions of relatively warm and humid climate causing up to 50% yield losses. Application of silicon- (Si-) based products have been extensively studied against various oomycete, fungal, bacterial, and viral plant diseases, but studies on Si application in their nanosize are limited. In this study, the field application of silica nanoparticles (SiNPs) on Thompson Seedless grapevines (H4 strain) infected with downy mildew was evaluated. In addition, molecular, physiological, ultrastructural, and toxicity investigations were also conducted. The obtained results revealed that spraying of grapevines with SiNPs at 150 ppm significantly overexpressed the transcription factor jasmonate and ethylene-responsive factor 3 recording 8.7-fold, and the defense-related genes β-1,3-glucanase (11-fold), peroxidase (10.7-fold) pathogenesis-related-protein 1 (10.6-fold), and chitinase (6.5-fold). Moreover, a reduction up to 81.5% in the disease severity was achieved in response to this treatment. Shoot length and yield per grapevine were considerably enhanced recording up to 26.3 and 23.7% increase, respectively. The berries quality was also improved. Furthermore, this treatment led to an enhancement in the photosynthetic pigments, induction of phenolic and ascorbic acid contents, an increase in the activity of peroxidase and polyphenol oxidase enzymes, and a reduction in the cellular electrolyte leakage, lipid peroxidation, and H₂O₂ content. Scanning electron microscopy observations showed an increase up to 86.6% in the number of closed stomata and a reduction up to 55% in the average stomatal pore area in response to this treatment. Observations of the transmission electron microscopy showed ultrastructural alterations in the cells of a grapevine leaf due to the infection with downy mildew, including plasmolysis and disruption of the cellular components, abnormal chloroplasts, and thickening of the cell wall and cell membrane. These abnormal alterations were reduced in response to SiNPs spray. In contrast, this study also showed that this treatment had considerable cytotoxic and genotoxic effects at this direct dose/concentration. So, additional investigations to determine the SiNPs residue in the produced edible plant parts are urgently needed. In addition, the pre-harvest interval, toxicity index, and risk assessment should be evaluated before any recommendation for use.

Soil Salinity, a Serious Environmental Issue and Plant Responses: A Metabolomics Perspective

The effects of global warming have increasingly led to devastating environmental stresses, such as heat, salinity, and drought. Soil salinization is a serious environmental issue and results in detrimental abiotic stress, affecting 7% of land area and 33% of irrigated lands worldwide. The proportion of arable land facing salinity is expected to rise due to increasing climate change fuelled by anthropogenic activities, exacerbating the threat to global food security for the exponentially growing populace. As sessile organisms, plants have evolutionarily developed mechanisms that allow ad hoc responses to salinity stress. The orchestrated mechanisms include signalling cascades involving phytohormones, kinases, reactive oxygen species (ROS), and calcium regulatory networks. As a pillar in a systems biology approach, metabolomics allows for comprehensive interrogation of the biochemistry and a deconvolution of molecular mechanisms involved in plant responses to salinity. Thus, this review highlights soil salinization as a serious environmental issue and points to the negative impacts of salinity on plants. Furthermore, the review summarises mechanisms regulating salinity tolerance on molecular, cellular, and biochemical levels with a focus on metabolomics perspectives. This critical synthesis of current literature is an opportunity to revisit the current models regarding plant responses to salinity, with an invitation to further fundamental research for novel and actionable insights.

Phytohormones: Key players in the modulation of heavy metal stress tolerance in plants

Heavy metal (HM) stress in plants has received considerable global attention as it threatens sustainable growth in agriculture worldwide. Hence, desperate efforts have been undertaken for combating the effects of this stress in plants. Interestingly, the use of phytohormones in reducing the impact of HM toxicity has gained much momentum in the recent past. Phytohormones act as chemical messengers that improve the HM stress resistance in plants, thus allowing them to retain their growth and developmental plasticity. Their exogenous application as well as manipulation of endogenous levels through precise targeting of their biosynthesis/signaling components is a promising approach for providing a protective shield against HM stress in plants. However, for the successful use of phytohormones for field plants exposed to HM toxicity, in-depth knowledge of the key pathways regulated by them is of prime importance. Hence, the present review mainly summarizes the key conceptual developments on the involvement of phytohormones in the mitigation of HM stress in plants. The role of various genes, proteins, and signaling components involved in phytohormones associated HM stress tolerance and their modulation has also been discussed. Thus, this update will pave the way for improving HM stress tolerance in plants with the advent of phytohormones for sustainable agriculture growth in the future.

Roles of Glutathione in Mediating Abscisic Acid Signaling and Its Regulation of Seed Dormancy and Drought Tolerance

Plant growth and development and interactions with the environment are regulated by phytohormones and other signaling molecules. During their evolution, plants have developed strategies for efficient signal perception and for the activation of signal transduction cascades to maintain proper growth and development, in particular under adverse environmental conditions. Abscisic acid (ABA) is one of the phytohormones known to regulate plant developmental events and tolerance to environmental stresses. The role of ABA is mediated by both its accumulated level, which is regulated by its biosynthesis and catabolism, and signaling, all of which are influenced by complex regulatory mechanisms. Under stress conditions, plants employ enzymatic and non-enzymatic antioxidant strategies to scavenge excess reactive oxygen species (ROS) and mitigate the negative effects of oxidative stress. Glutathione (GSH) is one of the main antioxidant molecules playing a critical role in plant survival under stress conditions through the detoxification of excess ROS, maintaining cellular redox homeostasis and regulating protein functions. GSH has recently emerged as an important signaling molecule regulating ABA signal transduction and associated developmental events, and response to stressors. This review highlights the current knowledge on the interplay between ABA and GSH in regulating seed dormancy, germination, stomatal closure and tolerance to drought.

Alfalfa (Medicago sativa L.) MsCML46 gene encoding calmodulin-like protein confers tolerance to abiotic stress in tobacco

KEY MESSAGE

MsCML46 enhances tolerance to abiotic stresses through alleviating osmotic stress and oxidative damage by regulating the expression of stress-related genes to optimize osmolytes levels and antioxidant enzyme activity in transgenic tobacco. Abiotic stresses are major environmental factors that constraint crop productivity worldwide. Various stimuli regulate intracellular calcium levels and calcium-mediated signal transduction, and cellular responses. Ca2+ signals are perceived by different Ca2+ receptors. Calmodulin-like protein (CML) is one of the best-characterized Ca2+ sensors which shares sequence similarity with highly conserved calmodulin (CaM) ubiquitously expressed in plants. Currently, the molecular and physiological functions of CMLs are largely unknown. In this study, the MsCML46 was characterized in alfalfa (Medicago sativa cv. Zhaodong) under freezing stress. Results showed that MsCML46 was localized to the cytoplasm of Arabidopsis, and its expression was strongly elevated by cold, drought, salt, saline-alkali, and ABA treatments. Overexpressing MsCML46 in tobacco enhanced tolerance to freezing, drought, and salt stresses as evidenced by improved contents of osmotic regulatory solutes and antioxidant enzyme activity but decreased reactive oxygen species (ROS) accumulation. Furthermore, cold, drought, and salt stresses increased the expression of stress-related genes in transgenic tobacco. MsCML46 binds free Ca2+ to promote signal transduction and maintain higher K+/Na+ ratio. In this way, it protects intracellular homeostasis under sodium ion toxicity. These results suggest that MsCML46 plays a crucial role in resisting abiotic stresses and can be exploited in genetic engineering for crops.

Multiomics analyses reveal the roles of the ASR1 transcription factor in tomato fruits

The transcription factor ASR1 (ABA, STRESS, RIPENING 1) plays multiple roles in plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression of ASR1 in tomato fruits, large scale analyses to uncover its function in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multiomics analysis of ASR1-antisense transgenic tomato fruits at the transcriptome and metabolome levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism, as well as abiotic stress pathways. Moreover, we found that ASR1-antisense fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. Given that ASR1 could be regulated by fruit ripening regulators such as FRUITFULL1/FRUITFULL2 (FUL1/FUL2), NON-RIPENING (NOR), and COLORLESS NON-RIPENING (CNR), we positioned it in the regulatory cascade of red ripe tomato fruits. These data extend the known range of functions of ASR1 as an important auxiliary regulator of tomato fruit ripening.

Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination

Abiotic stresses, including cold and drought, negatively affect maize (Zea mays L.) seed field emergence and later yield and quality. In order to reveal the molecular mechanism of maize seed resistance to abiotic stress at seed germination, the global transcriptome of high- vigour variety Zhongdi175 exposed to cold- and drought- stress was analyzed by RNA-seq. In the comparison between the control and different stressed sample, 12,299 differentially expressed genes (DEGs) were detected, of which 9605 and 7837 DEGs were identified under cold- and drought- stress, respectively. Functional annotation analysis suggested that stress response mediated by the pathways involving ribosome, phenylpropanoid biosynthesis and biosynthesis of secondary metabolites, among others. Of the obtained DEGs (12,299), 5,143 genes are common to cold- and drought- stress, at least 2248 TFs in 56 TF families were identified that are involved in cold and/or drought treatments during seed germination, including bHLH, NAC, MYB and WRKY families, which suggested that common mechanisms may be originated during maize seed germination in response to different abiotic stresses. This study will provide a better understanding of the molecular mechanism of response to abiotic stress during maize seed germination, and could be useful for cultivar improvement and breeding of high vigour maize cultivars.

Wood Formation under Severe Drought Invokes Adjustment of the Hormonal and Transcriptional Landscape in Poplar

Drought is a severe environmental stress that exerts negative effects on plant growth. In trees, drought leads to reduced secondary growth and altered wood anatomy. The mechanisms underlying wood stress adaptation are not well understood. Here, we investigated the physiological, anatomical, hormonal, and transcriptional responses of poplar to strong drought. Drought-stressed xylem was characterized by higher vessel frequencies, smaller vessel lumina, and thicker secondary fiber cell walls. These changes were accompanied by strong increases in abscisic acid (ABA) and antagonistic changes in salicylic acid in wood. Transcriptional evidence supported ABA biosynthesis and signaling in wood. Since ABA signaling activates the fiber-thickening factor NST1, we expected upregulation of the secondary cell wall (SCW) cascade under stress. By contrast, transcription factors and biosynthesis genes for SCW formation were down-regulated, whereas a small set of cellulose synthase-like genes and a huge array of genes involved in cell wall modification were up-regulated in drought-stressed wood. Therefore, we suggest that ABA signaling monitors normal SCW biosynthesis and that drought causes a switch from normal to "stress wood" formation recruiting a dedicated set of genes for cell wall biosynthesis and remodeling. This proposition implies that drought-induced changes in cell wall properties underlie regulatory mechanisms distinct from those of normal wood.

Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.

Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale)

Background

Cytochrome P450s play crucial roles in various biosynthetic reactions. Ginger (Zingiber officinale), which is often threatened by Ralstonia solanacearum, is the most economically important crop in the family Zingiberaceae. Whether the cytochrome P450 complement (CYPome) significantly responds to this pathogen has remained unclear.

Methods

Transcriptomic responses to R. solanacearum and soil moisture were analyzed in ginger, and expression profiles of the CYPome were determined based on transcriptome data.

Results

A total of 821 P450 unigenes with ORFs ≥ 300 bp were identified. Forty percent soil moisture suppressed several key P450 unigenes involved in the biosynthesis of flavonoids, gingerols, and jasmonates, including unigenes encoding flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, steroid 22-alpha-hydroxylase, cytochrome P450 family 724 subfamily B polypeptide 1, and allene oxide synthase. Conversely, the expression of P450 unigenes involved in gibberellin biosynthesis and abscisic acid catabolism, encoding ent-kaurene oxidase and abscisic acid 8'-hydroxylase, respectively, were promoted by 40% soil moisture. Under R. solanacearum infection, the expression of P450 unigenes involved in the biosynthesis of the above secondary metabolites were changed, but divergent expression patterns were observed under different soil moisture treatments. High moisture repressed expression of genes involved in flavonoid, brassinosteroid, gingerol, and jasmonate biosynthesis, but promoted expression of genes involved in GA anabolism and ABA catabolism. These results suggest possible mechanisms for how high moisture causes elevated susceptibility to R. solanacearum infection.

Transcriptome-Wide Identification and Characterization of the JAZ Gene Family in Mentha canadensis L

Jasmonate ZIM-domain (JAZ) proteins are the crucial transcriptional repressors in the jasmonic acid (JA) signaling process, and they play pervasive roles in plant development, defense, and plant specialized metabolism. Although numerous JAZ gene families have been discovered across several plants, our knowledge about the JAZ gene family remains limited in the economically and medicinally important Chinese herb Mentha canadensis L. Here, seven non-redundant JAZ genes named McJAZ1–McJAZ7 were identified from our reported M. canadensis transcriptome data. Structural, amino acid composition, and phylogenetic analysis showed that seven McJAZ proteins contained the typical zinc-finger inflorescence meristem (ZIM) domain and JA-associated (Jas) domain as conserved as those in other plants, and they were clustered into four groups (A-D) and distributed into five subgroups (A1, A2, B1, B2, and D). Quantitative real-time PCR (qRT-PCR) analysis showed that seven McJAZ genes displayed differential expression patterns in M. canadensis tissues, and preferentially expressed in flowers. Furthermore, the McJAZ genes expression was differentially induced after Methyl jasmonate (MeJA) treatment, and their transcripts were variable and up- or down-regulated under abscisic acid (ABA), drought, and salt treatments. Subcellular localization analysis revealed that McJAZ proteins are localized in the nucleus or cytoplasm. Yeast two-hybrid (Y2H) assays demonstrated that McJAZ1-5 interacted with McCOI1a, a homolog of Arabidopsis JA receptor AtCOI1, in a coronatine-dependent manner, and most of McJAZ proteins could also form homo- or heterodimers. This present study provides valuable basis for functional analysis and exploitation of the potential candidate McJAZ genes for developing efficient strategies for genetic improvement of M. canadensis.

Genome-Wide Identification and Characterization of the Brassinazole-resistant (BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat (Triticum aestivum L.)

Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat.

Function and Mechanism of Jasmonic Acid in Plant Responses to Abiotic and Biotic Stresses

As sessile organisms, plants must tolerate various environmental stresses. Plant hormones play vital roles in plant responses to biotic and abiotic stresses. Among these hormones, jasmonic acid (JA) and its precursors and derivatives (jasmonates, JAs) play important roles in the mediation of plant responses and defenses to biotic and abiotic stresses and have received extensive research attention. Although some reviews of JAs are available, this review focuses on JAs in the regulation of plant stress responses, as well as JA synthesis, metabolism, and signaling pathways. We summarize recent progress in clarifying the functions and mechanisms of JAs in plant responses to abiotic stresses (drought, cold, salt, heat, and heavy metal toxicity) and biotic stresses (pathogen, insect, and herbivore). Meanwhile, the crosstalk of JA with various other plant hormones regulates the balance between plant growth and defense. Therefore, we review the crosstalk of JAs with other phytohormones, including auxin, gibberellic acid, salicylic acid, brassinosteroid, ethylene, and abscisic acid. Finally, we discuss current issues and future opportunities in research into JAs in plant stress responses.

Xylooligosaccharides induce stomatal closure via salicylic acid signaling-regulated reactive oxygen species and nitric oxide production in Arabidopsis

Xylooligosaccharides (XOS) are the major coproducts of biofuel production and the most representative functional sugar enhancing animal physiology. However, little is known regarding the biological relevance of XOS to plants. Here, we found XOS triggered stomatal closure in Arabidopsis in a dose-dependent manner. Pamarcological data showed that XOS-induced stomatal closure was markedly inhibited by catalase (CAT, a reactive oxygen species [ROS] scavenger), salicylhydroxamic acid (SHAM, a peroxidase inhibitor), and 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO, a nitric oxide [NO] scavenger). Moreover, XOS induced the production of ROS and NO in guard cells of Arabidopsis. ROS production was strongly restricted by CAT and SHAM, but was unaffected by treatment with diphenyleneiodonium chloride (DPI, an NADPH oxidase inhibitor) or cPTIO. NO production was suppressed by CAT, SHAM, and cPTIO, but not by DPI. The elevation of ROS level mediated by SHAM-sensitive peroxidases occurred upstream of NO. Additionally, XOS-triggered stomatal closure and ROS and NO accumulation were significantly impaired in npr1 (salicylic acid signaling) mutant plants, but were not in jar1 (jasmonic acid signaling) or ein2 (ethylene signaling) mutant plants. Furthermore, XOS-induced stomatal closure was unaffected in both ost1 and atrbohD atrbohF (abscisic acid [ABA] signaling) mutant plants. Therefore, these results indicated that the biotic sugar, XOS, can elicit stomatal closure via salicylic acid signaling-mediated production of ROS and NO, in a manner independent of ABA signaling.

Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes

Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and, ultimately, the formation of nitrogen-fixing root nodules. Here, we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti while, conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of early nodulin 11 (ENOD11) shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic but not the osmotic component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with S. meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggest that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, functions to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Jasmonic acid: a key frontier in conferring abiotic stress tolerance in plants

Abiotic stresses are the primary sources of crop losses globally. The identification of key mechanisms deployed and established by plants in response to abiotic stresses is necessary for the maintenance of their growth and persistence. Recent discoveries have revealed that phytohormones or plant growth regulators (PGRs), mainly jasmonic acid (JA), have increased our knowledge of hormonal signaling of plants under stressful environments. Jasmonic acid is involved in various physiological and biochemical processes associated with plant growth and development as well as plant defense mechanism against wounding by pathogen and insect attacks. Recent findings suggest that JA can mediate the effect of abiotic stresses and help plants to acclimatize under unfavorable conditions. As a vital PGR, JA contributes in many signal transduction pathways, i.e., gene network, regulatory protein, signaling intermediates and enzymes, proteins, and other molecules that act to defend cells from the harmful effects of various environmental stresses. However, JA does not work as an independent regulator, but acts in a complex signaling pathway along other PGRs. Further, JA can protect and maintain the integrity of plant cells under several stresses by up-regulating the antioxidant defense. In this review, we have documented the biosynthesis and metabolism of JA and its protective role against different abiotic stresses. Further, JA-mediated antioxidant potential and its crosstalk with other PGRs have also been discussed.

Morphological Analysis, Protein Profiling and Expression Analysis of Auxin Homeostasis Genes of Roots of Two Contrasting Cultivars of Rice Provide Inputs on Mechanisms Involved in Rice Adaptation towards Salinity Stress

Plants remodel their root architecture in response to a salinity stress stimulus. This process is regulated by an array of factors including phytohormones, particularly auxin. In the present study, in order to better understand the mechanisms involved in salinity stress adaptation in rice, we compared two contrasting rice cultivars—Luna Suvarna, a salt tolerant, and IR64, a salt sensitive cultivar. Phenotypic investigations suggested that Luna Suvarna in comparison with IR64 presented stress adaptive root traits which correlated with a higher accumulation of auxin in its roots. The expression level investigation of auxin signaling pathway genes revealed an increase in several auxin homeostasis genes transcript levels in Luna Suvarna compared with IR64 under salinity stress. Furthermore, protein profiling showed 18 proteins that were differentially regulated between the roots of two cultivars, and some of them were salinity stress responsive proteins found exclusively in the proteome of Luna Suvarna roots, revealing the critical role of these proteins in imparting salinity stress tolerance. This included proteins related to the salt overly sensitive pathway, root growth, the reactive oxygen species scavenging system, and abscisic acid activation. Taken together, our results highlight that Luna Suvarna involves a combination of morphological and molecular traits of the root system that could prime the plant to better tolerate salinity stress.

Analysis of Phytohormone Signal Transduction in Sophora alopecuroides under Salt Stress

Salt stress seriously restricts crop yield and quality, leading to an urgent need to understand its effects on plants and the mechanism of plant responses. Although phytohormones are crucial for plant responses to salt stress, the role of phytohormone signal transduction in the salt stress responses of stress-resistant species such as Sophora alopecuroides has not been reported. Herein, we combined transcriptome and metabolome analyses to evaluate expression changes of key genes and metabolites associated with plant hormone signal transduction in S. alopecuroides roots under salt stress for 0 h to 72 h. Auxin, cytokinin, brassinosteroid, and gibberellin signals were predominantly involved in regulating S. alopecuroides growth and recovery under salt stress. Ethylene and jasmonic acid signals may negatively regulate the response of S. alopecuroides to salt stress. Abscisic acid and salicylic acid are significantly upregulated under salt stress, and their signals may positively regulate the plant response to salt stress. Additionally, salicylic acid (SA) might regulate the balance between plant growth and resistance by preventing reduction in growth-promoting hormones and maintaining high levels of abscisic acid (ABA). This study provides insight into the mechanism of salt stress response in S. alopecuroides and the corresponding role of plant hormones, which is beneficial for crop resistance breeding.

Current status of microRNA-mediated regulation of drought stress responses in cereals

Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.

Ginsenosides in Panax genus and their biosynthesis

Ginsenosides are a series of glycosylated triterpenoids which belong to protopanaxadiol (PPD)-, protopanaxatriol (PPT)-, ocotillol (OCT)- and oleanane (OA)-type saponins known as active compounds of Panax genus. They are accumulated in plant roots, stems, leaves, and flowers. The content and composition of ginsenosides are varied in different ginseng species, and in different parts of a certain plant. In this review, we summarized the representative saponins structures, their distributions and the contents in nearly 20 Panax species, and updated the biosynthetic pathways of ginsenosides focusing on enzymes responsible for structural diversified ginsenoside biosynthesis. We also emphasized the transcription factors in ginsenoside biosynthesis and non-coding RNAs in the growth of Panax genus plants, and highlighted the current three major biotechnological applications for ginsenosides production. This review covered advances in the past four decades, providing more clues for chemical discrimination and assessment on certain ginseng plants, new perspectives for rational evaluation and utilization of ginseng resource, and potential strategies for production of specific ginsenosides.

Transcriptome Analysis of Tolerant and Susceptible Maize Genotypes Reveals Novel Insights about the Molecular Mechanisms Underlying Drought Responses in Leaves

Maize (Zea mays L.) is the most essential food crop in the world. However, maize is highly susceptible to drought stress, especially at the seedling stage, and the molecular mechanisms underlying drought tolerance remain elusive. In this study, we conducted comparative transcriptome and physiological analyses of drought-tolerant (CML69) and susceptible (LX9801) inbred lines subjected to drought treatment at the seedling stage for three and five days. The tolerant line had significantly higher relative water content in the leaves, as well as lower electrolyte leakage and malondialdehyde levels, than the susceptible line. Using an RNA-seq-based approach, we identified 10,084 differentially expressed genes (DEGs) with 6906 and 3178 DEGs been annotated and unannotated, respectively. Two critical sets of drought-responsive DEGs, including 4687 genotype-specific and 2219 common drought-responsive genes, were mined out of the annotated DEGs. The tolerant-line DEGs were predominantly associated with the cytoskeleton, cell wall modification, glycolysis/gluconeogenesis, transport, osmotic regulation, drought avoidance, ROS scavengers, defense, and transcriptional factors. For the susceptible line, the DEGs were highly enriched in the photosynthesis, histone, and carbon fixation pathways. The unannotated DEGs were implicated in lncRNAs, including 428 previously reported and 22% putative TE-lncRNAs. There was consensus on both the physiological response and RNA-seq outcomes. Collectively, our findings will provide a comprehensive basis of the molecular networks mediating drought stress tolerance of maize at the seedling stage.

Fusarium head blight resistance in European winter wheat: insights from genome-wide transcriptome analysis

Background

Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially the extent of extruded anthers, are strongly associated with FHB resistance.

Results

To characterize the genetic basis of FHB resistance, we generated and analyzed phenotypic and gene expression data on the response to Fusarium graminearum (Fg) infection in 96 European winter wheat genotypes, including several lines containing introgressions from the highly resistant Asian cultivar Sumai3. The 96 lines represented a broad range in FHB resistance and were assigned to sub-groups based on their phenotypic FHB severity score. Comparative analyses were conducted to connect sub-group-specific expression profiles in response to Fg infection with FHB resistance level. Collectively, over 12,300 wheat genes were Fusarium responsive. The core set of genes induced in response to Fg was common across different resistance groups, indicating that the activation of basal defense response mechanisms was largely independent of the resistance level of the wheat line. Fg-induced genes tended to have higher expression levels in more susceptible genotypes. Compared to the more susceptible non-Sumai3 lines, the Sumai3-derivatives demonstrated higher constitutive expression of genes associated with cell wall and plant-type secondary cell wall biogenesis and higher constitutive and Fg-induced expression of genes involved in terpene metabolism. Gene expression analysis of the FHB QTL Qfhs.ifa-5A identified a constitutively expressed gene encoding a stress response NST1-like protein (TraesCS5A01G211300LC) as a candidate gene for FHB resistance. NST1 genes are key regulators of secondary cell wall biosynthesis in anther endothecium cells. Whether the stress response NST1-like gene affects anther extrusion, thereby affecting FHB resistance, needs further investigation.

Conclusion

Induced and preexisting cell wall components and terpene metabolites contribute to resistance and limit fungal colonization early on. In contrast, excessive gene expression directs plant defense response towards programmed cell death which favors necrotrophic growth of the Fg pathogen and could thus lead to increased fungal colonization.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07800-1.

CRISPR Genome Editing Technology: A Powerful Tool Applied to Developing Agribusiness

The natural increase of the world's population implies boosting agricultural demand. In the current non-optimistic global scenario, where adverse climate changes come associated with substantial population growth, the main challenge in agribusiness is food security. Recently, the CRISPR/Cas system has emerged as a friendly gene editing biotechnological tool, enabling a precise manipulation of genomes and enhancement of desirable traits in several organisms. This review highlights the CRISPR/Cas system as a paramount tool for the improvement of agribusiness products and brings up-to-date findings showing its potential applications in improving agricultural-related traits in major plant crops and farm animals, all representing economic-relevant commodities responsible for feeding the world. Several applied pieces of research have successfully demonstrated the CRISPR/Cas ability in boosting interesting traits in agribusiness products, including animal productivity and welfare, crop yield growth, and seed quality, reflecting positive impacts in both socioeconomics and human health aspects. Hence, the CRISPR/Cas system has revolutionized bioscience and biotechnology, and its concrete application in agribusiness goods is on the horizon.

Proteomic analysis validates previous findings on wounding-responsive plant hormone signaling and primary metabolism contributing to the biosynthesis of secondary metabolites based on metabolomic analysis in harvested broccoli (Brassica oleracea L. var. italica)

The plant wound-response is a complex process that generates physiological modifications for protecting the wounded tissue. In this study, tandem mass tag (TMT)-based quantitative proteomic analysis was performed to clarify the comprehensive molecular mechanism for the wound-response of broccoli subjected to two wounding intensities (0.04 and 1.85 m² kg^-1 for florets and shreds, respectively). Furthermore, integrated proteomic and metabolomic analysis was performed to reveal the interaction among the critical metabolic pathway responses to wounding. The results show that a total of 399 proteins and 266 proteins were identified as differentially expressed proteins (DEPs) in florets and shreds broccoli compared to control, respectively. Furthermore, 167 DEPs were detected in shreds broccoli compared to the florets broccoli. Salicylic acid (SA) and ethylene (ET) biosynthesis were more susceptible to being induced by wounding with lower intensities, whereas, phenylpropanoid biosynthesis, aliphatic glucosinolate synthesis and jasmonic acid (JA) biosynthesis were more susceptible to being activated by wounding with higher intensities. The activation of starch and sucrose metabolism, TCA cycle, glycolysis, pentose phosphate could provide carbon sources and ATP for the production of amino acids including phenylalanine, valine, threonine, isoleucine, L-methionine, methionine and histidine. The motivation of carbohydrate metabolic pathways and amino acid biosynthesis-related pathways promotes the precursor levels for phenolic substances and glucosinolate synthesis. Furthermore, the accumulation of SA, ET and JA may activated secondary metabolite biosynthesis through the regulation of critical proteins involved in the corresponding metabolic pathways.

Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species

Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the selective oxidative cleavage steps from carotenoids to apocarotenoids, which are essential for the synthesis of biologically important molecules such as retinoids, and the phytohormones abscisic acid (ABA) and strigolactones. In addition, CCDs play important roles in plant biotic and abiotic stress responses. Till now, a comprehensive characterization of the CCD gene family in the economically important crop cotton (Gossypium spp.) is still missing. Here, we performed a genome-wide analysis and identified 33, 31, 16 and 15 CCD genes from two allotetraploid Gossypium species, G. hirsutum and G. barbadense, and two diploid Gossypium species, G. arboreum and G. raimondii, respectively. According to the phylogenetic tree analysis, cotton CCDs are classified as six subgroups including CCD1, CCD4, CCD7, CCD8, nine-cis-epoxycarotenoid dioxygenase (NCED) and zaxinone synthase (ZAS) sub-families. Evolutionary analysis shows that purifying selection dominated the evolution of these genes in G. hirsutum and G. barbadense. Predicted cis-acting elements in 2 kb promoters of CCDs in G. hirsutum are mainly involved in light, stress and hormone responses. The transcriptomic analysis of GhCCDs showed that different GhCCDs displayed diverse expression patterns and were ubiquitously expressed in most tissues; moreover, GhCCDs displayed specific inductions by different abiotic stresses. Quantitative reverse-transcriptional PCR (qRT-PCR) confirmed the induction of GhCCDs by heat stress, salinity, polyethylene glycol (PEG) and ABA application. In summary, the bioinformatics and expression analysis of CCD gene family provide evidence for the involvement in regulating abiotic stresses and useful information for in-depth studies of their biological functions in G. hirsutum.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02805-9.

Exogenous EBR Ameliorates Endogenous Hormone Contents in Tomato Species under Low-Temperature Stress

Low-temperature stress is a type of abiotic stress that limits plant growth and production in both subtropical and tropical climate conditions. In the current study, the effects of 24-epi-brassinolide (EBR) as analogs of brassinosteroids (BRs) were investigated, in terms of hormone content, antioxidant enzyme activity, and transcription of several cold-responsive genes, under low-temperature stress (9 °C) in two different tomato species (cold-sensitive and cold-tolerant species). Results indicated that the treatment with exogenous EBR increases the content of gibberellic acid (GA3) and indole-3-acetic acid (IAA), whose accumulation is reduced by low temperatures in cold-sensitive species. Furthermore, the combination or contribution of BR and abscisic acid (ABA) as a synergetic interaction was recognized between BR and ABA in response to low temperatures. The content of malondialdehyde (MDA) and proline was significantly increased in both species, in response to low-temperature stress; however, EBR treatment did not affect the MDA and proline content. Moreover, in the present study, the effect of EBR application was different in the tomato species under low-temperature stress, which increased the catalase (CAT) activity in the cold-tolerant species and increased the glutathione peroxidase (GPX) activity in the cold-sensitive species. Furthermore, expression levels of cold-responsive genes were influenced by low-temperature stress and EBR treatment. Overall, our findings revealed that a low temperature causes oxidative stress while EBR treatment may decrease the reactive oxygen species (ROS) damage into increasing antioxidant enzymes, and improve the growth rate of the tomato by affecting auxin and gibberellin content. This study provides insight into the mechanism by which BRs regulate stress-dependent processes in tomatoes, and provides a theoretical basis for promoting cold resistance of the tomato.

Potential Role and Utilization of Plant Growth Promoting Microbes in Plant Tissue Culture

Plant growth promoting microbes (PGPMs) play major roles in diverse ecosystems, including atmospheric nitrogen fixation, water uptake, solubilization, and transport of minerals from the soil to the plant. Different PGPMs are proposed as biofertilizers, biostimulants, and/or biocontrol agents to improve plant growth and productivity and thereby to contribute to agricultural sustainability and food security. However, little information exists regarding the use of PGPMs in micropropagation such as the in vitro plant tissue culture. This review presents an overview of the importance of PGPMs and their potential application in plant micropropagation. Our analysis, based on published articles, reveals that the process of in vitro classical tissue culture techniques, under strictly aseptic conditions, deserves to be reviewed to allow vitroplants to benefit from the positive effect of PGPMs. Furthermore, exploiting the potential benefits of PGPMs will lead to lessen the cost production of vitroplants during micropropagation process and will make the technique of plant tissue culture more efficient. The last part of the review will indicate where research is needed in the future.

Plant RABs: Role in Development and in Abiotic and Biotic Stress Responses

Endosomal trafficking plays an integral role in various eukaryotic cellular activities and is vital for higher-order functions in multicellular organisms. RAB GTPases are important proteins that influence various aspects of membrane traffic, which consequently influence many cellular functions and responses. Compared to yeast and mammals, plants have evolved a unique set of plant-specific RABs that play a significant role in their development. RABs form the largest family of small guanosine triphosphate (GTP)-binding proteins, and are divided into eight sub-families named RAB1, RAB2, RAB5, RAB6, RAB7, RAB8, RAB11 and RAB18. Recent studies on different species suggest that RAB proteins play crucial roles in intracellular trafficking and cytokinesis, in autophagy, plant microbe interactions and in biotic and abiotic stress responses. This review recaptures and summarizes the roles of RABs in plant cell functions and in enhancing plant survival under stress conditions.

Post-translational Modifications of bZIP Transcription Factors in Abscisic Acid Signaling and Drought Responses

Under drought stress, plants have developed various mechanisms to survive in the reduced water supply, of which the regulation of stress-related gene expression is responsible for several transcription factors. The basic leucine zippers (bZIPs) are one of the largest and most diverse transcription factor families in plants. Among the 10 Arabidopsis bZIP groups, group A bZIP transcription factors function as a positive or negative regulator in ABA signal transduction and drought stress response. These bZIP transcription factors, which are involved in the drought response, have also been isolated in various plant species such as rice, pepper, potato, and maize. Recent studies have provided substantial evidence that many bZIP transcription factors undergo the post-translational modifications, through which the regulation of their activity or stability affects plant responses to various intracellular or extracellular stimuli. This review aims to address the modulation of the bZIP proteins in ABA signaling and drought responses through phosphorylation, ubiquitination and sumoylation.

Roles of Phytohormones and Their Signaling Pathways in Leaf Development and Stress Responses

Phytohormones participate in various processes over the course of a plant's lifecycle. In addition to the five classical phytohormones (auxins, cytokinins, gibberellins, abscisic acid, and ethylene), phytohormones such as brassinosteroids, jasmonic acid, salicylic acid, strigolactones, and peptides also play important roles in plant growth and stress responses. Given the highly interconnected nature of phytohormones during plant development and stress responses, it is challenging to study the biological function of a single phytohormone in isolation. In the current Review, we describe the combined functions and signaling cascades (especially the shared points and pathways) of various phytohormones in leaf development, in particular, during leaf primordium initiation and the establishment of leaf polarity and leaf morphology as well as leaf development under various stress conditions. We propose a model incorporating the roles of multiple phytohormones in leaf development and stress responses to illustrate the underlying combinatorial signaling pathways. This model provides a reference for breeding stress-resistant crops.

Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

BACKGROUND

As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family.

RESULTS

Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses.

CONCLUSIONS

In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

Functional Characterization of PsnNAC036 under Salinity and High Temperature Stresses

Plant growth and development are challenged by biotic and abiotic stresses including salinity and heat stresses. For Populus simonii × P. nigra as an important greening and economic tree species in China, increasing soil salinization and global warming have become major environmental challenges. We aim to unravel the molecular mechanisms underlying tree tolerance to salt stress and high temprerature (HT) stress conditions. Transcriptomics revealed that a PsnNAC036 transcription factor (TF) was significantly induced by salt stress in P. simonii × P. nigra. This study focuses on addressing the biological functions of PsnNAC036. The gene was cloned, and its temporal and spatial expression was analyzed under different stresses. PsnNAC036 was significantly upregulated under 150 mM NaCl and 37 °C for 12 h. The result is consistent with the presence of stress responsive cis-elements in the PsnNAC036 promoter. Subcellular localization analysis showed that PsnNAC036 was targeted to the nucleus. Additionally, PsnNAC036 was highly expressed in the leaves and roots. To investigate the core activation region of PsnNAC036 protein and its potential regulatory factors and targets, we conducted trans-activation analysis and the result indicates that the C-terminal region of 191-343 amino acids of the PsnNAC036 was a potent activation domain. Furthermore, overexpression of PsnNAC036 stimulated plant growth and enhanced salinity and HT tolerance. Moreover, 14 stress-related genes upregulated in the transgenic plants under high salt and HT conditions may be potential targets of the PsnNAC036. All the results demonstrate that PsnNAC036 plays an important role in salt and HT stress tolerance.

Plant Defense Responses to Biotic Stress and Its Interplay With Fluctuating Dark/Light Conditions

Plants are subjected to a plethora of environmental cues that cause extreme losses to crop productivity. Due to fluctuating environmental conditions, plants encounter difficulties in attaining full genetic potential for growth and reproduction. One such environmental condition is the recurrent attack on plants by herbivores and microbial pathogens. To surmount such attacks, plants have developed a complex array of defense mechanisms. The defense mechanism can be either preformed, where toxic secondary metabolites are stored; or can be inducible, where defense is activated upon detection of an attack. Plants sense biotic stress conditions, activate the regulatory or transcriptional machinery, and eventually generate an appropriate response. Plant defense against pathogen attack is well understood, but the interplay and impact of different signals to generate defense responses against biotic stress still remain elusive. The impact of light and dark signals on biotic stress response is one such area to comprehend. Light and dark alterations not only regulate defense mechanisms impacting plant development and biochemistry but also bestow resistance against invading pathogens. The interaction between plant defense and dark/light environment activates a signaling cascade. This signaling cascade acts as a connecting link between perception of biotic stress, dark/light environment, and generation of an appropriate physiological or biochemical response. The present review highlights molecular responses arising from dark/light fluctuations vis-à-vis elicitation of defense mechanisms in plants.