Out of Shape During Stress: A Key Role for Auxin

Overexpression of auxin synthesis gene PagYUC6a in poplar (Populus alba × P. glandulosa) enhances salt tolerance

YUCCA proteins play a crucial role in auxin biosynthesis. However, their specific functions in poplar in response to abiotic stress are unclear. Here, we isolated the auxin biosynthesis gene PagYUC6a, one of the Arabidopsis AtYUC6 homologs, from '84 K' poplar (Populus alba × P. glandulosa), and investigated its role in salt tolerance in transgenic poplar plants. PagYUC6a was predominantly expressed in young stems and significantly upregulated upon 200 mM NaCl treatment. Overexpression of PagYUC6a enhanced the growth and salt tolerance of transgenic poplar, as well as the content of indole-3-acetic acid (IAA). Further analysis revealed that the level of reactive oxygen species (ROS) accumulation in the leaves of transgenic plants was significantly lower than that in the leaves of wild type plants, accompanied with a higher activity of catalase (CAT), superoxide dismutase (SOD) and ascorbate peroxidase (APX). The transcript level of CAT2, SOD1 and APX1 was also higher in the leaves of transgenic plants under salt stress conditions. These results demonstrated that PagYUC6a improved salt tolerance by enhancing ROS scavenging capacity. Our findings provide valuable information on the molecular mechanisms of PagYUC6a mediated salinity tolerance and highlight its potential for the breeding of salt-tolerant tree species.

Exogenous proline mediates OsNPR1 to regulate the innate pool of IAA in response to Cr exposure in rice plants

Indole acetic acid (IAA) orchestrates a myriad of physiological and biochemical responses in plants under stressful conditions, highlighting its indispensable role in plant resilience. The widespread contamination of chromium (Cr) poses a significant threat to rice cultivation, as its accumulation in plants disrupts various metabolic processes, consequently hindering growth. Of course, the utilization of exogenous growth regulators, including proline (Pro), has notably surged as a strategy to mitigate stress in plants. Pro can trigger the activation of other growth-regulating molecules, including IAA, to coordinate stress responses. To explore the complex interaction between exogenous Pro and the endogenous pool of IAA under Cr(VI) toxicity, a hydroponic system was established. The rice plants treated with exogenous Pro in coupled with Cr(VI) [Cr(VI)+Pro] showed significantly greater content of IAA than the plants not treated with exogenous Pro [Cr(VI)-Pro]. The expression analysis of genes involved in the speciation of IAA reactions reveals that the downregulation of OsNPR1 under "Cr(VI)+Pro" treatments might be the crucial player in increasing the IAA content in rice plants. The increase in IAA by Pro treatment under Cr toxicity might lead to an improvement in root activity and root architecture elements. Importantly, no significant difference was observed in the accumulation of Cr in [Cr(VI)-Pro]- and [Cr(VI)+Pro]-treated rice plants. These results reveal that exogenous Pro can improve plant growth by inducing IAA accumulation in plant tissues exposed to Cr(VI) toxicity, without increasing Cr toxicity in plants.

ABCB transporters: functionality extends to more than auxin transportation

MAIN CONCLUSION

ABCs transport diverse compounds; with plant's most abundant ABCG and ABCB subfamilies. ABCBs are multi-functional transporter proteins having role in plant adaptation. ATP-binding cassette (ABC) proteins have been known for the transportation of various structurally diverse compounds in all kingdoms of life. Plants possess a particularly high number of ABC transporters compared to other eukaryotes: the most abundant being ABCG followed by the ABCB subfamilies. While members of the ABCB subfamily are primarily known for auxin transportation, however, studies have shown their involvement in variety of other functions viz. growth and development, biotic and abiotic stresses, metal toxicity and homeostasis, cellular redox state stability, stomatal regulation, cell shape maintenance, and transport of secondary metabolites and phytohormones. These proteins are able to perform various biological processes due to their widespread localization in the plasma membrane, mitochondrial membrane, chloroplast, and tonoplast facilitating membrane transport influenced by various environmental and biological cues. The current review compiles published insights into the role of ABCB transporters, and also provides brief insights into the role of ABCB transporters in a medicinal plant, where the synthesis of its bioactive secondary metabolite is linked to the primary function of ABCBs, i.e., auxin transport. The review discusses ABCB subfamily members as multi-functional protein and comprehensively examines their role in various biological processes that help plants to survive under unfavorable environmental conditions.

How to survive mild winters: Cold acclimation, deacclimation, and reacclimation in winter wheat and barley

Cold acclimation and vernalization represent the major evolutionary adaptive responses to ensure winter survival of temperate plants. Due to climate change, mild winters can paradoxically worsen plant winter survival due to cold deacclimation induced by warm periods during winter. It seems that the ability of cold reacclimation in overwintering Triticeae cereals is limited, especially in vernalized plants. In the present review, the major factors determining cold acclimation (CA), deacclimation (DA) and reacclimation (RA) processes in winter-type Triticeae, namely wheat and barley, are discussed. Recent knowledge on cold sensing and signaling is briefly summarized. The impacts of chilling temperatures, photoperiod and light spectrum quality as the major environmental factors, and the roles of soluble proteins and sugars (carbohydrates) as well as cold stress memory molecular mechanisms as the major plant-based factors determining CA, DA, and RA processes are discussed. The roles of plant stress memory mechanisms and development processes, namely vernalization, in winter Triticeae reacclimation are elucidated. Recent findings about the role of O-glucose N-acetylation of target proteins during vernalization and their impacts on the expression of VRN1 gene and other target proteins resulting in cold-responsive modules reprogramming are presented.

Salinity survival: molecular mechanisms and adaptive strategies in plants

Soil salinity is a significant environmental challenge that threatens plant growth and development, adversely affecting global food crop production. This underscores the critical need to elucidate the molecular mechanisms underlying plant salt tolerance, which has profound implications for agricultural advancement. Recent progress in plant salt tolerance has greatly improved our understanding of the molecular mechanisms of plant responses to salt stress and precision design breeding as an effective strategy for developing new salt-tolerant crop varieties. This review focuses on the model plant species Arabidopsis thaliana and important crops, namely, wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa). It summarizes current knowledge on plant salt tolerance, emphasizing key aspects such as the perception and response to salt stress, Na+ transport, Na+ compartmentalization and clearance, changes in reactive oxygen species induced by salt stress, and regulation of plant stem cell development under salt stress conditions. The review might provide new and valuable information for understanding the molecular mechanisms of plant response and adaptation to salt stress.

Molecular insight into auxin signaling and associated network modulating stress responses in rice

Phytohormones are vital regulators of various signaling networks in plants. Among different phytohormones, auxin has been thoroughly studied for its role in regulating plants' growth, development, and stress response. One major function of auxin is modulating the developmental processes in response to environmental cues. Although extensive studies on Arabidopsis have advanced the knowledge of auxin biology, several studies on rice have uncovered key players regulated by auxin that play critical roles in coordinating auxin homeostasis and signaling involved in defense response. The emerging knowledge on auxin biology, auxin-regulated gene expression, and auxin-signaling in rice during various environmental stresses has provided insights into the possible mechanism of rice susceptibility or resistance to different abiotic and biotic stresses. The current review enumerates the possible mechanisms of stress-induced auxin homeostasis in rice. In addition, we provide an overview of the state of knowledge on auxin-mediated defense signaling in rice, highlighting its pivotal role in stress response. In particular, we discuss the auxin pathways and the dynamic regulation in response to biotic and abiotic stress. We highlight the novel findings in the diversity of auxin signaling in the model plant Arabidopsis with an aim to emphasize the need to translate these findings into agronomically and economically important cereals like rice. Addressing the complexity of auxin induction, signaling, and its associated molecular network, an in-depth investigation in rice is required to comprehend auxin-mediated spatial-temporal regulation of developmental processes during stress.

Unlocking Biochar's Potential: Innovative Strategies for Sustainable Remediation of Heavy Metal Stress in Tobacco Plants

Tobacco, being a globally cultivated crop, holds significant social and economic importance. Tobacco plants are susceptible to the adverse effects of heavy metals (HMs), particularly cadmium (Cd), which hinders root development, disrupts water balance, and impedes nutrient absorption. Higher concentrations of HMs, especially Cd, naturally accumulate in tobacco leaves due to complex interactions within the plant-soil continuum. The uptake of Cd by plants from the soil is influenced by several factors, including soil type, pH, irrigation water quality, and the chemical composition of the metal involved. Different techniques, such as bioremediation, phytoremediation, and mycoremediation, have been employed to tackle the issue of HMs. The use of biochar offers a practical solution to mitigate this problem. With its large surface area and porous nature, biochar can effectively alleviate HMs contamination. Under biochar application, metal adsorption primarily occurs through physical adsorption, where metal ions are trapped within the pores of the biochar. Additionally, electrostatic attraction, in which negatively charged biochar surfaces attract positively charged metal ions, is another major mechanism of metal remediation facilitated by biochar. In this review, we documented, compiled, and interpreted novel and recent information on HMs stress on tobacco plants and explored biochar's role in alleviating HMs toxicity. By providing a comprehensive review of the persistent threat posed by Cd to tobacco crops and exploring biochar's potential as a remediation measure, this work aims to enhance our understanding of HMs stress in tobacco and contribute to the development of sustainable agricultural practices.

Fungal endophytes modulate the negative effects induced by Persistent Organic Pollutants in the antarctic plant Colobanthus quitensis

Antarctica has one of the most sensitive ecosystems to the negative effects of Persistent Organic Pollutants (POPs) on its biodiversity. This is because of the lower temperatures and the persistence of POPs that promote their accumulation or even biomagnification. However, the impact of POPs on vascular plants is unknown. Moreover, fungal symbionts could modulate the effects on host plants to cope with this stress factor. This study investigates the molecular and ecophysiological responses of the Sub-Antarctic and Antarctic plant Colobanthus quitensis to POPs in different populations along a latitudinal gradient (53°- 67° S), emphasizing the role of endophytic fungi. The results show that exposure of POPs in C. quitensis generates oxidative stress and alters its ecophysiological performance. Nevertheless, C. quitensis in association with fungal endophytes and POPs exposure, shows lower lipid peroxidation, higher proline content and higher photosynthetic capacity, as well as higher biomass and survival percentage, compared to plants in the absence of fungal endophytes. On the other hand, the antarctic plant population (67°S) with endophytic fungi presents better stress modulating upon POPs exposure. Endophytic fungi would be more necessary for plant performance towards higher latitudes with extreme conditions, contributing significantly to their general functional adaptation. We develop a transcriptomics analyses n the C. quitensis-fungal endophytes association from the Peninsula population. We observed that fungal endophytes promote tolerance to POPs stress through upregulated genes for the redox regulation based on ascorbate and scavenging mechanisms (peroxidases, MDAR, VTC4, CCS), transformation (monooxygenases) and conjugation of compounds or metabolites (glutathione transferases, glycosyltransferases, S-transferases), and the storage or elimination of conjugates (ABC transporters, C and G family) that contribute to detoxification cell. This work highlights the contribution of endophytic fungi to plant resistance in situations of environmental stress, especially in extreme conditions such as in antarctica exposed to anthropogenic impact. The implications of these findings are relevant for the biosecurity of one of the last pristine bastions worldwide.

Sextuple knockouts of a highly conserved and coexpressed AUXIN/INDOLE-3-ACETIC ACID gene set confer shade avoidance-like responses in Arabidopsis

AUXIN/INDOLE-3-ACETIC ACIDs are transcriptional repressors for auxin signalling. Aux/IAAs of Arabidopsis thaliana display some functional redundancy. The IAA3/SHY2 clade (IAA1, IAA2, IAA3 and IAA4) show strong sequence similarity, but no higher-order mutants have been reported. Here, through CRISPR/Cas9 genome editing, we generated loss-of-function iaa1/2/3/4 mutants. The quadruple mutants only exhibited a weak phenotype. Thus, we additionally knocked out IAA7/AXR2 and IAA16, which are coexpressed with IAA1/2/3/4. Remarkably, under white light control conditions, the iaa1/2/3/4/7/16 mutants exhibited a shade avoidance-like phenotype with over-elongated hypocotyls and petioles and hyponastic leaves. The sextuple mutants were highly sensitive to low light intensity, and the hypocotyl cells of the mutants were excessively elongated. Transcriptome profiling and qRT-PCR analyses revealed that the sextuple mutation upregulated IAA19/MSG2 and IAA29, two shared shade/auxin signalling targets. Besides, genes encoding cell wall-remodelling proteins and shade-responsive transcription regulators were upregulated. Using dual-luciferase reporter assays, we verified that IAA2/IAA7 targeted the promoters of cell wall-remodelling genes to inhibit their transcription. Our work indicates that the IAA1/2/3/4/7/16 gene set is required for the optimal integration of auxin and shade signalling. The mutants generated here should be valuable for exploring the complex interactions among signal sensors, transcription activators and transcription repressors during hormone/environmental responses.

Emerging roles of auxin in plant abiotic stress tolerance

Plants are continuously attacked by several biotic and abiotic factors. Among abiotic factors, heat, cold, drought, and salinity are common stresses. Plants produce several hormones as their main weapon in fightback against these stresses. Among these hormones, the role of auxin is well established in regulating plant growth and development at various scales. However, in recent literature, the important role of auxin in abiotic stress tolerance has emerged. Several auxin signalling and transport mutants exhibit heat, drought, and salinity-related phenotypes. Among them, auxin-mediated hypocotyl elongation and root growth in response to increased heat are of importance due to the continuous rise in global temperature. Auxin is also involved in regulating and recruiting specialized metabolites like aliphatic glucosinolate to defend themselves from drought stress. Aliphatic glucosinolate (A-GLS) regulates guard cell closure using auxin, which is independent of the major abiotic stress hormone abscisic acid. This regulatory mechanism serves as an additional layer of guard cell movement to protect plants from drought. Transferring the aliphatic glucosinolate pathway into non-brassica plants such as rice and soybean holds the promise to improve drought tolerance. In addition to these, post-translational modification of auxin signalling components and redistribution of auxin efflux transporters are also playing important roles in drought and salt tolerance and, hence, may be exploited to breed drought-tolerant crops. Also, reactive oxygen species, along with peptide hormone and auxin signalling, are important in root growth under stress. In conclusion, we summarize recent discoveries that suggest auxin is involved in various abiotic stresses.

Understanding of Plant Salt Tolerance Mechanisms and Application to Molecular Breeding

Soil salinization is a widespread hindrance that endangers agricultural production and ecological security. High salt concentrations in saline soils are primarily caused by osmotic stress, ionic toxicity and oxidative stress, which have a negative impact on plant growth and development. In order to withstand salt stress, plants have developed a series of complicated physiological and molecular mechanisms, encompassing adaptive changes in the structure and function of various plant organs, as well as the intricate signal transduction networks enabling plants to survive in high-salinity environments. This review summarizes the recent advances in salt perception under different tissues, physiological responses and signaling regulations of plant tolerance to salt stress. We also examine the current knowledge of strategies for breeding salt-tolerant plants, including the applications of omics technologies and transgenic approaches, aiming to provide the basis for the cultivation of salt-tolerant crops through molecular breeding. Finally, future research on the application of wild germplasm resources and muti-omics technologies to discover new tolerant genes as well as investigation of crosstalk among plant hormone signaling pathways to uncover plant salt tolerance mechanisms are also discussed in this review.

Small chemical molecules regulating the phytohormone signalling alter the plant's physiological processes to improve stress adaptation, growth and productivity

Small chemical molecules are attractive agents for improving the plant processes associated with plant growth and stress tolerance. Recent advances in chemical biology and structure-assisted drug discovery approaches have opened up new avenues in plant biology to discover new drug-like molecules to improve plant processes for sustained food production. Several compounds targeting phytohormone biosynthesis or signalling cascades were designed to alter plant physiological mechanisms. Altering Abscisic acid synthesis and its signalling process can improve drought tolerance, and the processes targeted are reversible. Molecules targeting cytokinin, Auxin, and gibberellic acid regulate plant physiological processes and can potentially improve plant growth, biomass and productivity. The potential of molecules may be exploited as agrochemicals to enhance agricultural productivity. The discovery of small molecules provides new avenues to improve crop production in changing climatic conditions and the nutritional quality of foods. We present the rational combinations of small molecules with inhibitory and co-stimulatory effects and discuss future opportunities in this field.

Phytohormonal balance and differential gene expression in chronically irradiated Scots pine populations from the chernobyl affected zone

The impact of chronic radiation exposure on phytohormone content and expression of phytohormone- and stress-related genes of Scots pine in the zone affected by the Chernobyl accident was studied. Needle samples were collected from three plots with contrasting levels of radioactive contamination in the Polesye State Radiation-Ecological Reserve, Republic of Belarus, and two reference plots in the Kozeluzhsky forest in June 2022. The experimental plots were located within the artificial plantations of Scots pine established in 1982, before the accident in 1986. The activity of radionuclides 137Cs, 90Sr, 241Am, 238Pu, and 239+240Pu in soil and needles ensured dose rates ranging from 3.3 to 87 mGy × year-1, while at the reference plots, the range was 0.7‒0.8 mGy × year-1. Concentrations of plant hormones, including indole-3-acetic acid (IAA), indole-3-butyric acid (IBA), zeatin, and abscisic acid (ABA) in needles were evaluated using high-performance liquid chromatography (HPLC). We demonstrate that chronic radiation exposure is a significant stress factor that affects both phytohormonal balance and the expression of some important phytohormone- and stress-related genes. We found a tendency toward decreased ABA and auxin concentrations in trees from plots contaminated with radionuclides. The ratio (IAA + IBA + zeatin)/ABA was drastically raised at the most contaminated plots Masany and Kulazhin, reflecting the functional rearrangements of cellular metabolism that ensure plant adaptation under chronic radiation exposure. Changes in gene expression indicated modulation of ABA and Ca2+ signalling pathways, decreased potential of zeatin biosynthesis, and activation of heat shock proteins biosynthesis.

Raffinose catabolism enhances maize waterlogging tolerance by stimulating adventitious root growth and development

Raffinose mitigates plant heat, drought, and cold stresses; however, whether raffinose contributes to plant waterlogging tolerance is unknown. The maize raffinose synthase mutant zmrafs-1 had seedlings that lack raffinose, generated fewer and shorter adventitious roots, and were more sensitive to waterlogging stress, while overexpression of the raffinose synthase gene, ZmRAFS, increased raffinose content, stimulated adventitious root formation, and enhanced waterlogging tolerance of maize seedlings. Transcriptome analysis of null segregant seedlings compared with zmrafs-1, particularly when waterlogged, revealed that the expression of genes related to galactose metabolism and the auxin biosynthetic pathway were up-regulated by raffinose. Additionally, indole-3-acetic acid content was significantly decreased in zmrafs-1 seedlings and increased in ZmRAFS-overexpressing seedlings. Inhibition of the hydrolysis of raffinose by 1-deoxygalactonojirimycin decreased the waterlogging tolerance of maize seedlings, the expression of genes encoding proteins related to auxin transport-related genes, and the indole-3-acetic acid level in the seedlings, indicating that the hydrolysis of raffinose is necessary for maize waterlogging tolerance. These data demonstrate that raffinose catabolism stimulates adventitious root formation via the auxin signaling pathway to enhance maize waterlogging tolerance.

Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50

Auxins, mainly in the form of indole-3-acetic acid (IAA), regulate several aspects of plant and algal growth and development. Consequently, plant and algae-associated bacteria developed the ability to modulate IAA levels, including IAA catabolism. In this work, we present and analyse the genome sequence of the IAA-degrading and marine algae-associated bacterium, Marinomonas sp. NFXS50, analyse its IAA catabolism gene cluster and study the prevalence of IAA catabolism genes in other Marinomonas genomes. Our findings revealed the presence of homologs of the Pseudomonas iac gene cluster, implicated in IAA catabolism, in the genome of strain NFXS50; however, differences were observed in the content and organization of the Marinomonas iac gene cluster when compared to that of the model iac-containing Pseudomonas putida 1290. These variations suggest potential adaptations in the IAA catabolism pathway, possibly influenced by substrate availability and evolutionary factors. The prevalence of iac genes across several Marinomonas species underscores the significance of IAA catabolism in marine environments, potentially influencing plant/algae-bacteria interactions. This study provides novel insights into the IAA catabolism in Marinomonas, laying the groundwork for future investigations into the role of iac genes in Marinomonas physiology and the regulation of marine plant/algae-bacteria interactions.

Overexpression of EgrZFP6 from Eucalyptus grandis increases ROS levels by downregulating photosynthesis in plants

In plants, abiotic stressors are frequently encountered during growth and development. To counteract these challenges, zinc finger proteins play a critical role as transcriptional regulators. The EgrZFP6 gene, which codes for a zinc finger protein of the C2H2 type, was shown to be considerably elevated in the leaves of Eucalyptus grandis seedlings in the current study when they were subjected to a variety of abiotic stimuli, including heat, salinity, cold, and drought. Analysis conducted later showed that in EgrZFP6 transgenic Arabidopsis thaliana, EgrZFP6 was essential for causing hyponastic leaves and controlling the stress response. Furthermore, the transgenic plants showed elevated levels of reactive oxygen species (ROS), such as superoxide and hydrogen peroxide (H2O2). Additionally, in EgrZFP6-overexpressing plants, transcriptome sequencing analysis demonstrated a considerable downregulation of many genes involved in photosynthesis, decreasing electron transport efficiency and perhaps promoting the buildup of ROS. Auxin levels were higher and auxin signal transduction was compromised in the transgenic plants. Stress-related genes were also upregulated in Arabidopsis as a result of EgrZFP6 overexpression. It is hypothesized that EgrZFP6 can downregulate photosynthesis, which would cause the production of ROS in chloroplasts. As a result, this protein may alter plant stress responses and leaf morphology via a retrograde mechanism driven by ROS. These results highlight the significance of zinc finger proteins in this sophisticated process and advance our understanding of the complex link between gene regulation, ROS signaling, and plant stress responses.

Comprehensive transcriptome analysis of Asparagus officinalis in response to varying levels of salt stress

BACKGROUND

Salt stress is a major abiotic factor that affects the distribution and growth of plants. Asparagus officinalis is primarily resistant to salt stress and is suitable for cultivation in saline-alkali soil.

RESULTS

The study integrated the morphology, physiological indexes, and transcriptome of A. officinalis exposed to different levels of NaCl, with the aim of understanding its biological processes under salt stress. The findings indicated that exposure to salt stress led to decreases in the height and weight of A. officinalis plants. Additionally, the levels of POD and SOD, as well as the amounts of MDA, proline, and soluble sugars, showed an increase, whereas the chlorophyll content decreased. Analysis of the transcriptome revealed that 6,203 genes that showed differential expression at different salt-stress levels. Various TFs, including FAR1, MYB, NAC, and bHLH, exhibited differential expression under salt stress. KEGG analysis showed that the DEGs were primarily associated with the plant hormone signal transduction and lignin biosynthesis pathways.

CONCLUSION

These discoveries provide a solid foundation for an in-depth exploration of the pivotal genes, including Aux/IAA, TCH4, COMT, and POD, among others, as well as the pathways involved in asparagus's salt stress responses. Consequently, they have significant implications for the future analysis of the molecular mechanisms underlying asparagus's response to salt stress.

ABSCISIC ACID INSENSITIVE 3 promotes auxin signalling by regulating SHY2 expression to control primary root growth in response to dehydration stress

Plants combat dehydration stress through different strategies including root architectural changes. Here we show that when exposed to varying levels of dehydration stress, primary root growth in Arabidopsis is modulated by regulating root meristem activity. Abscisic acid (ABA) in concert with auxin signalling adjust primary root growth according to stress levels. ABSCISIC ACID INSENSITIVE 3 (ABI3), an ABA-responsive transcription factor, stands at the intersection of ABA and auxin signalling and fine-tunes primary root growth in response to dehydration stress. Under low ABA or dehydration stress, induction of ABI3 expression promotes auxin signalling by decreasing expression of SHY2, a negative regulator of auxin response. This further enhances the expression of auxin transporter gene PIN1 and cell cycle gene CYCB1;1, resulting in an increase in primary root meristem size and root length. Higher levels of dehydration stress or ABA repress ABI3 expression and promote ABSCISIC ACID INSENSITIVE 5 (ABI5) expression. This elevates SHY2 expression, thereby impairing primary root meristem activity and retarding root growth. Notably, ABI5 can promote SHY2 expression only in the absence of ABI3. Such ABA concentration-dependent expression of ABI3 therefore functions as a regulatory sensor of dehydration stress levels and orchestrates primary root growth by coordinating its downstream regulation.

AZGs: a new family of cytokinin transporters

Cytokinins (CKs) are phytohormones structurally similar to purines that play important roles in various aspects of plant physiology and development. The local and long-distance distribution of CKs is very important to control their action throughout the plant body. Over the past decade, several novel CK transporters have been described, many of which have been linked to a physiological function rather than simply their ability to transport the hormone in vitro. Purine permeases, equilibrative nucleotide transporters and ATP-binding cassette transporters are involved in the local and long-range distribution of CK. In addition, members of the Arabidopsis AZA-GUANINE RESISTANT (AZG) protein family, AZG1 and AZG2, have recently been shown to mediate CK uptake at the plasma membrane and endoplasmic reticulum. Despite sharing ∼50% homology, AZG1 and AZG2 have unique transport mechanisms, tissue-specific expression patterns, and subcellular localizations that underlie their distinct physiological functions. AZG2 is expressed in a small group of cells in the overlying tissue around the lateral root primordia, where its expression is induced by auxins and it is involved in the regulation of lateral root growth. AZG1 is ubiquitously expressed, with high levels in the division zone of the root apical meristem. Here, it binds and stabilises the auxin efflux carrier PIN1, thereby shaping root architecture, particularly under salt stress. This review highlights the latest findings on the protein properties, transport mechanisms and cellular functions of this new family of CK transporters and discusses perspectives for future research in this field.

Unveiling nutrient flow-mediated stress in plant roots using an on-chip phytofluidic device

The initial emergence of the primary root from a germinating seed is a pivotal phase that influences a plant's survival. Abiotic factors such as pH, nutrient availability, and soil composition significantly affect root morphology and architecture. Of particular interest is the impact of nutrient flow on thigmomorphogenesis, a response to mechanical stimulation in early root growth, which remains largely unexplored. This study explores the intricate factors influencing early root system development, with a focus on the cooperative correlation between nutrient uptake and its flow dynamics. Using a physiologically as well as ecologically relevant, portable, and cost-effective microfluidic system for the controlled fluid environments offering hydraulic conductivity comparable to that of the soil, this study analyzes the interplay between nutrient flow and root growth post-germination. Emphasizing the relationship between root growth and nitrogen uptake, the findings reveal that nutrient flow significantly influences early root morphology, leading to increased length and improved nutrient uptake, varying with the flow rate. The experimental findings are supported by mechanical and plant stress-related fluid flow-root interaction simulations and quantitative determination of nitrogen uptake using the total Kjeldahl nitrogen (TKN) method. The microfluidic approach offers novel insights into plant root dynamics under controlled flow conditions, filling a critical research gap. By providing a high-resolution platform, this study contributes to the understanding of how fluid-flow-assisted nutrient uptake and pressure affect root cell behavior, which, in turn, induces mechanical stress leading to thigmomorphogenesis. The findings hold implications for comprehending root responses to changing environmental conditions, paving the way for innovative agricultural and environmental management strategies.

Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L

In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.

Drought and salt stress mitigation in crop plants using stress-tolerant auxin-producing endophytic bacteria: a futuristic approach towards sustainable agriculture

Abiotic stresses, especially drought stress and salt stress in crop plants are accelerating due to climate change. The combined impact of drought and salt is anticipated to lead to the loss of up to 50% of arable land globally, resulting in diminished growth and substantial yield losses threatening food security. Addressing the challenges, agriculture through sustainable practices emerges as a potential solution to achieve Zero Hunger, one of the sustainable development goals set by the IUCN. Plants deploy a myriad of mechanisms to effectively address drought and salt stress with phytohormones playing pivotal roles as crucial signaling molecules for stress tolerance. The phytohormone auxin, particularly indole acetic acid (IAA) emerges as a paramount regulator integral to numerous aspects of plant growth and development. During both drought and salt stress conditions, auxin plays crucial roles for tolerance, but stress-induced processes lead to decreased levels of endogenous free auxin in the plant, leading to an urgent need for auxin production. With an aim to augment this auxin deficiency, several researchers have extensively investigated auxin production, particularly IAA by plant-associated microorganisms, including endophytic bacteria. These endophytic bacteria have been introduced into various crop plants subjected to drought or salt stress and potential isolates promoting plant growth have been identified. However, post-identification, essential studies on translational research to advance these potential isolates from the laboratory to the field are lacking. This review aims to offer an overview of stress tolerant auxin-producing endophytic bacterial isolates while identifying research gaps that need to be fulfilled to utilize this knowledge for the formulation of crop-specific and stress-specific endophyte bioinoculants for the plant to cope with auxin imbalance occurring during these stress conditions.

A rapid and robust colorimetric method for measuring relative abundance of auxins in plant tissues

INTRODUCTION

Auxin estimation in plant tissues is a crucial component of auxin signaling studies. Despite the availability of various high-throughput auxin quantification methods like LC-MS, GC-MS, HPLC, biosensors, and DR5-gus/gfp-based assays, auxin quantification remains troublesome because these techniques are very expensive and technology intensive and they mostly involve elaborate sample preparation or require the development of transgenic plants.

OBJECTIVES

To find a solution to these problems, we made use of an old auxin detection system to quantify microbe derived auxins and modified it to effectively measure auxin levels in rice plants.

MATERIALS AND METHODS

Auxins from different tissues of rice plants, including root samples of seedlings exposed to IAA/TIBA or subjected to different abiotic stresses, were extracted in ethanol. The total auxin level was measured by the presently described colorimetric assay and counterchecked by other auxin estimation methods like LC-MS or gus staining of DR5-gus overexpressing lines.

RESULTS

The presented colorimetric method could measure (1) the auxin levels in different tissues of rice plants, thus identifying the regions of higher auxin abundance, (2) the differential accumulation of auxins in rice roots when auxin or its transport inhibitor was supplied exogenously, and (3) the levels of auxin in roots of rice seedlings subjected to various abiotic stresses. The thus obtained auxin levels correlated well with the auxin levels determined by other methods like LC-MS or gus staining and the expression pattern of auxin biosynthesis pathway genes.

CONCLUSIONS

The auxin estimation method described here is simple, rapid, cost-effective, and sensitive and allows for the efficient detection of relative auxin abundances in plant tissues.

An auxin regulated Universal stress protein (TaUSP_3B-1) interacts with TaGolS and provides tolerance under drought stress and ER stress

A previously identified wheat drought stress responsive Universal stress protein, TaUSP_3B-1 has been found to work in an auxin dependent manner in the plant root tissues in the differentiation zone. We also found a novel interacting partner, TaGolS, which physically interacts with TaUSP_3B-1 and colocalizes in the endoplasmic reticulum. TaGolS is a key enzyme in the RFO (Raffinose oligosaccharides) biosynthesis which is well reported to provide tolerance under water deficit conditions. TaUSP_3B-1 overexpression lines showed an early flowering phenotype under drought stress which might be attributed to the increased levels of AtTPPB and AtTPS transcripts under drought stress. Moreover, at the cellular levels ER stress induced TaUSP_3B-1 transcription and provides tolerance in both adaptive and acute ER stress via less ROS accumulation in the overexpression lines. TaUSP_3B-1 overexpression plants had increased silique numbers and a denser root architecture as compared to the WT plants under drought stress.

Identification of ARF genes in Juglans Sigillata Dode and analysis of their expression patterns under drought stress

BACKGROUND

Auxin response factor (ARF), a transcription factors that controls the expression of genes responsive to auxin, plays a key role in the regulation of plant growth and development. Analyses aimed at identifying ARF family genes and characterizing their functions in Juglans sigillata Dode are lacking.

METHODS AND RESULTS

We used bioinformatic approaches to identify members of the J. sigillata ARF gene family and analyze their evolutionary relationships, collinearity, cis-acting elements, and tissue-specific expression patterns. The expression patterns of ARF gene family members under natural drought conditions were also analyzed. The J. sigillata ARF gene family contained 31 members, which were unevenly distributed across 16 chromosomes. We constructed a phylogenetic tree of JsARF genes and other plant ARF genes. Cis-acting elements in the promoters of JsARF were predicted. JsARF28 showed higher expressions in both the roots and leaves. A heat map of the transcriptome data of the cluster analysis under drought stress indicated that JsARF3/9/11/17/20/26 are responsive to drought. The expression of the 11 ARF genes varied under PEG treatment and JsARF18 and JsARF20 were significantly up-regulated.

CONCLUSIONS

The interactions between abiotic stresses and plant hormones are supported by our cumulative data, which also offers a theoretical groundwork for comprehending the ARF mechanism and drought resistance in J. sigillata.

Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses

Abiotic stresses are predominant and main causes of the losses in the crop yield. A complexity of systems biology and involvement of numerous genes in the response to abiotic factors have challenged efforts to create tolerant cultivars with sustainable production. The root is the main organ of the plant and determines a plant tolerance under stressful conditions. In this study, we carried out a meta-analysis of expression datasets from wheat root to identify differentially expressed genes, followed by the weighted gene co-expression network analysis (WGCNA) to construct the weighted gene co-expression network. The aim was to identify consensus differentially expressed genes with regulatory functions, gene networks, and biological pathways involved in response of wheat root to a set of abiotic stresses. The meta-analysis using Fisher method (FDR<0.05) identified consensus 526 DEGs from 55,367 probe sets. Although the annotated expression data are limited for wheat, the functional analysis based on the data from model plants could identify the up-regulated seven regulatory genes involved in chromosome organization and response to oxygen-containing compounds. WGCNA identified four gene modules that were mostly associated with the ribosome biogenesis and polypeptide synthesis. This study's findings enhance our understanding of key players and gene networks related to wheat root response to multiple abiotic stresses.

Humic acid improves wheat growth by modulating auxin and cytokinin biosynthesis pathways

Humic acids have been widely used for centuries to enhance plant growth and productivity. The beneficial effects of humic acids have been attributed to different functional groups and phytohormone-like compounds enclosed in macrostructure. However, the mechanisms underlying the plant growth-promoting effects of humic acids are only partially understood. We hypothesize that the bio-stimulatory effect of humic acids is mainly due to the modulation of innate pathways of auxin and cytokinin biosynthesis in treated plants. A physiological investigation along with molecular characterization was carried out to understand the mechanism of bio-stimulatory effects of humic acid. A gene expression analysis was performed for the genes involved in auxin and cytokinin biosynthesis pathways in wheat seedlings. Furthermore, Arabidopsis thaliana transgenic lines generated by fusing the auxin-responsive DR5 and cytokinin-responsive ARR5 promoter to ß-glucuronidase (GUS) reporter were used to study the GUS expression analysis in humic acid treated seedlings. This study demonstrates that humic acid treatment improved the shoot and root growth of wheat seedlings. The expression of several genes involved in auxin (Tryptophan Aminotransferase of Arabidopsis and Gretchen Hagen 3.2) and cytokinin (Lonely Guy3) biosynthesis pathways were up-regulated in humic acid-treated seedlings compared to the control. Furthermore, GUS expression analysis showed that bioactive compounds of humic acid stimulate endogenous auxin and cytokinin-like activities. This study is the first report in which using ARR5:GUS lines we demonstrate the biostimulants activity of humic acid.

Endogenous melatonin involved in plant salt response by impacting auxin signaling

KEY MESSAGE

The study on melatonin biosynthesis mutant snat1snat2 revealed that endogenous melatonin plays an important role in salt responsiveness by mediating auxin signaling. Melatonin is a pleiotropic signaling molecule, which, besides being involved in multiple growth and developmental processes, also mediates environmental stress responses. However, whether and how endogenous melatonin is involved in salt response has not been determined. In this study, we elucidated the involvement of endogenous melatonin in salt response by investigatiing the impact of salt stress on a double mutant of Arabidopsis (snat1snat2) defective in melatonin biosynthesis genes SNAT1 and SNAT2. This mutant was found to exhibit salt sensitivity, manifested by unhealthy growth, ion imbalance and ROS accumulation under salt stress. Transcriptomic profiles of snat1snat2 revealed that the expression of a large number of salt-responsive genes was affected by SNAT defect, and these genes were closely related to the synthesis of auxin and several signaling pathways. In addition, the salt-sensitive growth phenotype of snat1snat2 was alleviated by the application of exogenous auxin. Our results show that endogenous melatonin may be essential for plant salt tolerance, a function that could be correlated with diverse activity in mediating auxin signaling.

The chromosome-level genome assembly of an endangered herb Bergenia scopulosa provides insights into local adaptation and genomic vulnerability under climate change

BACKGROUND

Global climate change poses severe threats to biodiversity and ecosystem stability. Rapid climate oscillations potentially lead to species geographic range shifts, population declines, and even extinctions. The rare and endangered species, being critical components of regional biodiversity, hold the key to understanding local adaptation and evolutionary processes shaping species distributions. Therefore, assessing the evolutionary mechanisms of local adaptation and population vulnerability under climate change is crucial for developing conservation strategies of endangered species.

RESULTS

In this study, we assembled a high-quality, chromosome-level genome of the rare and endangered herb Bergenia scopulosa in the Qinling Mountains in East Asia and resequenced 37 individual genomes spanning its entire geographic distributional ranges. By integrating population genetics, landscape genomics, and climate datasets, a substantial number of adaptive single-nucleotide polymorphism loci associated with climate variables were identified. The genotype-environment association analysis showed that some cold-tolerant genes have played pivotal roles in cold environmental adaptation of B. scopulosa. These findings are further corroborated through evolutionary analysis of gene family and quantitative PCR validation. Population genomic analysis revealed 2 distinct genetic lineages in B. scopulosa. The western lineage showed higher genomic vulnerability and more rare cold-tolerance alleles, suggesting its heightened sensitivity to impending climate shifts, and should be given priority conservation in the management practices.

CONCLUSIONS

These findings provide novel insights into local adaptation and genomic vulnerability of B. scopulosa under climate change in the Qinling Mountains in East Asia. Additionally, the study also offers valuable guidance for formulating conservation strategies for the rare and endangered plants.

The IAA17.1/HSFA5a module enhances salt tolerance in Populus tomentosa by regulating flavonol biosynthesis and ROS levels in lateral roots

Auxin signaling provides a promising approach to controlling root system architecture and improving stress tolerance in plants. However, how the auxin signaling is transducted in this process remains unclear. The Aux indole-3-acetic acid (IAA) repressor IAA17.1 is stabilized by salinity, and primarily expressed in the lateral root (LR) primordia and tips in poplar. Overexpression of the auxin-resistant form of IAA17.1 (IAA17.1m) led to growth inhibition of LRs, markedly reduced salt tolerance, increased reactive oxygen species (ROS) levels, and decreased flavonol content. We further identified that IAA17.1 can interact with the heat shock protein HSFA5a, which was highly expressed in roots and induced by salt stress. Overexpression of HSFA5a significantly increased flavonol content, reduced ROS accumulation, enhanced LR growth and salt tolerance in transgenic poplar. Moreover, HSFA5a could rescue the defective phenotypes caused by IAA17.1m. Expression analysis showed that genes associated with flavonol biosynthesis were altered in IAA17.1m- and HAFA5a-overexpressing plants. Furthermore, we identified that HSFA5a directly activated the expression of key enzyme genes in the flavonol biosynthesis pathway, while IAA17.1 suppressed HSFA5a-mediated activation of these genes. Collectively, the IAA17.1/HSFA5a module regulates flavonol biosynthesis, controls ROS accumulation, thereby modulating the root system of poplar to adapt to salt stress.

The Contribution of Hormonal Changes to the Protective Effect of Endophytic Bacterium Bacillus subtilis on Two Wheat Genotypes with Contrasting Drought Sensitivities under Osmotic Stress

A comparative analysis was conducted to evaluate the effects of seed priming with endophytic bacterium Bacillus subtilis 10-4 (BS) on the hormonal system and cell wall tolerance (lipid peroxidation (LPO), electrolyte leakage (EL), and root lignin deposition) of two Triticum aestivum L. (wheat) varieties with contrasting drought sensitivities (Ekada 70-drought-tolerant (DT); Salavat Yulaev-drought-sensitive (DS)) under normal conditions and 12% polyethylene glycol-6000 (PEG)-induced osmotic stress. The results showed that under normal conditions, the growth stimulation in wheat plants by BS was attributed to changes in the hormonal balance, particularly an increase in endogenous indole-3-acetic acid (IAA) accumulation. However, under stress, a significant hormonal imbalance was observed in wheat seedlings, characterized by a pronounced accumulation of abscisic acid (ABA) and a decrease in the levels of IAA and cytokinins (CK). These effects were reflected in the inhibition of plant growth. BS exhibited a protective effect on stressed plants, as evidenced by a significantly lower amplitude of stress-induced changes in the hormonal system: maintaining the content of IAA at a level close to the control, reducing stress-induced ABA accumulation, and preventing CK depletion. These effects were further reflected in the normalization of growth parameters in dehydrated seedlings, as well as a decrease in leaf chlorophyll degradation, LPO, and EL, along with an increase in lignin deposition in the basal part of the roots in both genotypes. Overall, the findings demonstrate that BS, producing phytohormones, specifically IAA and ABA, had a more pronounced protective effect on DT plants, as evidenced by a smaller amplitude of stress-induced hormonal changes, higher leaf chlorophyll content, root lignin deposition, and lower cell membrane damage (LPO) and permeability (EL) compared to DS plants.

Auxin homeostasis in plant responses to heavy metal stress

Expeditious industrialization and anthropogenic activities have resulted in large amounts of heavy metals (HMs) being released into the environment. These HMs affect crop yields and directly threaten global food security. Therefore, significant efforts have been made to control the toxic effects of HMs on crops. When HMs are taken up by plants, various mechanisms are stimulated to alleviate HM stress, including the biosynthesis and transport of auxin in the plant. Interestingly, researchers have noted the significant potential of auxin in mediating resistance to HM stress, primarily by reducing uptake of metals, promoting chelation and sequestration in plant tissues, and mitigating oxidative damage. Both exogenous administration of auxin and manipulation of intrinsic auxin status are effective strategies to protect plants from the negative consequences of HMs stress. Regulation of genes and transcription factors related to auxin homeostasis has been shown to be related to varying degrees to the type and concentration of HMs. Therefore, to derive the maximum benefit from auxin-mediated mechanisms to attenuate HM toxicities, it is essential to gain a comprehensive understanding of signaling pathways involved in regulatory actions. This review primarily emphases on the auxin-mediated mechanisms participating in the injurious effects of HMs in plants. Thus, it will pave the way to understanding the mechanism of auxin homeostasis in regulating HM tolerance in plants and become a tool for developing sustainable strategies for agricultural growth in the future.

Genetic Architecture of Salt Tolerance in Cowpea (Vigna unguiculata (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach

Cowpea (Vigna unguiculata (L.) Walp.) is a diploid legume crop used for human consumption, feed for livestock, and cover crops. Earlier reports have shown that salinity has been a growing threat to cowpea cultivation. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify SNP markers and to investigate candidate genes for salt tolerance in cowpea. A total of 331 cowpea genotypes were evaluated for salt tolerance by supplying a solution of 200 mM NaCl in our previous work. The cowpea panel was genotyped using a whole genome resequencing approach, generating 14,465,516 SNPs. Moreover, 5,884,299 SNPs were used after SNP filtering. GWAS was conducted on a total of 296 cowpea genotypes that have high-quality SNPs. BLINK was used for conducting GWAS. Results showed (1) a strong GWAS peak on an 890-bk region of chromosome 2 for leaf SPAD chlorophyll under salt stress in cowpea and harboring a significant cluster of nicotinamide adenine dinucleotide (NAD) dependent epimerase/dehydratase genes such as Vigun02g128900.1, Vigun02g129000.1, Vigun02g129100.1, Vigun02g129200.1, and Vigun02g129500.1; (2) two GWAS peaks associated with relative tolerance index for chlorophyll were identified on chromosomes 1 and 2. The peak on chromosome 1 was defined by a cluster of 10 significant SNPs mapped on a 5 kb region and was located in the vicinity of Vigun01g086000.1, encoding for a GATA transcription factor. The GWAS peak on chromosome 2 was defined by a cluster of 53 significant SNPs and mapped on a 68 bk region of chromosome 2, and (3) the highest GWAS peak was identified on chromosome 3, and this locus was associated with leaf score injury. This peak was within the structure of a potassium channel gene (Vigun03g144700.1). To the best of our knowledge, this is one the earliest reports on the salt tolerance study of cowpea using whole genome resequencing data.

Transcriptomic and physiological comparison of Shatangju (Citrus reticulata) and its late-maturing mutant provides insights into auxin regulation of citrus fruit maturation

Previous studies have shown that abscisic acid (ABA) and ethylene are involved in pulp maturation and peel coloration in the nonclimacteric citrus fruits. There are also signs indicating that other plant hormones may play some roles in citrus fruit ripening. In this study, we compared profiles of genome-wide gene expression and changes in hormones and peel pigments between fruits of Shatangju mandarin (Citrus reticulata Blanco, designated WT) and its natural mutant, Yuenongwanju (designated MT). The MT fruit matures ~2 months later than the WT fruit. Significant differences in fruit diameter, total soluble solids, titratable acid content, chlorophylls and carotenoids were detected between the fruits of the two genotypes at the sampled time points. Genome-wide transcriptome profiling showed that many genes involved in auxin and ABA metabolism and/or signaling pathways were differentially expressed between the MT and the WT fruits. Importantly, the expression of CrYUCCA8 was significantly lower and the expression of CrNCED5 was significantly higher in WT than in MT fruits at 230 and 250 DPA, respectively. In addition, the indole-3-acetic acid (IAA) level in the MT fruit was significantly higher than that in the WT counterpart, whereas a significantly lower level of ABA was detected in the mutant. Treatment of the WT fruit with exogenous IAA significantly delayed fruit maturation. Our results provide experimental evidence supporting the notion that auxin is a negative regulator of fruit maturation in citrus.

PIN2/3/4 auxin carriers mediate root growth inhibition under conditions of boron deprivation in Arabidopsis

The mechanistic basis by which boron (B) deprivation inhibits root growth via the mediation of root apical auxin transport and distribution remains elusive. This study showed that B deprivation repressed root growth of wild-type Arabidopsis seedlings, which was related to higher auxin accumulation (observed with DII-VENUS and DR5-GFP lines) in B-deprived roots. Boron deprivation elevated the auxin content in the root apex, coinciding with upregulation of the expression levels of auxin biosynthesis-related genes (TAA1, YUC3, YUC9, and NIT1) in shoots, but not in root apices. Phenotyping experiments using auxin transport-related mutants revealed that the PIN2/3/4 carriers are involved in root growth inhibition caused by B deprivation. B deprivation not only upregulated the transcriptional levels of PIN2/3/4, but also restrained the endocytosis of PIN2/3/4 carriers (observed with PIN-Dendra2 lines), resulting in elevated protein levels of PIN2/3/4 in the plasma membrane. Overall, these results suggest that B deprivation not only enhances auxin biosynthesis in shoots by elevating the expression levels of auxin biosynthesis-related genes but also promotes the polar auxin transport from shoots to roots by upregulating the gene expression levels of PIN2/3/4, as well as restraining the endocytosis of PIN2/3/4 carriers, ultimately resulting in auxin accumulation in root apices and root growth inhibition.

Recent advances in auxin biosynthesis and homeostasis

The plant proliferation is linked with auxins which in turn play a pivotal role in the rate of growth. Also, auxin concentrations could provide insights into the age, stress, and events leading to flowering and fruiting in the sessile plant kingdom. The role in rejuvenation and plasticity is now evidenced. Interest in plant auxins spans many decades, information from different plant families for auxin concentrations, transcriptional, and epigenetic evidences for gene regulation is evaluated here, for getting an insight into pattern of auxin biosynthesis. This biosynthesis takes place via an tryptophan-independent and tryptophan-dependent pathway. The independent pathway initiated before the tryptophan (trp) production involves indole as the primary substrate. On the other hand, the trp-dependent IAA pathway passes through the indole pyruvic acid (IPyA), indole-3-acetaldoxime (IAOx), and indole acetamide (IAM) pathways. Investigations on trp-dependent pathways involved mutants, namely yucca (1-11), taa1, nit1, cyp79b and cyp79b2, vt2 and crd, and independent mutants of tryptophan, ins are compiled here. The auxin conjugates of the IAA amide and ester-linked mutant gh3, iar, ilr, ill, iamt1, ugt, and dao are remarkable and could facilitate the assimilation of auxins. Efforts are made herein to provide an up-to-date detailed information about biosynthesis leading to plant sustenance. The vast information about auxin biosynthesis and homeostasis is consolidated in this review with a simplified model of auxin biosynthesis with keys and clues for important missing links since auxins can enable the plants to proliferate and override the environmental influence and needs to be probed for applications in sustainable agriculture.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-023-03709-6.

Root system architecture and genomic plasticity to salinity provide insights into salt-tolerant traits in tall fescue

Salinity is detrimental to soil health, plant growth, and crop productivity. Understanding salt tolerance mechanisms offers the potential to introduce superior crops, especially in coastal regions. Root system architecture (RSA) plasticity is vital for plant salt stress adaptation. Tall fescue is a promising forage grass in saline regions with scarce RSA studies. Here, we used the computer-integrated and -automated programs EZ-Rhizo II and ROOT-Vis II to analyze and identify natural RSA variations and adaptability to high salt stress at physiological and genetic levels in 17 global tall fescue accessions. Total root length rather than the number of lateral roots contribute more to water uptake and could be used to separate salt-tolerant (LS-11) and -sensitive accessions (PI531230). Comparative evaluation of LS-11 and PI531230 demonstrated that the lateral root length rather than the main root contributed more towards the total root length in LS-11. Also, high water uptake was associated with a larger lateral root vector and position while low water intake was associated with an insignificant correlation between root length, vector, and position. To examine candidate gene expression, we performed transcriptome and transcription analyses using high-throughput RNA sequencing and real-time quantitative PCR, respectively of the lateral and main roots. The main root displayed more differentially expressed genes than the lateral root. A Poisson comparison of LS-11 vs PI531230 demonstrated significant upregulation of PLASMA MEMBRANE AQUAPORIN 1 and AUXIN RESPONSE FACTOR 22 in both the main and lateral root, which are associated with transmembrane water transport and the auxin-activated signaling system, respectively. There is also an upregulation of BASIC HELIX-LOOP-HELIX 5 in the main root and a downregulation in the lateral root, which is ascribed to sodium ion transmembrane transport, as well as an upregulation of THE MEDIATOR COMPLEX 1 assigned to water transport in the lateral root and a downregulation in the main root. Gene-protein interaction analysis found that more genes interacting with aquaporins proteins were upregulated in the lateral root than in the main root. We inferred that deeper main roots with longer lateral roots emanating from the bottom of the main root were ideal for tall fescue water uptake and salt tolerance, rather than many shallow roots, and that, while both main lateral roots may play similar roles in salt sensing and water uptake, there are intrinsic genomic differences.

Wheat type one protein phosphatase promotes salt and osmotic stress tolerance in arabidopsis via auxin-mediated remodelling of the root system

The control of optimal root growth and plant stress responses depends largely on a variety of phytohormones among which auxin and brassinosteroids (BRs) are the most influential. We have previously reported that the durum wheat type 1 protein phosphatase TdPP1 participates in the control of root growth by modulating BR signaling. In this study, we pursue our understanding of how TdPP1 fulfills this regulatory function on root growth by evaluating the physiological and molecular responses of Arabidopsis TdPP1 over-expressing lines to abiotic stresses. Our results showed that when exposed to 300 mM Mannitol or 100 mM NaCl, the seedlings of TdPP1 over-expressors exhibit modified root architecture with higher lateral root density, and longer root hairs concomitant with a lower inhibition of the primary root growth. These lines also exhibit faster gravitropic response and a decrease in primary root growth inhibition when exposed to high concentrations of exogenous IAA. On another hand, a cross between TdPP1 overexpressors and DR5:GUS marker line was performed to monitor auxin accumulation in roots. Remarkably, the TdPP1 overexpression resulted in an enhanced auxin gradient under salt stress with a higher accumulation in primary and lateral root tips. Moreover, TdPP1 transgenics exhibit a significant induction of a subset of auxin-responsive genes under salt stress conditions. Therefore, our results reveal a role of PP1 in enhancing auxin signaling to help shape greater root plasticity thus improving plant stress resilience.

Salt stress responses and alleviation strategies in legumes: a review of the current knowledge

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.

Biosynthetic Pathways of Hormones in Plants

Phytohormones exhibit a wide range of chemical structures, though they primarily originate from three key metabolic precursors: amino acids, isoprenoids, and lipids. Specific amino acids, such as tryptophan, methionine, phenylalanine, and arginine, contribute to the production of various phytohormones, including auxins, melatonin, ethylene, salicylic acid, and polyamines. Isoprenoids are the foundation of five phytohormone categories: cytokinins, brassinosteroids, gibberellins, abscisic acid, and strigolactones. Furthermore, lipids, i.e., α-linolenic acid, function as a precursor for jasmonic acid. The biosynthesis routes of these different plant hormones are intricately complex. Understanding of these processes can greatly enhance our knowledge of how these hormones regulate plant growth, development, and physiology. This review focuses on detailing the biosynthetic pathways of phytohormones.

Lanthanum Supplementation Alleviates Tomato Root Growth Suppression under Low Light Stress

Supplementation with rare earth elements (REEs) such as lanthanum and cerium has been shown to promote plant elongation and/or increase crop yields. On the other hand, there are reports that REE supplementation of plants has no such effect. The appropriate modes for REE utilization and the underlying mechanism are not fully understood. In this study, we investigated how REE supplementation of plants under low light stress affects plant growth and gene expression. Under low light stress conditions, tomato root elongation was observed to be reduced by about half. This suppression of root elongation was found to be considerably alleviated by 20 mM lanthanum ion supplementation. This effect was plant-species-dependent and nutrient-condition-dependent. Under low light stress, the expression of the genes for phytochrome-interacting factor, which induces auxin synthesis, and several auxin-synthesis-related proteins were markedly upregulated by lanthanum ion supplementation. Thus, we speculate that REE supplementation of plants results in auxin-induced cell elongation and alleviates growth suppression under stress conditions.

Effective root responses to salinity stress include maintained cell expansion and carbon allocation

Acclimation of root growth is vital for plants to survive salt stress. Halophytes are great examples of plants that thrive even under severe salinity, but their salt tolerance mechanisms, especially those mediated by root responses, are still largely unknown. We compared root growth responses of the halophyte Schrenkiella parvula with its glycophytic relative species Arabidopsis thaliana under salt stress and performed transcriptomic analysis of S. parvula roots to identify possible gene regulatory networks underlying their physiological responses. Schrenkiella parvula roots do not avoid salt and experience less growth inhibition under salt stress. Salt-induced abscisic acid levels were higher in S. parvula roots compared with Arabidopsis. Root transcriptomic analysis of S. parvula revealed the induction of sugar transporters and genes regulating cell expansion and suberization under salt stress. ¹⁴ C-labeled carbon partitioning analyses showed that S. parvula continued allocating carbon to roots from shoots under salt stress while carbon barely allocated to Arabidopsis roots. Further physiological investigation revealed that S. parvula roots maintained root cell expansion and enhanced suberization under severe salt stress. In summary, roots of S. parvula deploy multiple physiological and developmental adjustments under salt stress to maintain growth, providing new avenues to improve salt tolerance of plants using root-specific strategies.

Hydrogen sulfide alleviates osmotic stress-induced root growth inhibition by promoting auxin homeostasis

Hydrogen sulfide (H2 S) promotes plant tolerance against various environmental cues, and d-cysteine desulfhydrase (DCD) is an enzymatic source of H2 S to enhance abiotic stress resistance. However, the role of DCD-mediated H2 S production in root growth under abiotic stress remains to be further elucidated. Here, we report that DCD-mediated H2 S production alleviates osmotic stress-mediated root growth inhibition by promoting auxin homeostasis. Osmotic stress up-regulated DCD gene transcript and DCD protein levels and thus H2 S production in roots. When subjected to osmotic stress, a dcd mutant showed more severe root growth inhibition, whereas the transgenic lines DCDox overexpressing DCD exhibited less sensitivity to osmotic stress in terms of longer root compared to the wild-type. Moreover, osmotic stress inhibited root growth through repressing auxin signaling, whereas H2 S treatment significantly alleviated osmotic stress-mediated inhibition of auxin. Under osmotic stress, auxin accumulation was increased in DCDox but decreased in dcd mutant. H2 S promoted auxin biosynthesis gene expression and auxin efflux carrier PIN-FORMED 1 (PIN1) protein level under osmotic stress. Taken together, our results reveal that mannitol-induced DCD and H2 S in roots promote auxin homeostasis, contributing to alleviating the inhibition of root growth under osmotic stress.

Functionalized Hydrogel-Based Wearable Gas and Humidity Sensors

Breathing is an inherent human activity; however, the composition of the air we inhale and gas exhale remains unknown to us. To address this, wearable vapor sensors can help people monitor air composition in real time to avoid underlying risks, and for the early detection and treatment of diseases for home healthcare. Hydrogels with three-dimensional polymer networks and large amounts of water molecules are naturally flexible and stretchable. Functionalized hydrogels are intrinsically conductive, self-healing, self-adhesive, biocompatible, and room-temperature sensitive. Compared with traditional rigid vapor sensors, hydrogel-based gas and humidity sensors can directly fit human skin or clothing, and are more suitable for real-time monitoring of personal health and safety. In this review, current studies on hydrogel-based vapor sensors are investigated. The required properties and optimization methods of wearable hydrogel-based sensors are introduced. Subsequently, existing reports on the response mechanisms of hydrogel-based gas and humidity sensors are summarized. Related works on hydrogel-based vapor sensors for their application in personal health and safety monitoring are presented. Moreover, the potential of hydrogels in the field of vapor sensing is elucidated. Finally, the current research status, challenges, and future trends of hydrogel gas/humidity sensing are discussed.

Efficient strategies for controlled release of nanoencapsulated phytohormones to improve plant stress tolerance

Climate change due to different human activities is causing adverse environmental conditions and uncontrolled extreme weather events. These harsh conditions are directly affecting the crop areas, and consequently, their yield (both in quantity and quality) is often impaired. It is essential to seek new advanced technologies to allow plants to tolerate environmental stresses and maintain their normal growth and development. Treatments performed with exogenous phytohormones stand out because they mitigate the negative effects of stress and promote the growth rate of plants. However, the technical limitations in field application, the putative side effects, and the difficulty in determining the correct dose, limit their widespread use. Nanoencapsulated systems have attracted attention because they allow a controlled delivery of active compounds and for their protection with eco-friendly shell biomaterials. Encapsulation is in continuous evolution due to the development and improvement of new techniques economically affordable and environmentally friendly, as well as new biomaterials with high affinity to carry and coat bioactive compounds. Despite their potential as an efficient alternative to phytohormone treatments, encapsulation systems remain relatively unexplored to date. This review aims to emphasize the potential of phytohormone treatments as a means of enhancing plant stress tolerance, with a specific focus on the benefits that can be gained through the improved exogenous application of these treatments using encapsulation techniques. Moreover, the main encapsulation techniques, shell materials and recent work on plants treated with encapsulated phytohormones have been compiled.

Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice

Introduction

Saline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve rice saline-alkali tolerance at the germination stage.

Methods

To understand the genetic basis of saline-alkali tolerance and facilitate breeding efforts for developing saline-alkali tolerant rice varieties, the genetic basis of rice saline-alkali tolerance was dissected by phenotyping seven germination-related traits of 736 diverse rice accessions under the saline-alkali stress and control conditions using genome-wide association and epistasis analysis (GWAES).

Results

Totally, 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified as significantly associated with saline-alkali tolerance, which explained a significant portion of the total phenotypic variation of the saline-alkali tolerance traits in the 736 rice accessions. Most of these QTNs were located in genomic regions either harboring saline-alkali tolerance QTNs or known genes for saline-alkali tolerance reported previously. Epistasis as an important genetic basis of rice saline-alkali tolerance was validated by genomic best linear unbiased prediction in which inclusion of both main-effect and epistatic QTNs showed a consistently better prediction accuracy than either main-effect or epistatic QTNs alone. Candidate genes for two pairs of important epistatic QTNs were suggested based on combined evidence from the high-resolution mapping plus their reported molecular functions. The first pair included a glycosyltransferase gene LOC_Os02g51900 (UGT85E1) and an E3 ligase gene LOC_Os04g01490 (OsSIRP4), while the second pair comprised an ethylene-responsive transcriptional factor, AP59 (LOC_Os02g43790), and a Bcl-2-associated athanogene gene, OsBAG1 (LOC_Os09g35630) for salt tolerance. Detailed haplotype analyses at both gene promoter and CDS regions of these candidate genes for important QTNs identified favorable haplotype combinations with large effects on saline-alkali tolerance, which can be used to improve rice saline-alkali tolerance by selective introgression.

Discussion

Our findings provided saline-alkali tolerant germplasm resources and valuable genetic information to be used in future functional genomic and breeding efforts of rice saline-alkali tolerance at the germination stage.

Regulatory networks of hormone-involved transcription factors and their downstream pathways during somatic embryogenesis of Arabidopsis thaliana

Somatic embryogenesis (SE) depends on a variety of developmental pathways that are influenced by several environmental factors. Therefore, it is important to understand the relationship between environmental and genetic factors by identifying the gene networks involved in SE through gene set enrichment analysis (GSEA). For determination of SE effective transcription factors, upstream sequences of core-enriched genes were analyzed. The results indicated that response to hormones is one of the biological pathways activated by the enriched TFs at all stages of somatic embryogenesis and about half of the hormonal pathways were enriched. On the fifth day after 2,4-Dichlorophenoxyacetic acid (2,4-D) treatment, the activity of hormone-affecting genes reached its maximum. At this time, more transcription factors regulated the enriched genes compared to the other stages of somatic embryogenesis. MYBs, AT-HOOKs, and HSFs are the main families of transcription factors which affect core-enriched genes during SE. CCA1, PRR7, and TOC1 and their related genes at the center of protein-protein interaction of SE-key transcription factors, involved in the regulation of the circadian clock. Gene expression analysis of CCA1, PRR7, and TOC1 revealed that the genes involved in circadian clock reached their maximum activity when embryonic cells formed. Also, auxin response elements were identified at the upstream of SE-circadian clock transcription factors, indicating that they might mediate between auxin signaling and SE-related hormonal pathways as well as SE marker genes such as AGL15, BBM, and LECs. Based on these results, it is possible that the cellular circadian rhythm activates various developmental pathways under the influence of auxin signal transduction and their interactions determine the induction of somatic embryogenesis. According to the results of this study, modifying pathways affected by SE-related transcription factors such as circadian rhythm may result in cell reprogramming and increase somatic embryogenesis efficiency.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03546-7.

Salinity-Triggered Responses in Plant Apical Meristems for Developmental Plasticity

Salt stress severely affects plant growth and development. The plant growth and development of a sessile organism are continuously regulated and reformed in response to surrounding environmental stress stimuli, including salinity. In plants, postembryonic development is derived mainly from primary apical meristems of shoots and roots. Therefore, to understand plant tolerance and adaptation under salt stress conditions, it is essential to determine the stress response mechanisms related to growth and development based on the primary apical meristems. This paper reports that the biological roles of microRNAs, redox status, reactive oxygen species (ROS), nitric oxide (NO), and phytohormones, such as auxin and cytokinin, are important for salt tolerance, and are associated with growth and development in apical meristems. Moreover, the mutual relationship between the salt stress response and signaling associated with stem cell homeostasis in meristems is also considered.

Transcriptional regulatory network of high-value active ingredients in medicinal plants

High-value active ingredients in medicinal plants have attracted research attention because of their benefits for human health, such as the antimalarial artemisinin, anticardiovascular disease tanshinones, and anticancer Taxol and vinblastine. Here, we review how hormones and environmental factors promote the accumulation of active ingredients, thereby providing a strategy to produce high-value drugs at a low cost. Focusing on major hormone signaling events and environmental factors, we review the transcriptional regulatory network mediating biosynthesis of representative active ingredients. In this network, many transcription factors (TFs) simultaneously control multiple synthase genes; thus, understanding the molecular mechanisms affecting transcriptional regulation of active ingredients will be crucial to developing new breeding possibilities.

Boron supply restores aluminum-blocked auxin transport by the modulation of PIN2 trafficking in the root apical transition zone

The supply of boron (B) alleviates the toxic effects of aluminum (Al) on root growth; however, the mechanistic basis of this process remains elusive. This study filled this knowledge gap, demonstrating that boron modifies auxin distribution and transport in Al-exposed Arabidopsis roots. In B-deprived roots, treatment with Al induced an increase in auxin content in the root apical meristem zone (MZ) and transition zone (TZ), whereas in the elongation zone (EZ) the auxin content was decreased beyond the level required for adequate growth. These distribution patterns are explained by the fact that basipetal auxin transport from the TZ to the EZ was disrupted by Al-inhibited PIN-FORMED 2 (PIN2) endocytosis. Experiments involving the modulation of protein biosynthesis by cycloheximide (CHX) and transcriptional regulation by cordycepin (COR) demonstrated that the Al-induced increase of PIN2 membrane proteins was dependent upon the inhibition of PIN2 endocytosis, rather than on the transcriptional regulation of the PIN2 gene. Experiments reporting on the profiling of Al³⁺ and PIN2 proteins revealed that the inhibition of endocytosis of PIN2 proteins was the result of Al-induced limitation of the fluidity of the plasma membrane. The supply of B mediated the turnover of PIN2 endosomes conjugated with indole-3-acetic acid (IAA), and thus restored the Al-induced inhibition of IAA transport through the TZ to the EZ. Overall, the reported results demonstrate that boron supply mediates PIN2 endosome-based auxin transport to alleviate Al toxicity in plant roots.