Zinc solubilization and organic acid production by the entomopathogenic fungus, Metarhizium pingshaense sheds light on its key ecological role in the environment

We report for the first-time higher zinc (Zn) solubilization efficiency and plant growth promotion by an entomopathogenic fungus (EPF), Metarhizium pingshaense IISR-EPF-14, which was earlier isolated from Conogethes punctiferalis, a pest of global importance. The Zn solubilizing efficiency of the fungus varied depending on the type of insoluble source of Zn used, which was observed to be 1.6 times higher in Zn3(PO4)2-amended media compared to ZnO media. In liquid media, there was a 6.2-fold increase in available Zn in ZnO-amended media, whereas a 20.2-fold increase in available Zn was recorded in Zn3(PO4)2 medium. We ascribe the production of various organic acids such as gluconic, keto-gluconic, oxalic, tartaric, malonic, succinic and formic acids, which in general, interact with insoluble Zn sources and make them soluble by forming metal cations and displacing anions as the major mechanism for Zn solubilization by M. pingshaense. However, the type and amount of organic acid produced in the media varied depending on the source of Zn used and the incubation period. Application of the fungus alone and in combination with insoluble Zn sources enhanced various plant growth parameters in rice and cardamom plants. Moreover, the uptake of Zn in rice plants was enhanced up to ~2.5-fold by fungal application. The fungus also exhibited various other plant growth-promoting traits, such as production of Indole-3-acetic acid, ammonia, siderophores, solubilization of mineral phosphate, and production of hydrolytic enzymes such as α-amylase, protease, and pectinase. Hence, apart from its use as a biological control agent, M. pingshaense has the potential to be used as a bio-fortifier to enhance the solubilization and uptake of Zn from nutrient poor soils under field conditions. Our findings shed light on the broader ecological role played by this fungus and widen its scope for utilization in sustainable agriculture.

BRZ-INSENSITIVE-LONG HYPOCOTYL8 inhibits kinase-mediated phosphorylation to regulate brassinosteroid signaling

Glycogen synthase kinase 3 (GSK3) is an evolutionarily conserved serine/threonine protein kinase in eukaryotes. In plants, the GSK3-like kinase BRASSINOSTEROID-INSENSITIVE 2 (BIN2) functions as a central signaling node through which hormonal and environmental signals are integrated to regulate plant development and stress adaptation. BIN2 plays a major regulatory role in brassinosteroid (BR) signaling and is critical for phosphorylating/inactivating BRASSINAZOLE-RESISTANT 1 (BZR1), also known as BRZ-INSENSITIVE-LONG HYPOCOTYL 1 (BIL1), a master transcription factor of BR signaling, but the detailed regulatory mechanism of BIN2 action has not been fully revealed. In this study, we identified BIL8 as a positive regulator of BR signaling and plant growth in Arabidopsis (Arabidopsis thaliana). Genetic and biochemical analyses showed that BIL8 is downstream of the BR receptor BRASSINOSTEROID-INSENSITIVE 1 (BRI1) and promotes the dephosphorylation of BIL1/BZR1. BIL8 interacts with and inhibits the activity of the BIN2 kinase, leading to the accumulation of dephosphorylated BIL1/BZR1. BIL8 suppresses the cytoplasmic localization of BIL1/BZR1, which is induced via BIN2-mediated phosphorylation. Our study reveals a regulatory factor, BIL8, that positively regulates BR signaling by inhibiting BIN2 activity.

WRKY transcription factors modulate flowering time and response to environmental changes

WRKY transcription factors (TFs), originating in green algae, regulate flowering time and responses to environmental changes in plants. However, the molecular mechanisms underlying the role of WRKY TFs in the correlation between flowering time and environmental changes remain unclear. Therefore, this review summarizes the association of WRKY TFs with flowering pathways to accelerate or delay flowering. WRKY TFs are implicated in phytohormone pathways, such as ethylene, auxin, and abscisic acid pathways, to modulate flowering time. WRKY TFs can modulate salt tolerance by regulating flowering time. WRKY TFs exhibit functional divergence in modulating environmental changes and flowering time. In summary, WRKY TFs are involved in complex pathways and modulate response to environmental changes, thus regulating flowering time.

Low-cost and efficient strategy for brown algal hydrolysis: Combination of alginate lyase and cellulase

Brown algae are rich in biostimulants that not only stimulate the overall development and growth of plants but also have great beneficial effects on the whole soil-plant system. However, alginate, the major component of brown algae, is comparatively difficult to degrade. The cost of preparing alginate oligosaccharides (AOSs) is still too high to produce seaweed fertilizer. In this work, the marine bacterium Vibrio sp. B1Z05 is found to be capable of efficient alginate depolymerization and harbors an extended pathway for alginate metabolism. The B1Z05 extracellular cell-free supernatant exhibited great potential for AOS production at low cost, which, together with cellulase, can efficiently hydrolyze seaweed. The brown algal hydrolysis rates were significantly greater than those of the commercial alginate lyase product CE201, and the obtained seaweed extracts were rich in phytohormones. This work provides a low-cost but efficient strategy for the sustainable production of desirable AOSs and seaweed fertilizer.

Maize multi-omics reveal leaf water status controlling of differential transcriptomes, proteomes and hormones as mechanisms of age-dependent osmotic stress response in leaves

Drought-induced osmotic stress severely affects the growth and yield of maize. However, the mechanisms underlying the different responses of young and old maize leaves to osmotic stress remain unclear. To gain a systematic understanding of age-related stress responses, we compared osmotic-stress-induced changes in maize leaves of different ages using multi-omics approaches. After short-term osmotic stress, old leaves suffered more severe water deficits than young leaves. The adjustments of transcriptomes, proteomes, and hormones in response to osmotic stress were more dynamic in old leaves. Metabolic activities, stress signaling pathways, and hormones (especially abscisic acid) responded to osmotic stress in an age-dependent manner. We identified multiple functional clusters of genes and proteins with potential roles in stress adaptation. Old leaves significantly accumulated stress proteins such as dehydrin, aquaporin, and chaperones to cope with osmotic stress, accompanied by senescence-like cellular events, whereas young leaves exhibited an effective water conservation strategy mainly by hydrolyzing transitory starch and increasing proline production. The stress responses of individual leaves are primarily determined by their intracellular water status, resulting in differential transcriptomes, proteomes, and hormones. This study extends our understanding of the mechanisms underlying plant responses to osmotic stress.

Papiliotrema flavescens, a plant growth-promoting fungus, alters root system architecture and induces systemic resistance through its volatile organic compounds in Arabidopsis

The current trend in agricultural development is the establishment of sustainable agricultural systems. This involves utilizing and implementing eco-friendly biofertilizers and biocontrol agents as alternatives to conventional fertilizers and pesticides. A plant growth-promoting fungal strain, that could alter root system architecture and promote the growth of Arabidopsis seedlings in a non-contact manner by releasing volatile organic compounds (VOCs) was isolated in this study. 26S rDNA sequencing revealed that the strain was a yeast-like fungus, Papiliotrema flavescens. Analysis of plant growth-promoting traits revealed that the fungus could produce indole-3-acetic acid and ammonia and fix nitrogen. Transcriptome analysis in combination with inhibitor experiments revealed that P. flavescens VOCs triggered metabolic alterations, promoted auxin accumulation and distribution in the roots, and coordinated ethylene signaling, thus inhibiting primary root elongation and inducing lateral root formation in Arabidopsis. Additionally, transcriptome analysis and fungal infection experiments confirmed that pretreatment with P. flavescens stimulated the defense response of Arabidopsis to boost its resistance to the pathogenic fungus Botrytis cinerea. Solid-phase microextraction, which was followed by gas chromatography-mass spectrometry analysis, identified three VOCs (acetoin, naphthalene and indole) with significant plant growth-promoting attributes. Their roles were confirmed using further pharmacological experiments and upregulated expression of auxin- and ethylene-related genes. Our study serves as an essential reference for utilizing P. flavescens as a potential biological fertilizer and biocontrol agent.

Polysome-bound mRNAs and translational mechanisms regulate drought tolerance in rice

Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. Drought stress at the anthesis stage in rice affects productivity due to the inefficiency of protein synthesis machinery. The effect of translational mechanisms on different pathways involved in cellular tolerance plays an important role. We report differential responses of translation-associated mechanisms in rice using polysome bound mRNA sequencing at anthesis stage drought stress in resistant Apo and sensitive IR64 genotypes. Apo maintained higher polysomes with 60 S-to-40 S and polysome-to-monosome ratios which directly correlate with protein levels under stress. IR64 has less protein levels under stress due to defective translation machinery and reduced water potential. Many polysome-bound long non-coding RNAs (lncRNA) were identified in both genotypes under drought, influencing translation. Apo had higher levels of N6-Methyladenosine (m6A) mRNA modifications that contributed for sustained translation. Translation machinery in Apo could maintain higher levels of photosynthetic machinery-associated proteins in drought stress, which maintain gas exchange, photosynthesis and yield under stress. The protein stability and ribosome biogenesis mechanisms favoured improved translation in Apo. The phytohormone signalling and transcriptional responses were severely affected in IR64. Our results demonstrate that, the higher translation ability of Apo favours maintenance of photosynthesis and physiological responses that are required for drought stress adaptation.

Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils

Background

Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils.

Results

Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs.

Conclusions

We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.

Waterlogging faced by bulbil expansion improved the growth of Pinellia ternata and its effect reinforced by brassinolide

The bulbil expansion of P. ternata is a key period for its yield formation, and the process of bulbil expansion is often subjected to short-term heavy precipitation. It is not clear whether the short-term waterlogging can affect bulbil expansion. Brassinolide (BR) is widely believed to enhance plant tolerance to abiotic stress. The study investigated the effects of normal water (C), waterlogging (W), waterlogging + BR (W + B), waterlogging + propiconazole (W + P) on P. ternata at the bulbil expansion period in order to assess P. ternata's ability to cope with waterlogging during the bulbil expansion stage and the regulation effects of BR on the process. The biomass of P. ternata was significantly increased after waterlogging. W treatment significantly reduced the H2O2 and MDA contents, the rate of O2⋅- production and the activities of antioxidant enzymes compared with the C group. AsA and GSH contents were significantly reduced by W treatment. However, the ratios of AsA/DHA and GSH/GSSG were slightly affected by W treatment. The rate of O2∙- production and H2O2 content in W + B group were significantly lower than those in W group. The POD, APX, and GR activities, and GSH content in W + B group were evidently increased compared with the W group. Soluble sugar and active ingredients contents were significantly increased after waterlogging, and the enhancement was reinforced by BR. In conclusion, waterlogging reduced oxidative stress in P. ternata under the experimental conditions. BR treatment under waterlogging had a positive effect on P. ternata by enhancing antioxidant capacity and promoting the accumulation of soluble sugars and active ingredients.

A comprehensive review of TGA transcription factors in plant growth, stress responses, and beyond

TGA transcription factors (TFs), belonging to the D clade of the basic region leucine zipper (bZIP) family, exhibit a specific ability to recognize and bind to regulatory elements with TGACG as the core recognition sequence, enabling the regulation of target gene expression and participation in various biological regulatory processes. In plant growth and development, TGA TFs influence organ traits and phenotypes, including initial root length and flowering time. They also play a vital role in responding to abiotic stresses like salt, drought, and cadmium exposure. Additionally, TGA TFs are involved in defending against potential biological stresses, such as fungal bacterial diseases and nematodes. Notably, TGA TFs are sensitive to the oxidative-reductive state within plants and participate in pathways that aid in the elimination of reactive oxygen species (ROS) generated during stressful conditions. TGA TFs also participate in multiple phytohormonal signaling pathways (ABA, SA, etc.). This review thoroughly examines the roles of TGA TFs in plant growth, development, and stress response. It also provides detailed insights into the mechanisms underlying their involvement in physiological and pathological processes, and their participation in plant hormone signaling. This multifaceted exploration distinguishes this review from others, offering a comprehensive understanding of TGA TFs.

Genome-wide identification of B-box zinc finger (BBX) gene family in Medicago sativa and their roles in abiotic stress responses

BACKGROUND

B-box (BBX) family is a class of zinc finger transcription factors (TFs) that play essential roles in regulating plant growth, development, as well as abiotic stress. However, no systematic analysis of BBX genes has yet been conducted in alfalfa (Medica go sativa L.), and their functions have not been elucidated up to now.

RESULTS

In this study, 28 MsBBX genes were identified from the alfalfa genome, which were clustered into 4 subfamilies according to an evolutionary tree of BBX proteins. Exon-intron structure and conserved motif analysis reflected the evolutionary conservation of MsBBXs in alfalfa. Collinearity analysis showed that segmental duplication promoted the expansion of the MsBBX family. Analysis of cis-regulatory elements suggested that the MsBBX genes possessed many growth/development-, light-, phytohormone-, and abiotic stress-related elements. MsBBX genes were differentially expressed in leaves, flowers, pre-elongated stems, elongated stems, roots and nodules, and most MsBBXs were remarkably induced by drought, salt and various plant growth regulators (ABA, JA, and SA). Further functional verification demonstrated that overexpressing of the MsBBX11 gene clearly promoted salt tolerance in transgenic Arabidopsis by regulating growth and physiological processes of seedlings.

CONCLUSIONS

This research provides insights into further functional research and regulatory mechanisms of MsBBX family genes under abiotic stress of alfalfa.

AsHSP26.2, a creeping bentgrass chloroplast small heat shock protein positively regulates plant development

KEY MESSAGE

The creeping bentgrass small heat shock protein AsHSP26.2 positively regulates plant growth and is a novel candidate for use in crop genetic engineering for enhanced biomass production and grain yield. Small heat shock proteins (sHSPs), a family of proteins with high level of diversity, significantly influence plant stress tolerance and plant development. We have cloned a creeping bentgrass chloroplast-localized sHSP gene, AsHSP26.2 responsive to IAA, GA and 6-BA stimulation. Transgenic creeping bentgrass overexpressing AsHSP26.2 exhibited significantly enhanced plant growth with increased stolon number and length as well as enlarged leaf blade width and leaf sheath diameters, but inhibited leaf trichomes initiation and development in the abaxial epidermis. These phenotypes are completely opposite to those displayed in the transgenic plants overexpressing AsHSP26.8, another chloroplast sHSP26 isoform that contains additional seven amino acids (AEGQGDG) between the consensus regions III and IV (Sun et al., Plant Cell Environ 44:1769-1787, 2021). Furthermore, AsHSP26.2 overexpression altered phytohormone biosynthesis and signaling transduction, resulting in elevated auxin and gibberellins (GA) accumulation. The results obtained provide novel insights implicating the sHSPs in plant growth and development regulation, and strongly suggest AsHSP26.2 to be a novel candidate for use in crop genetic engineering for enhanced plant biomass production and grain yield.

Salicylic acid enhances cell growth, fatty acid and astaxanthin production in heterotrophic Chromochloris zofingiensis without reactive oxygen species elevation

BACKGROUND

The induction of lipid and astaxanthin accumulation in microalgae is often achieved through abiotic stress. However, this approach usually leads to oxidative stress, which results in relatively low growth rate. Phytohormones, as important small molecule signaling substances, not only affect the growth and metabolism of microalgae but also influence the intracellular reactive oxygen species level. This study aimed to screen phytohormones that could promote the fatty acids and astaxanthin yield of heterotrophic Chromochloris zofingiensis without causing oxidative damage, and further investigate the underlying mechanisms.

RESULTS

In the present study, among all the selected phytohormones, the addition of exogenous salicylic acid (SA) could effectively promote cell growth along with the yield of total fatty acids (TFA) and astaxanthin in heterotrophic C. zofingiensis. Notably, the highest yields of TFA and astaxanthin were achieved at 100 μM SA, 43% and 97.2% higher compared with the control, respectively. Interestingly, the intracellular reactive oxygen species (ROS) levels, which are usually increased with elevated TFA content under abiotic stresses, were significantly decreased by SA treatment. Comparative transcriptome analysis unveiled significant alterations in overall carbon metabolism by SA. Specifically, the upregulation of fatty acid synthesis pathway, upregulation of β-carotene-4-ketolase (BKT) in carotenoid synthesis aligned with biochemical findings. Weighted gene co-expression network analysis highlighted ABC transporters and GTF2B-like transcription factor as potential key regulators.

CONCLUSION

This study found that salicylic acid can serve as an effective regulator to promote the celling growth and accumulation of fatty acids and astaxanthin in heterotrophic C. zofingiensis without ROS elevation, which provides a promising approach for heterotrophic production of TFA and astaxanthin without growth inhibition.

Rapid profiling of cytokinins using supercritical fluid chromatography coupled with tandem mass spectrometry

BACKGROUND

The determination of plant hormones is still a very challenging analytical discipline, mainly due to their low concentration in complex plant matrices. Therefore, the involvement of very sensitive high-throughput techniques is required. Cytokinins (CKs) are semi-polar basic plant hormones regulating plant growth and development. Modern methods for CK determination are currently based on ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), which enables the separation of CK isomeric forms occurring endogenously in plants. Here, ultra-high performance supercritical fluid chromatography coupled with tandem mass spectrometry (UHPSFC-MS/MS) was used for the simultaneous determination of 37 CK metabolites.

RESULTS

The chromatographic conditions were tested on three different columns with various retention mechanisms. Hybrid silica modified with 2-picolylamine was selected as the stationary phase. Several parameters such as column temperature, back pressure regulation, mobile phase composition and make-up solvent were investigated to achieve efficient separation of CK isomers and reasonable sensitivity. Compared to UHPLC-MS/MS, a 9-min chromatographic analysis using a mobile phase of supercritical CO2 and 5 mM ammonia in methanol represents a three-fold acceleration of total run time. The quantification limit of UHPSFC-MS/MS method was in the range of 0.03-0.19 fmol per injection and the method validation showed high accuracy and precision (below 15 % for most analytes). The method was finally applied to the complex plant matrix of the model plant Arabidopsis thaliana and the obtained profiles of CK metabolites were compared with the results from the conventional UHPLC-MS/MS method.

SIGNIFICANCE

The presented work offers a novel approach for quantification of endogenous CKs in plants. Compared to the conventional UHPLC-MS/MS, the total run time is shorter and the matrix effect lower for the key CK metabolites. This approach opens the opportunity to utilize UHPSFC-MS/MS instrumentation for targeted plant hormonomics including other plant hormone families.

Tomato growth and physiology as well as soil physicochemical and biological properties affected by ozonated water in a saline agroecosystem

Current trends in agriculture are focused on implementing sustainable practices that avoid the use of chemical compounds. It is important to propose environmentally friendly methods, which may enhance plant growth physiology and yield without affecting soil microbial community as much. In this context, irrigation with ozonated water could be a potential strategy to reduce some chemical compounds in soils due to the degradative power of ozone. Here, we studied the impact of irrigation with ozonated water on the microbial community of a Mediterranean soil, and on Solanum lycopersicum L. agro-physiology and productivity in a greenhouse experiment. To this end, we evaluated: i) soil physicochemical properties, soil enzyme activities, microbial biomass via fatty acid analysis, microbial diversity (via amplicon sequencing), and ii) the nutrient content, physiology, phytohormone content, yield, and fruit quality of tomato plants. Our results indicate that soil physicochemical properties were significantly affected by the irrigation with ozonated water (OZ). We observed an increase in the content of total organic carbon (TOC), water-soluble nitrogen (WSN) and ammonium, and a decrease in soil pH due to the OZ treatment. In addition, a significant increase in alkaline phosphatase and fungal and bacterial biomass was also observed in the OZ treatment. It was observed that the prokaryotic community structure was affected by the OZ treatment, while that of fungi was undisturbed. The OZ treatment increased the photosynthetic rates of tomato plants and maintained water conditions when compared to control plants. The increased trans-Zeatin riboside (tZ-Rib) could provide rapid apical and root growth allowing adaptation to the new growing conditions. However, a more in-depth study on the physiological response of the plant to this treatment would be of interest, as it would help with the implementation of this strategy in agricultural fields in a safe manner, and with obtaining higher plant yields.

The miR156-SPL4/SPL9 module regulates leaf and lateral branch development in Betula platyphylla

The miR156 gene is known to play an important role in regulating growth and development in plants. This gene is involved in the transition from juvenile to adult stages, leaf morphology, and root development, among other processes. While the function of miR156 is similar in many plants, there are also differences in the function of this gene between herbaceous and native species. We obtained BpmiR156 overexpression transgenic lines in Betula platyphylla, and the transgenic lines exhibited traits such as delayed development, dwarfism, increased leaf epidermal hairs, larger leaf basal angle and altered stem curvature, which were highly consistent with the overexpression miR156 in Arabidopsis, rice and tomato. However, we also observed a lack of apical dominance, increased number of lateral branches and increased diameter of lateral branches in transgenic B. platyphylla, which is different from the effects reported in other plants. Transgenic plants showed changes in the distribution of IAA, GA3, and Zeatin in lateral branches and main stem, and the ratio of the content of the three hormones was significantly higher than in the non-transgenic plants served as control. Additionally, overexpression of BpmiR156 caused down-regulation of BpSPL4 and BpSPL9 expression, as well as differential expression of genes involved in auxin and cytokinin synthesis such as BpARR3, BpARR11 and BpmiR172.

The response of rhubarb to smut infection is revealed through a comparative transcriptome and metabolome study

MAIN CONCLUSION

Integrated transcriptome and metabolome analysis have unveiled the physiological and molecular responses of rhubarb to infection by smut fungi. Rhubarb is an important medicinal plant that is easily infected by smut fungi during its growth. Thus far, no research on the influence of smut fungi on the growth of rhubarb and its secondary metabolism has been conducted. In this study, petioles of Chinese rhubarb (Rheum officinale) [healthy or infected with smut fungus (Thecaphora schwarzmaniana)] were characterized. Microscopic structure, global gene expression profiling, global metabolic profiling, and key enzyme activity and metabolite levels in infected plants were analyzed. Infection by smut fungi resulted in numerous holes inside the petiole tissue and led to visible tumors on the external surface of the petiole. Through metabolic changes, T. schwarzmaniana induced the production of specific sugars, lipids, and amino acids, and inhibited the metabolism of phenolics and flavonoids in R. officinale. The concentrations of key medicinal compounds (anthraquinones) were decreased because of smut fungus infection. In terms of gene expression, the presence of T. schwarzmaniana led to upregulation of the genes associated with nutrient (sugar, amino acid, etc.) transport and metabolism. The gene expression profiling showed a stimulated cell division activity (the basis of tumor formation). Although plant antioxidative response was enhanced, the plant defense response against pathogen was suppressed by T. schwarzmaniana, as indicated by the expression profiling of genes involved in biotic and abiotic stress-related hormone signaling and the synthesis of plant disease resistance proteins. This study demonstrated physiological and molecular changes in R. officinale under T. schwarzmaniana infection, reflecting the survival tactics employed by smut fungus for parasitizing rhubarb.

Jasmonates and salicylic acid: Evolution of defense hormones in land plants

The emergence of plant hormone signaling pathways is deeply intertwined with land plant evolution. In angiosperms, two plant hormones, salicylic Acid (SA) and Jasmonates (JAs), play a key role in plant defense, where JAs-mediated defenses are typically activated in response to herbivores and necrotrophic pathogens, whereas SA is prioritized against hemi/biotrophic pathogens. Thus, studying the evolution of SA and JAs and their crosstalk is essential to understand the evolution of molecular plant-microbe interactions (EvoMPMI) in land plants. Recent advances in the evolution of SA and JAs biosynthesis, signaling, and crosstalk in land plants illustrated that the insight gained in angiosperms does not necessarily apply to non-seed plant lineages, where the receptors perceive different ligands and the hormones activate pathways independently on the canonical receptors. In this review, recent findings on the two main defense hormones (JAs and SA) in non-seed plants, including functional studies in the bryophyte model Marchantia polymorpha, will be discussed.

Abscisic acid biosynthesis is necessary for full auxin effects on hypocotyl elongation

In concert with other phytohormones, auxin regulates plant growth and development. However, how auxin and other phytohormones coordinately regulate distinct processes is not fully understood. In this work, we uncover an auxin-abscisic acid (ABA) interaction module in Arabidopsis that is specific to coordinating activities of these hormones in the hypocotyl. From our forward genetics screen, we determine that ABA biosynthesis is required for the full effects of auxin on hypocotyl elongation. Our data also suggest that ABA biosynthesis is not required for the inhibitory effects of auxin treatment on root elongation. Our transcriptome analysis identified distinct auxin-responsive genes in root and shoot tissues, which is consistent with differential regulation of growth in these tissues. Further, our data suggest that many gene targets repressed upon auxin treatment require an intact ABA pathway for full repression. Our results support a model in which auxin stimulates ABA biosynthesis to fully regulate hypocotyl elongation.

Highly sensitive analysis of photoregulation and dynamic distribution of phytohormones based on nanoconfined liquid phase nanoextraction

BACKGROUND

As a vital energy source, light is one of the most significant environmental signals for plants' growth and development. The crosstalk amongst phytohormones regulated by light exhibits quantitative dynamic changes, but methodologies to analyze their distribution during plant growth are still limited. Rapid, highly sensitive, low-invasive detection and simultaneous assessment of the levels of multiple classes of phytohormones have important phytology applications, however the existing sample pretreatment strategies remain intricate, laborious, and far from being developed for in vivo high-sensitivity testing. (81) RESULTS: We applied a nanoconfined liquid phase nanoextraction (NLPNE) technique based on acidified carbon nanofibers (ACNFs) in combination with LC-ESI-MS/MS for highly sensitive analysis of acidic phytohormones' photoregulation and dynamic distribution. In this system, the mass transfer ability of analytes entering the nanoconfined space is significantly improved given the nanoconfined effect. In particular, the accelerated and strong adsorption of alkaline compounds to the ACNFs surface provide minimum interference for acidic compounds (photosensitive phytohormones), which facilitates their simple, fast, and selective quantification with improved sensitivity. The ACNFs-NLPNE strategy achieved quantitative enrichment of multi-class phytohormones in less than 5 min, and detection limits down to 0.49 fg mL-1. Moreover, we monitored the phytohormone changes under red and blue monochromatic light with relative standard deviations <13.4 %. The results further indicated that short-time red light regulation promoted Lepidium sativum L. growth while blue light inhibited it. (141) SIGNIFICANCE: A nanoconfinement effect-based sample pretreatment platform was developed for monitoring photoregulation phytohormones dynamic distribution with higher sensitivity and stability. Our findings highlighted the importance of the NLPNE approach in providing an accurate plant crosstalk information at the molecular level, which opens a promising avenue for investigating internal hormonal responses to external stimuli. (52).

Effects of phytohormone on Chlorella vulgaris grown in wastewater-flue gas: C/N/S fixation, wastewater treatment and metabolome analysis

Chlorella vulgaris (C. vulgaris) can provide the means to fix CO2 from complicated flue gas, treat wastewater and reach a sustainable production of petrochemical substitutes simultaneously. However, a prerequisite to achieving this goal is to promote C. vulgaris growth and improve the CO2-to-fatty acids conversion efficiency under different conditions of flue gas and wastewater. Thus, the addition of indole-3-acetic acid (IAA) in C. vulgaris cultivation was proposed. Results showed that C. vulgaris were more easily inhibited by 100 ppm NO and 200 ppm SO2 under low nitrogen (N) condition. NO and SO2 decreased the carbon (C) fixation; but increased N and sulfur (S) fixation. IAA adjusted the content of superoxide dismutase (SOD) and malondialdehyde (MDA), improved the expression of psbA, rbcL, and accD, attenuated the toxicity of NO and SO2 on C. vulgaris, and ultimately improved cell growth (2014.64-2458.16 mgdw·L-1) and restored CO2 fixation rate (170.98-220.92 mg CO2·L-1·d-1). Moreover, wastewater was found to have a high treatment efficiency because C. vulgaris grew well in all treatments, and the maximal removal rates of both N and phosphorus (P) reached 100%. Metabonomic analysis showed that IAA, "NO and SO2" were involved in the down-regulated and up-regulated expression of multiple metabolites, such as fatty acids, amino acids, and carbohydrates. IAA was beneficial for improving lipid accumulation with 24584.21-27634.23 μg g-1, especially monounsaturated fatty acids (MUFAs) dominated by 16-18 C fatty acids, in C. vulgaris cells. It was concluded that IAA enhanced the CO2 fixation, fatty acids production of C. vulgaris and its nutrients removal rate.

Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple (Malus domestica Borkh. Cv. Red delicious)

BACKGROUND

Bud sport is a kind of somatic mutation that usually occurred in apple. 'Red Delicious' is considered to be a special plant material of bud sport, whereas the genetic basis of plant mutants is still unknown. In this study, we used whole-genome resequencing and transcriptome sequencing to identify genes related to spur-type and skin-color in the 'Red Delicious' (G0) and its four generation mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee Spur' (G4).

RESULTS

The number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels) and structural variations (SVs) were decreased in four generation mutants compared to G0, and the number of unique SNPs and InDels were over 9-fold and 4-fold higher in G1 versus (vs.) G2 and G2 vs. G3, respectively. Chromosomes 2, 5, 11 and 15 carried the most SNPs, InDels and SVs, while chromosomes 1 and 6 carried the least. Meanwhile, we identified 4,356 variation genes by whole-genome resequencing and transcriptome, and obtained 13 and 16 differentially expressed genes (DEGs) related to spur-type and skin-color by gene expression levels. Among them, DELLA and 4CL7 were the potential genes that regulate the difference of spur-type and skin-color characters, respectively.

CONCLUSIONS

Our study identified potential genes associated with spur-type and skin-color differences in 'Red Delicious' and its four generation mutants, which provides a theoretical foundation for the mechanism of the apple bud sport.

Changing turn-over rates regulate abundance of tryptophan, GS biosynthesis, IAA transport and photosynthesis proteins in Arabidopsis growth defense transitions

BACKGROUND

Shifts in dynamic equilibria of the abundance of cellular molecules in plant-pathogen interactions need further exploration. We induced PTI in optimally growing Arabidopsis thaliana seedlings for 16 h, returning them to growth conditions for another 16 h.

METHODS

Turn-over and abundance of 99 flg22 responding proteins were measured chronologically using a stable heavy nitrogen isotope partial labeling strategy and targeted liquid chromatography coupled to mass spectrometry (PRM LC-MS). These experiments were complemented by measurements of mRNA and phytohormone levels.

RESULTS

Changes in synthesis and degradation rate constants (Ks and Kd) regulated tryptophane and glucosinolate, IAA transport, and photosynthesis-associated protein (PAP) homeostasis in growth/PTI transitions independently of mRNA levels. Ks values increased after elicitation while protein and mRNA levels became uncorrelated. mRNA returned to pre-elicitation levels, yet protein abundance remained at PTI levels even 16 h after media exchange, indicating protein levels were robust and unresponsive to transition back to growth. The abundance of 23 PAPs including FERREDOXIN-NADP( +)-OXIDOREDUCTASE (FNR1) decreased 16 h after PAMP exposure, their depletion was nearly abolished in the myc234 mutant. FNR1 Kd increased as mRNA levels decreased early in PTI, its Ks decreased in prolonged PTI. FNR1 Kd was lower in myc234, mRNA levels decreased as in wild type.

CONCLUSIONS

Protein Kd and Ks values change in response to flg22 exposure and constitute an additional layer of protein abundance regulation in growth defense transitions next to changes in mRNA levels. Our results suggest photosystem remodeling in PTI to direct electron flow away from the photosynthetic carbon reaction towards ROS production as an active defense mechanism controlled post-transcriptionally and by MYC2 and homologs. Target proteins accumulated later and PAP and auxin/IAA depletion was repressed in myc234 indicating a positive effect of the transcription factors in the establishment of PTI.

Phytohormones and candidate genes synergistically regulate fruitlet abscission in Areca catechu L

BACKGROUND

The fruit population of most plants is under the control of a process named "physiological drop" to selectively abort some developing fruitlets. However, frequent fruitlet abscission severely restricts the yield of Areca catechu. To reveal the physiological and molecular variations in this process, we detected the variation of phytohormone levels in abscised and non-abscised fruitlets in A. catechu.

RESULTS

The levels of gibberellin acid, jasmonic acid, salicylic acid, abscisic acid and zeatin were elevated, while the indole-3-acetic acid and indole-3-carboxaldehyde levels were declined in the "about-to-abscise" part (AB) of abscission zone (AZ) compared to the "non-abscised" part (CK). Then the differentially expressed genes (DEGs) between AB and CK were screened based on transcriptome data. DEGs involved in phytohormone synthesis, response and transportation were identified as key genes. Genes related to cell wall biosynthesis, degradation, loosening and modification, and critical processes during fruit abscission were identified as role players. In addition, genes encoding transcription factors, such as NAC, ERF, WRKY, MADS and Zinc Finger proteins, showed differentially expressed patterns between AB and CK, were also identified as candidates.

CONCLUSIONS

These results unraveled a phytohormone signaling cross talk and key genes involved in the fruitlet abscission process in A. catechu. This study not only provides a theoretical basis for fruitlet abscission in A. catechu, but also identified many candidate genes or potential molecular markers for further breeding of fruit trees.

Transcriptome analysis reveals the effect of acidic environment on adventitious root differentiation in Camellia sinensis

The generation of adventitious roots (ARs) is the key to the success of cuttings. The appropriate environment for AR differentiation in tea plants is acidic. However, the mechanism is unclear. In this study, pH 4.5 was suitable condition for the differentiation of AR in tea plants. At the base of cuttings, the root primordia differentiated ARs more rapidly at pH 4.5 than pH 7.0, and nine AR differentiation-related genes were found to be differentially expressed in 30 days, the result was also validated by qRT-PCR. The promoter regions of these genes contained auxin and brassinosteroid response elements. The expression levels of several genes which were involved in auxin and brassinosteroid synthesis as well as signaling at pH 4.5 compared to pH 7.0 occurred differential expression. Brassinolide (BL) and indole-3-acetic acid (IAA) could affect the differentiation of ARs under pH 4.5 and pH 7.0. By qRT-PCR analysis of genes during ARs generation, BL and IAA inhibited and promoted the expression of CsIAA14 gene, respectively, to regulate auxin signal transduction. Meanwhile, the expression levels of CsKNAT4, CsNAC2, CsNAC100, CsWRKY30 and CsLBD18 genes were up-regulated upon auxin treatment and were positively correlated with ARs differentiation.This study showed that pH 4.5 was the most suitable environment for the root primordia differentiation of AR in tea plant. Proper acidic pH conditions promoted auxin synthesis and signal transduction. The auxin initiated the expression of AR differentiation-related genes, and promoted its differentiated. BL was involved in ARs formation and elongation by regulating auxin signal transduction.

Transcriptome profiling reveals ethylene formation in rice seeds by trichloroisocyanuric acid

KEY MESSAGE

Ethylene formation via methionine reacting with trichloroisocyanuric acid under FeSO4 condition in a non-enzymatical manner provides one economically and efficiently novel ethylene-forming approach in planta. Rice seed germination can be stimulated by trichloroisocyanuric acid (TCICA). However, the molecular basis of TCICA in stimulating rice seed germination remains unclear. In this study, the molecular mechanism on how TCICA stimulated rice seed germination was examined via comparative transcriptome. Results showed that clustering of transcripts of TCICA-treated seeds, water-treated seeds, and dry seeds was clearly separated. Twenty-two and three hundred differentially expressed genes were identified as TCICA treatment responsive genes and TCICA treatment potentially responsive genes, respectively. Two and one TCICA treatment responsive genes were involved in ethylene signal transduction and iron homeostasis, respectively. Seventeen of the three hundred TCICA treatment potentially responsive genes were significantly annotated to iron ion binding. Meanwhile, level of methionine (ethylene precursor) showed a 73.9% decrease in response to TCICA treatment. Ethylene was then proved to produce via methionine reacting with TCICA under FeSO4 condition in vitro. Revealing ethylene formation by TCICA not only may bring novel insights into crosstalk between ethylene and other phytohormones during rice seed germination, but also may provide one economically and efficiently novel approach to producing ethylene in planta independently of the ethylene biosynthesis in plants and thereby may broaden its applications in investigational and applied purposes.

Genes expression profiles in vascular cambium of Eucalyptus urophylla × Eucalyptus grandis at different ages

BACKGROUND

Wood is a secondary xylem generated by vascular cambium. Vascular cambium activities mainly include cambium proliferation and vascular tissue formation through secondary growth, thereby producing new secondary phloem inward and secondary xylem outward and leading to continuous tree thickening and wood formation. Wood formation is a complex biological process, which is strictly regulated by multiple genes. Therefore, molecular level research on the vascular cambium of different tree ages can lead to the identification of both key and related genes involved in wood formation and further explain the molecular regulation mechanism of wood formation.

RESULTS

In the present study, RNA-Seq and Pac-Bio Iso-Seq were used for profiling gene expression changes in Eucalyptus urophylla × Eucalyptus grandis (E. urograndis) vascular cambium at four different ages. A total of 59,770 non-redundant transcripts and 1892 differentially expressed genes (DEGs) were identified. The expression trends of the DEGs related to cell division and differentiation, cell wall biosynthesis, phytohormone, and transcription factors were analyzed. The DEGs encoding expansin, kinesin, cycline, PAL, GRP9, KNOX, C2C2-dof, REV, etc., were highly expressed in E. urograndis at three years old, leading to positive effects on growth and development. Moreover, some gene family members, such as NAC, MYB, HD-ZIP III, RPK, and RAP, play different regulatory roles in wood formation because of their sophisticated transcriptional network and function redundantly.

CONCLUSIONS

These candidate genes are a potential resource to further study wood formation, especially in fast-growing and adaptable eucalyptus. The results may also serve as a basis for further research to unravel the molecular mechanism underlying wood formation.

Salicylic acid alleviates Zn-induced inhibition of growth via enhancing antioxidant system and glutathione metabolism in alfalfa

Zinc (Zn) is considered as one of the heavy metal pollutants in soil affecting agriculture. Salicylic acid (SA) is an important phytohormone that can mitigate effects against various abiotic stresses in plants, however, its exploration to improve Zn stress tolerance in alfalfa plants is still elusive. Thus, in the present study, exogenous SA treatment was conducted on alfalfa plants under Zn stress. The effects of exogenous SA on the physiological effects of alfalfa plants and the expression levels related genes were studied. This study tested the biomass, relative water content, chlorophyll levels, photosynthetic capacity, proline and soluble sugar contents, detected the activity of antioxidant enzymes (such as peroxidase and superoxide dismutase), glutathione biosynthesis, and endogenous SA levels, and quantified the genes associated with the antioxidant system and glutathione metabolism-mediated Zn stress. The results showed that exogenous SA could elevate the physiological adaptability of alfalfa plants through enhancing photosynthesis, proline and soluble sugar levels, stimulating antioxidant system and glutathione metabolism, and inducing the transcription level of related genes, thereby diminishing oxidative stress, inhibiting excessive Zn accumulation of alfalfa plants, increasing tolerance to Zn stress, and reducing the toxicity of Zn. Collectively, the application of SA alleviates Zn toxicity in alfalfa plants. The findings gave first insights into the regulatory mechanism of the Zn stress tolerance of alfalfa by exogenous SA and this might have positive implications for managing other plants which are suffering Zn stress.

An arbuscular mycorrhizal fungus differentially regulates root traits and cadmium uptake in two maize varieties

Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi that colonize plant roots, and they are more common in Cd-polluted habitats. However, there is limited understanding of the response of root traits and cadmium (Cd) uptake to AMF in different crop varieties. Two maize varieties, Panyu 3 and Ludan 8, with high and low Cd uptake capacities, respectively, were cultivated as host plants in a pot experiment with Cd-polluted soil (17.1 mg/kg Cd). The effects of AMF on the growth, mineral nutrient concentration, root traits, phytohormone concentrations and Cd uptake of the two maize varieties and their comprehensive response to AMF fungal inoculation were investigated. AMF improved growth, mineral nutrient levels and root morphology and increased lignin and phytohormone concentrations in roots and Cd uptake in the two maize varieties. However, the two maize varieties, Panyu 3 and Ludan 8, had different responses to AMF, and their comprehensive response indices were 753.6% and 389.4%, respectively. The root biomass, branch number, abscisic acid concentrations, lignin concentrations and Cd uptake of maize Panyu 3 increased by 151.1%, 28.6%, 139.7%, 99.5% and 84.7%, respectively. The root biomass, average diameter, auxin concentration, lignin concentration and Cd uptake of maize Ludan 8 increased by 168.7%, 31.8%, 31.4%, 41.7% and 136.7%, respectively. Moreover, Cd uptake in roots presented very significant positive correlations with the average root diameter and abscisic acid concentration. A structural equation model indicated that the root abscisic acid concentration and root surface area had positive effects on Cd uptake by the Panyu 3 maize roots; the root abscisic acid concentration and root tip number had positive effects on Cd uptake by the Ludan 8 maize roots. Thus, AMF differentially regulated Cd uptake in the two maize varieties, and the regulatory effect was closely related to root traits and phytohormone concentrations.

Knockout of SlYTH2, encoding a YTH domain-containing protein, caused plant dwarfing, delayed fruit internal ripening, and increased seed abortion rate in tomato

The m6A is one of the most abundant and widespread modifications in eukaryotic mRNAs, which regulates gene expression at the post-transcriptional level and plays key roles in many physiological processes. The YT521-B homologous (YTH) domain-containing proteins act as m6A readers to regulate m6A-RNA metabolism processes and mediate the various functions of m6A modification. Previously, we reported tomato contains 9 YTH genes, among which SlYTH2 is relatively highly expressed. This study reports the physiological functions of SlYTH2 in tomato. SlYTH2 protein is distributed in the nucleus and cytoplasm, and its three-dimensional structure is highly similar to human HsYTHDF1. SlYTH2 knockout through Crispr/Cas9 gene editing technology leaded to pleiotropic phenotypes, including dwarfing plant, delayed fruit internal ripening process, and increased seed abortion rate. The deletion of SlYTH2 gene increased the accumulation of endogenous ABA, decreased the content of endogenous GA3, and enhanced the sensitivity of seed germination to exogenous ABA and seedling growth to exogenous GA3. RNA-Seq data showed that the expression levels of multiple hormone-related genes were altered in SlYTH2 knockout line. These facts suggested SlYTH2 plays its physiological roles related to ABA, gibberellin and other hormones in tomato.

Plant growth-promoting rhizobacteria: A good companion for heavy metal phytoremediation

Phytoremediation is an environment-friendly approach regarded as a potential candidate for remediating heavy metal (HM)-contaminated soils. However, the low efficacy of phytoremediation is a major limitation that hampers its large-scale application. Therefore, developing strategies to enhance phytoremediation efficacy for contaminated soils is crucial. Plant growth-promoting rhizobacteria (PGPR) considerably contribute to phytoremediation intensification. To improve the efficiency of plant-microbe symbiosis for remediation, the mechanisms underlying PGPR-stimulated HM accumulation and tolerance in plants should be comprehensively understood. This review focuses on hyperaccumulators, PGPR, and the mechanisms by which PGPR enhance phytoremediation from four aspects: providing nutrients to plants, secreting plant hormones and specific enzymes, inducing systemic resistance, and altering the bioavailability of HMs in soils. It also provides a theoretical and technical basis for future research on PGPR synergism in promoting the phytoextraction efficiency in HM-contaminated soils.

Multi-omics insights into the positive role of strigolactone perception in barley drought response

BACKGROUND

Drought is a major environmental stress that affects crop productivity worldwide. Although previous research demonstrated links between strigolactones (SLs) and drought, here we used barley (Hordeum vulgare) SL-insensitive mutant hvd14 (dwarf14) to scrutinize the SL-dependent mechanisms associated with water deficit response.

RESULTS

We have employed a combination of transcriptomics, proteomics, phytohormonomics analyses, and physiological data to unravel differences between wild-type and hvd14 plants under drought. Our research revealed that drought sensitivity of hvd14 is related to weaker induction of abscisic acid-responsive genes/proteins, lower jasmonic acid content, higher reactive oxygen species content, and lower wax biosynthetic and deposition mechanisms than wild-type plants. In addition, we identified a set of transcription factors (TFs) that are exclusively drought-induced in the wild-type barley.

CONCLUSIONS

Critically, we resolved a comprehensive series of interactions between the drought-induced barley transcriptome and proteome responses, allowing us to understand the profound effects of SLs in alleviating water-limiting conditions. Several new avenues have opened for developing barley more resilient to drought through the information provided. Moreover, our study contributes to a better understanding of the complex interplay between genes, proteins, and hormones in response to drought, and underscores the importance of a multidisciplinary approach to studying plant stress response mechanisms.

The Inferior Grain Filling Initiation Promotes the Source Strength of Rice Leaves

Poor grain-filling initiation in inferior spikelets severely impedes rice yield improvement, while photo-assimilates from source leaves can greatly stimulate the initiation of inferior grain-filling (sink). To investigate the underlying mechanism of source-sink interaction, a two-year field experiment was conducted in 2019 and 2020 using two large-panicle rice cultivars (CJ03 and W1844). The treatments included intact panicles and partial spikelet removal. These two cultivars showed no significant difference in the number of spikelets per panicle. However, after removing spikelet, W1844 showed higher promotion on 1000-grain weight and seed-setting rate than CJ03, particularly for inferior spikelets. The reason was that the better sink activity of W1844 led to a more effective initiation of inferior grain-filling compared to CJ03. The inferior grain weight of CJ03 and W1844 did not show a significant increase until 8 days poster anthesis (DPA), which follows a similar pattern to the accumulation of photo-assimilates in leaves. After removing spikelets, the source leaves of W1844 exhibited lower photosynthetic inhibition compared to CJ03, as well as stronger metabolism and transport of photo-assimilates. Although T6P levels remained constant in both cultivars under same conditions, the source leaves of W1844 showed notable downregulation of SnRK1 activity and upregulation of phytohormones (such as abscisic acid, cytokinins, and auxin) after removing spikelets. Hence, the high sink strength of inferior spikelets plays a role in triggering the enhancement of source strength in rice leaves, thereby fulfilling grain-filling initiation demands.

Oligosaccharides increased both leaf biomass and steviol glycosides content of Stevia rebaudiana

Steviol glycosides (SGs) are a variety of important natural sweeteners. They are 200-350 times sweeter than sucrose without calories. Currently, their production is still mainly dependent on extraction from Stevia rebaudiana Bertoni (stevia). Oligosaccharides are environmentally friendly elicitors that promote plant growth and accumulation of secondary metabolites. In the present study, different concentrations of chitosan oligosaccharides (COS) and alginate oligosaccharides (AOS) were applied to stevia to explore their effect on growth and SGs biosynthesis. It was found that both COS and AOS promoted biomass production by increasing the leaf number and photosynthetic efficiency, which may be related to the decreased content of abscisic acid. The content of SGs was significantly increased after 50 mg/L AOS treatment, which not only increased the contents of stevioside (STV) and rebaudioside A (Reb A) significantly, but some important minority glucosides, like Reb E, Reb D, and Reb M. The increased SGs contents were the combined effect of the higher expression of SGs biosynthesis related genes, including KAH, UGT74G1, UGT85C2, and UGT91D2. The geometry changes of stem induced by COS and AOS may help to increase the lodging resistance of stevia. Thus, COS and AOS can be used in the field planting of stevia to increase the yield of SGs for industrial purposes.

Comparison of two contrasting Leymus chinensis accessions reveals the roles of the cell wall and auxin in rhizome development

Leymus chinensis, a perennial native forage grass, is widely distributed in the steppes of Inner Mongolia as the dominant species. The main reproductive strategy of this grass is clonal propagation, which occurs via the proliferation of subterranean horizontal stems known as rhizomes. To elucidate the mechanism underlying rhizome development in this grass, we collected 60 accessions of L. chinensis and evaluated their rhizome development. One accession, which we named SR-74 (Strong Rhizomes), had significantly better rhizome development capacity than the accession WR-16 (Weak Rhizomes) in terms of rhizome number, total and primary rhizome length, and number of rhizome seedlings. Rhizome elongation was positively correlated with the number of internodes in the rhizome, which affected plant biomass. Compared to WR-16, SR-74 had higher rhizome tip hardness, higher abundance of transcripts participating in the biosynthesis of cell wall components, and higher levels of the metabolites L-phenylalanine, trans-cinnamic acid, 3-coumaric acid, ferulic acid, and coniferin. These metabolites in the phenylpropanoid biosynthesis pathway are precursors of lignin. In addition, SR-74 rhizomes contained higher amounts of auxin and auxin metabolites, including L-Trp, IPA, IBA, IAA and IAA-Asp, as well as upregulated expression of the auxin biosynthesis and signaling genes YUCCA6, YUCCA8, YUCCA10, YUCCA11, PIN1, PIN2, UGT1, UGT2, UGT4, UGT10, GH3, IAA7, IAA23, and IAA30. We propose a network between auxin signaling and the cell wall underlying rhizome development in L. chinensis.

Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis)

Circular RNAs (circRNAs) are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GAs) and auxins (1-naphthaleneacetic acid, NAA) remain unknown. Here, we systematically identified and characterized the expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We explored the function of circRNAs, including their roles in regulating microRNA (miRNA)-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of circRNAs. Finally, we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA. Collectively, our study provides insights into the biogenesis, function, and miRNA-mediated degradation of circRNAs in moso bamboo.

Promising drought and salinity tolerance features of Nigrospora species existing as endophytes in Oryza sativa

In this study, we report the discovery of novel Nigrospora species isolated from the extensively cultivated PUSA 44 rice variety in Punjab, India. Out of the 120 isolates examined, 6.6% and 5% isolates exhibited tolerance to high salinity and drought stress. Isolates 6OSFR2e and 7OSFS3a exhibited the highest indole acetic acid and gibberellic acid production, with 268.32 ± 08.10 and 25.72 ± 0.04 µg/mL. Additionally, isolates 7OSFS3a, 6OSFR2e and 6OSFL4c had highest antioxidant potential with IC50 345.45 ± 11.66, 391.58 ± 10.66, and 474.529 ± 11.08 µg/mL. The isolates 6OSFR2e and 6OSFL4c also exhibited phosphate solubilisation with a PI of 1.06 ± 0.00 and 1.04 ± 0.02. The highest cellulase and laccase production with EI 1.24 ± 0.00 and 1.16 ± 0.00 was observed by isolates 6OSFR2e and 6OSFL4c. Promising results were observed in the case of ammonia production. The isolates belonged to the same phylum, Ascomycota and were identified as Nigrospora zimmermanii (6OSFR2e) and Nigrospora oryzae (7OSFS3a), and Nigrospora sphaerica (6OSFL4c) using morpho-taxonomic and molecular identification. The present study provides a critical insight into the characteristics of these Nigrospora species, which could be used to develop a bio-consortium for the rejuvenation of PUSA-44 cultivation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03679-9.

Transcriptomic analysis of Cucumis sativus uncovers putative genes related to hormone signaling under low temperature (LT) and high humidity (HH) stress

Climate change has caused changes in environmental conditions, leading to both low temperature (LT) and high humidity (HH) stress on crops worldwide. Therefore, there is a growing need to enhance our understanding of the physiological and molecular mechanisms underlying LT and HH stress tolerance in cucumbers, given the significance of climate change. The findings of this study offer a comprehensive understanding of how the transcriptome and hormone profiles of cucumbers respond to LT and HH stress. In this study, cucumber seedlings were subjected to LT and HH stress (9/5 °C day/night temperature, 95% humidity) as well as control (CK) conditions (25/18 °C day/night temperature, 80% humidity) for 24, 48, and 72 h. It was observed that the LT and HH stress caused severe damage to the morphometric traits of the plants compared to the control treatment. The concentrations of phytohormones IAA, ethylene, and GA were lower, while ABA and JA were higher during LT and HH stress at most time points. To gain insights into the molecular mechanisms underlying this stress response, RNA-sequencing was performed. The analysis revealed a total of 10,459 differentially expressed genes (DEGs) with annotated pathways. These pathways included plant hormone signal transduction, protein processing in the endoplasmic reticulum, MAPK signaling pathway, carbon fixation in photosynthetic organisms, and glycerolipid metabolism. Furthermore, 123 DEGs associated with hormone signaling pathways were identified, and their responses to LT and HH stress were thoroughly discussed. Overall, this study sheds light on the LT and HH tolerance mechanisms in cucumbers, particularly focusing on the genes involved in the LT and HH response and the signaling pathways of endogenous phytohormones.

Overexpression of Taetr1-1 promotes enhanced seed dormancy and ethylene insensitivity in wheat

MAIN CONCLUSION

Taetr1-1 can promote enhanced seed dormancy and ethylene insensitivity in wheat, indicating a conserved function of ETR1 in regulating seed dormancy. Lots of wheat cultivars have weak dormant seed. Weak seed dormancy can cause pre-harvest sprouting (PHS) in grain which significantly reduces grain yield and quality. The mining of causal genes of PHS resistance will serve to enhance breeding selection and cultivar development. In a previous study in Arabidopsis, we identified reduced dormancy 3 as a loss-of-function mutant of the ethylene receptor 1 (ETR1), which can control seed dormancy through the ERF12-TPL-DOG1 pathway. However, it is unknown whether ETR1 also functions in the regulation of wheat seed dormancy. To identify the regulatory role of ETR1 in wheat, we cloned TaETR1 and overexpressed the gain-of-function mutant Taetr1-1. The result indicated that overexpression of Taetr1-1 can promote enhanced seed dormancy and ethylene insensitivity in wheat. This study contributed to our understanding of the molecular basis for the regulation of wheat PHS resistance.

The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

BACKGROUND

Pod size is an important yield target trait for peanut breeding. However, the molecular mechanism underlying the determination of peanut pod size still remains unclear.

RESULTS

In this study, two peanut varieties with contrasting pod sizes were used for comparison of differences on the transcriptomic and endogenous hormonal levels. Developing peanut pods were sampled at 10, 15, 20, 25 and 30 days after pegging (DAP). Our results showed that the process of peanut pod-expansion could be divided into three stages: the gradual-growth stage, the rapid-growth stage and the slow-growth stage. Cytological analysis confirmed that the faster increase of cell-number during the rapid-growth stage was the main reason for the formation of larger pod size in Lps. Transcriptomic analyses showed that the expression of key genes related to the auxin, the cytokinin (CK) and the gibberellin (GA) were mostly up-regulated during the rapid-growth stage. Meanwhile, the cell division-related differentially expressed genes (DEGs) were mostly up-regulated at 10DAP which was consistent with the cytological-observation. Additionally, the absolute quantification of phytohormones were carried out by liquid-chromatography coupled with the tandem-mass-spectrometry (LC-MS/MS), and results supported the findings from comparative transcriptomic studies.

CONCLUSIONS

It was speculated that the differential expression levels of TAA1 and ARF (auxin-related), IPT and B-ARR (CK-related), KAO, GA20ox and GA3ox (GA-related), and certain cell division-related genes (gene-LOC112747313 and gene-LOC112754661) were important participating factors of the determination-mechanism of peanut pod sizes. These results were informative for the elucidation of the underlying regulatory network in peanut pod-growth and would facilitate further identification of valuable target genes.

Effect of exogenous phytohormone treatment on antioxidant activity, enzyme activity and phenolic content in wheat sprouts and identification of metabolites of control and treated samples by UHPLC-MS analysis

Phytohormones, Indole acetic acid, Salicylic acid and Gibberellic acid, either alone or in combination was applied on wheat sprouts to improve its nutritional status. The experiment included estimation of total phenolic, flavonoids, peroxidase activity and phenylalanine ammonium lyase activity. Antioxidant activity was determined by DPPH and FRAP assay. The results showed an increase in phenolic compounds, enzyme activity and antioxidant activity after treatment with the phytohormones. Phytohormone combinations were found to be more effective as compared to pure treatments. UHPLC-ESI-MS analysis was used to identify compounds in the control and treated samples. Phenolic acids, polyphenols, simple sugars, amino acids, dipeptides, lipids and fatty acids were detected. A multifold increase in the levels of phenolic compounds was observed in the phytohormone treated wheat sprouts.

Pan-transcriptomic Profiling Demarcates Serendipita Indica-Phosphorus Mediated Tolerance Mechanisms in Rice Exposed to Arsenic Toxicity

Inadvertent accumulation of arsenic (As) in rice (Oryza sativa L.) is a concern for people depending on it for their subsistence, as it verily causes epigenetic alterations across the genome as well as in specific cells. To ensure food safety, certain attempts have been made to nullify this highest health hazard encompassing physiological, chemical and biological methods. Albeit, the use of mycorrhizal association along with nutrient reinforcement strategy has not been explored yet. Mechanisms of response and resistance of two rice genotypes to As with or without phosphorus (P) nutrition and Serendipita indica (S. indica; S.i) colonization were explored by root transcriptome profiling in the present study. Results revealed that the resistant genotype had higher auxin content and root plasticity, which helped in keeping the As accumulation and P starvation response to a minimum under alone As stress. However, sufficient P supply and symbiotic relationship switched the energy resources towards plant's developmental aspects rather than excessive root proliferation. Higher As accumulating genotype (GD-6) displayed upregulation of ethylene signaling/biosynthesis, root stunting and senescence related genes under As toxicity. Antioxidant defense system and cytokinin biosynthesis/signaling of both genotypes were strengthened under As + S.i + P, while the upregulation of potassium (K) and zinc (Zn) transporters depicted underlying cross-talk with iron (Fe) and P. Differential expression of phosphate transporters, peroxidases and GSTs, metal detoxification/transport proteins, as well as phytohormonal metabolism were responsible for As detoxification. Taken together, S. indica symbiosis fortified with adequate P-fertilizer can prove to be effective in minimizing As acquisition and accumulation in rice plants.

Genome-wide identification and expression analysis of VQ gene family under abiotic stress in Coix lacryma-jobi L

BACKGROUND

Valine-glutamine (VQ) proteins are non-specific plant proteins that have a highly conserved motif: FxxhVQxhTG. These proteins are involved in the development of various plant organs such as seeds, hypocotyls, flowers, leaves and also play a role in response to salt, drought and cold stresses. Despite their importance, there is limited information available on the evolutionary and structural characteristics of VQ family genes in Coix lacryma-jobi.

RESULTS

In this study, a total of 31 VQ genes were identified from the coix genome and classified into seven subgroups (I-VII) based on phylogenetic analysis. These genes were found to be unevenly distributed on 10 chromosomes. Gene structure analysis revealed that these genes had a similar type of structure within each subfamily. Moreover, 27 of ClVQ genes were found to have no introns. Conserved domain and multiple sequence alignment analysis revealed the presence of a highly conserved sequences in the ClVQ protein. This research utilized quantitative real-time PCR (qRT-PCR) and promoter analysis to investigate the expression of ClVQ genes under different stress conditions. Results showed that most ClVQ genes responded to polyethylene glycol, heat treatment, salt, abscisic acid and methyl jasmonate treatment with varying degrees of expression. Furthermore, some ClVQ genes exhibited significant correlation in expression changes under abiotic stress, indicating that these genes may act synergistically in response to adversarial stress. Additionally, yeast dihybrid verification revealed an interaction between ClVQ4, ClVQ12, and ClVQ26.

CONCLUSIONS

This study conducted a genome-wide analysis of the VQ gene family in coix, including an examination of phylogenetic relationships, conserved domains, cis-elements and expression patterns. The goal of the study was to identify potential drought resistance candidate genes, providing a theoretical foundation for molecular resistance breeding.

Genome-wide investigation of NLP gene family members in alfalfa (Medicago sativa L.): evolution and expression profiles during development and stress

BACKGROUND

NIN-like protein (NLP) transcription factors (TFs) compose a plant-specific gene family whose members play vital roles in plant physiological processes, especially in the regulation of plant growth and the response to nitrate-nitrogen. However, no systematic identification or analysis of the NLP gene family has been reported in alfalfa. The recently completed whole-genome sequence of alfalfa has allowed us to investigate genome-wide characteristics and expression profiles.

RESULTS

53 MsNLP genes were identified from alfalfa and renamed according to their respective chromosome distributions. Phylogenetic analysis demonstrated that these MsNLPs can be classified into three groups on the basis of their conserved domains. Gene structure and protein motif analyses showed that closely clustered MsNLP genes were relatively conserved within each subgroup. Synteny analysis revealed four fragment duplication events of MsNLPs in alfalfa. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of gene pairs indicated that the MsNLP genes underwent purifying selection during evolution. Examination of the expression patterns of different tissues revealed specific expression patterns of the MsNLP genes in the leaves, indicating that these genes are involved in plant functional development. Prediction of cis-acting regulatory elements and expression profiles further demonstrated that the MsNLP genes might play important roles in the response to abiotic stress and in phytohormone signal transduction processes.

CONCLUSION

This study represents the first genome-wide characterization of MsNLP in alfalfa. Most MsNLPs are expressed mainly in leaves and respond positively to abiotic stresses and hormonal treatments. These results provide a valuable resource for an improved understanding of the characteristics and biological roles of the MsNLP genes in alfalfa.

Development of a novel method for multiple phytohormone analysis by UHPLC-MS/MS from bio-enriched organic fertilizer prepared using banana pseudostem sap waste

Banana harvesting generates a large amount of banana pseudostem waste, which is generally burnt or thrown away, despite containing many nutrients. Bio-enriched organic fertilizer (BOF) was prepared from banana pseudostem sap (BPS), and it has been patented (Patent No. WO 2013/001478 Al). Several reports revealed that its application increases plant growth promotion of various horticulture crops. Apart from macro- and micronutrients, it also contained phytohormones. Hence, the present study aims to detect and quantify phytohormone in it. A novel method was developed to extract four phytohormones, viz., indole-3-acetic acid (IAA), indole-3-butyric acid (IBA), gibberellic acid (GA₃), and salicylic acid (SA) using single solvent from BPS and BOF. Extracted hormones were analyzed by ultrahigh-performance liquid chromatography coupled with heated electrospray ionization tandem mass spectrometry (UHPLC-HESI-MS/MS). BOF showed a higher concentration of IAA, IBA, GA₃, and SA than BPS. Thus, this is the first time a method has been reported to extract and detect phytohormones from banana pseudostem sap.

The Regulatory Roles of MYC TFs in Plant Stamen Development

The stamen, as the male reproductive organ of flowering plants, plays a critical role in completing the life cycle of plants. MYC transcription factors are members of the bHLH IIIE subgroup and participate in a number of plant biological processes. In recent decades, a number of studies have confirmed that MYC transcription factors actively participate in the regulation of stamen development and have a critical impact on plant fertility. In this review, we summarized how MYC transcription factors play a role in regulating secondary thickening of the anther endothecium, the development and degradation of the tapetum, stomatal differentiation, and the dehydration of the anther epidermis. With regard to anther physiological metabolism, MYC transcription factors control dehydrin synthesis, ion and water transport, and carbohydrate metabolism to influence pollen viability. Additionally, MYCs participate in the JA signal transduction pathway, where they directly or indirectly control the development of stamens through the ET-JA, GA-JA, and ABA-JA pathways. By identifying the functions of MYCs during plant stamen development, it will help us to obtain a more comprehensive understanding not only on the molecular functions of this TF family but also the mechanisms underlying stamen development.

Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis

Soil salinity stress is one of the major bottlenecks for crop production. Although, allantoin is known to be involved in nitrogen metabolism in plants, yet several reports in recent time indicate its involvement in various abiotic stress responses including salinity stress. However, the detail mechanism of allantoin involvement in salinity stress tolerance in plants is not studied well. Moreover, we demonstrated the role of exogenous application of allantoin as well as increased concentration of endogenous allantoin in rendering salinity tolerance in rice and Arabidopsis respectively, via., induction of abscisic acid (ABA) and brassinosteroid (BR) biosynthesis pathways. Exogenous application of allantoin (10 µM) provides  salt-tolerance to salt-sensitive rice genotype (IR-29). Transcriptomic data after exogenous supplementation of allantoin under salinity stress showed induction of ABA (OsNCED1) and BR (Oscytochrome P450) biosynthesis genes in IR-29. Further, the key gene of allantoin biosynthesis pathway i.e., urate oxidase of the halophytic species Oryza coarctata was also found to induce ABA and BR biosynthesis genes when over-expressed in transgenic Arabidopsis. Thus, indicating that ABA and BR biosynthesis pathways were involved in allantoin mediated salinity tolerance in both rice and Arabidopsis. Additionally, it has been found that several physio-chemical parameters such as biomass, Na⁺/K⁺ ratio, MDA, soluble sugar, proline, allantoin and chlorophyll contents were also associated with the allantoin-mediated salinity tolerance in urate oxidase overexpressed lines of Arabidopsis. These findings depicted the functional conservation of allantoin for salinity tolerance in both plant clades.

Transcription elongation factors OsSPT4 and OsSPT5 are essential for rice growth and development and act with APO2

KEY MESSAGE

The transcription elongation factor SPT4/SPT5 complex is essential for rice vegetative and reproductive growth and that OsSPT5-1, with its interactor APO2, is involved in multiple phytohormone pathways. The SPT4/SPT5 complex is a transcription elongation factor that regulates the processivity of transcription elongation. However, our understanding of the role of SPT4/SPT5 complex in developmental regulation remains limited. Here, we identified three SPT4/SPT5 genes (OsSPT4, OsSPT5-1, and OsSPT5-2) in rice, and investigated their roles in vegetative and reproductive growth. These genes are highly conserved with their orthologs in other species. OsSPT4 and OsSPT5-1 are widely expressed in various tissues. By contrast, OsSPT5-2 is expressed at a relatively low level, which could cause osspt5-2 null mutants have no phenotypes. Loss-of-function mutants of OsSPT4 and OsSPT5-1 could not be obtained; their heterozygotes showed severe reproductive growth defects. An incomplete mutant line (osspt5-1#12) displayed gibberellin-related dwarfed defects and a weak root system at an early vegetative phase, and a short life cycle in different planting environments. Furthermore, OsSPT5-1 interacts with the transcription factor ABERRANT PANICLE ORGANIZATION 2 (APO2) and plays a similar role in regulating the growth of rice shoots. RNA sequencing analysis verified that OsSPT5-1 is involved in multiple phytohormone pathways, including gibberellin, auxin, and cytokinin. Therefore, the SPT4/SPT5 complex is essential for both vegetative and reproductive growth in rice.

Cytokinins act synergistically with heat acclimation to enhance rice thermotolerance affecting hormonal dynamics, gene expression and volatile emission

Heat stress is a frequent environmental constraint. Phytohormones can significantly affect plant thermotolerance. This study compares the effects of exogenous cytokinin meta-topolin-9-(tetrahydropyran-2-yl)purine (mT9THP) on rice (Oryza sativa) under control conditions, after acclimation by moderate temperature (A; 37 °C, 2h), heat stress (HS; 45 °C, 6h) and their combination (AHS). mT9THP is a stable cytokinin derivative that releases active meta-topolin gradually, preventing the rapid deactivation reported after exogenous cytokinin application. Under control conditions, mT9THP negatively affected jasmonic acid in leaves and abscisic and salicylic acids in crowns (meristematic tissue crucial for tillering). Exogenous cytokinin stimulated the emission of volatile organic compounds (VOC), especially 2,3-butanediol. Acclimation upregulated trans-zeatin, expression of stress- and hormone-related genes, and VOC emission. The combination of acclimation and mT9THP promoted the expression of stress markers and antioxidant enzymes and moderately increased VOC emission, including 2-ethylhexyl salicylate or furanones. AHS and HS responses shared some common features, namely, increase of ethylene precursor aminocyclopropane-1-carboxylic acid (ACC), cis-zeatin and cytokinin methylthio derivatives, as well as the expression of heat shock proteins, alternative oxidases, and superoxide dismutases. AHS specifically induced jasmonic acid and auxin indole-3-acetic acid levels, diacylglycerolipids with fewer double bonds, and VOC emissions [e.g., acetamide, lipoxygenase (LOX)-derived volatiles]. Under direct HS, exogenous cytokinin mimicked some positive acclimation effects. The combination of mT9THP and AHS had the strongest thermo-protective effect, including a strong stimulation of VOC emissions (including LOX-derived ones). These results demonstrate for the first time the crucial contribution of volatiles to the beneficial effects of cytokinin and AHS on rice thermotolerance.

Genome Editing Reveals Both the Crucial Role of OsCOI2 in Jasmonate Signaling and the Functional Diversity of COI1 Homologs in Rice

Jasmonic acid (JA) regulates plant growth, development and stress responses. Coronatine insensitive 1 (COI1) and jasmonate zinc-finger inflorescence meristem-domain (JAZ) proteins form a receptor complex for jasmonoyl-l-isoleucine, a biologically active form of JA. Three COIs (OsCOI1a, OsCOI1b and OsCOI2) are encoded in the rice genome. In the present study, we generated mutants for each rice COI gene using genome editing to reveal the physiological functions of the three rice COIs. The oscoi2 mutants, but not the oscoi1a and oscoi1b mutants, exhibited severely low fertility, indicating the crucial role of OsCOI2 in rice fertility. Transcriptomic analysis revealed that the transcriptional changes after methyl jasmonate (MeJA) treatment were moderate in the leaves of oscoi2 mutants compared to those in the wild type or oscoi1a and oscoi1b mutants. MeJA-induced chlorophyll degradation and accumulation of antimicrobial secondary metabolites were suppressed in oscoi2 mutants. These results indicate that OsCOI2 plays a central role in JA response in rice leaves. In contrast, the assessment of growth inhibition upon exogenous application of JA to seedlings of each mutant revealed that rice COIs are redundantly involved in shoot growth, whereas OsCOI2 plays a primary role in root growth. In addition, a co-immunoprecipitation assay showed that OsJAZ2 and OsJAZ5 containing divergent Jas motifs physically interacted only with OsCOI2, whereas OsJAZ4 with a canonical Jas motif interacts with all three rice COIs. The present study demonstrated the functional diversity of rice COIs, thereby providing clues to the mechanisms regulating the various physiological functions of JA.