An integrated targeted metabolome of phytohormones and transcriptomics analysis provides insight into the new generation of crops: Polygonatum kingianum var. grandifolium and Polygonatum kingianum.

Huangjing is becoming a new generation of crop. Polygonatum kingianum var. grandifolium (XHJ) is a variant of P. kingianum (DHJ), and they are treated as Huangjing. Unlike other Polygonatum species, the rhizome bud of XHJ can germinate both in spring and autumn, which contributes to its high rhizome yield. However, the molecular mechanism of the autumn shooting of XHJ was still unknown. In the present study, cellular observation, comparative targeted metabolome of phytohormones, and transcriptome analysis between XHJ and DHJ in autumn were conducted. Interestingly, 'Diterpenoid biosynthesis' (ko00904) and 'Plant hormone signal transduction' (ko04075) were commonly enriched by differentially accumulated phytohormones (DAPs) and differentially expressed genes (DEGs) in all tissues, which indicated the high auxin content, low cytokinin (CTK) content, and low abscisic acid/gibberellin (ABA/GA) ratio might contribute to the XHJ rhizome buds' differentiation and germination in autumn. Moreover, according to the weighted gene co-expression network analysis (WCGNA), transcript factors (TFs) related to auxin, CTK, GA, and jasmonic acid (JA) metabolism were screened, such as AP2/ERFs, WRKY, and NAC, which deserve further research. In conclusion, we comprehensively illustrated the mechanism of XHJ natural autumn shooting through cytological, metabolic, and transcriptomic analysis, which improves our understanding of the high yield of XHJ rhizomes and the diversity of shooting mechanisms in Polygonatum to lay the foundation for the further development of the Huangjing industry.

PavSPLs are key regulators of growth, development, and stress response in sweet cherry.

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes are plant-specific transcription factors essential for plant growth, development, and stress responses; however, their roles in sweet cherry are not well understood. In this study, we identified and isolated 16 SPL genes from the sweet cherry genome, categorizing them into five subfamilies, with 12 PavSPLs predicted as miR156 targets. The promoter regions of PavSPLs contain cis-elements associated with light, stress, and phytohormone responses, indicating their role in biological processes and abiotic stress responses. Seasonal expression analysis showed that PavSPL regulates sweet cherry recovery after dormancy. Gibberellin (GA) treatment reduced PavSPL expression, indicating its role in GA-mediated processes. Overexpression of PavSPL14 in Arabidopsis thaliana resulted in earlier flowering, increased plant height, and enhanced growth. Yeast two-hybrid assays revealed an interaction between PavSPL14 and DELLA protein PavDWARF8, suggesting the involvement of PavSPLs in GA-regulated processes through protein interactions. These findings lay the groundwork for future studies on PavSPL function in sweet cherry.

Unveiling significant roles of phytohormone 6-benzylaminopurine in empowering Phaeodactylum tricornutum for high-salinity wastewater treatment and bioresource recovery.

High-salinity presents significant challenges in microalgal wastewater treatment and bioresource recovery due to salinity stress. This study explored the use of salt-tolerant microalgae in conjunction with phytohormone regulation. 1 µM 6-benzylaminopurine increased the biomass of Phaeodactylum tricornutum by 38.3 % and enhanced lipid production by 36.8 %. 6-benzylaminopurine significantly improved the removal of inorganic carbon, total nitrogen, and total phosphorus by 85.2 %, 27.4 %, and 31.9 %. Specifically, 6-benzylaminopurine improved K+ transportation by 71.0 %, increased the activity of Ca2+ transport ATPase and Ca2+ sensors by 49.0 %-83.0 %, optimized osmotic balance, and alleviated salt-induced damage. The contents of proline and extracellular polymers increased by 34.8 % and 35.5 %. A 38.4 % reduction in reactive oxygen species indicated that high-salinity stress was mitigated. The analysis of Sustainable Development Goals showed a 56.2 % improvement in Affordable and Clean Energy. Overall, these findings further highlighted the promising application of the phytohormone 6-benzylaminopurine in microalgal high-salinity wastewater treatment and lipid production.

An Enhanced Interaction of Graft and Exogenous SA on Photosynthesis, Phytohormone, and Transcriptome Analysis in Tomato under Salinity Stress.

Salt stress can adversely affect global agricultural productivity, necessitating innovative strategies to mitigate its adverse effects on plant growth and yield. This study investigated the effects of exogenous salicylic acid (SA), grafting (G), and their combined application (GSA) on various parameters in tomato plants subjected to salt stress. The analysis focused on growth characteristics, photosynthesis, osmotic stress substances, antioxidant enzyme activity, plant hormones, ion content, and transcriptome profiles. Salt stress severely inhibits the growth of tomato seedlings. However, SA, G, and GSA improved the plant height by 22.5%, 26.5%, and 40.2%; the stem diameter by 11.0%, 26.0%, and 23.7%; the shoot fresh weight by 76.3%, 113.2%, and 247.4%; the root fresh weight by 150.9%, 238.6%, and 286.0%; the shoot dry weight by 53.5%, 65.1%, and 162.8%; the root dry weight by 150.0%, 150.0%, and 166.7%, and photosynthesis by 4.0%, 16.3%, and 32.7%, with GSA presenting the most pronounced positive effect. Regarding the osmotic stress substances, the proline content increased significantly by more than 259.2% in all treatments, with the highest levels in GSA. Under salt stress, the tomato seedlings accumulated high Na+ levels; the SA, G, and GSA treatments enhanced the K+ and Ca2+ absorption while reducing the Na+ and Al3+ levels, thereby alleviating the ion toxicity. The transcriptome analysis indicated that SA, G, and GSA influenced tomato growth under salt stress by regulating specific signaling pathways, including the phytohormone and MAPK pathways, which were characterized by increased endogenous SA and decreased ABA content. The combined application of grafting and exogenous SA could be a promising strategy for enhancing plant tolerance to salt stress, offering potential solutions for sustainable agriculture in saline environments.

Polyacrylamide Regulated Phytohormone Balance and Starch Degradation to Promote Seed-Potato Sprouting and Emergence.

Potatoes are typically seeded as tubers, and their slow sprouting significantly impacts production. Therefore, the effects of polyacrylamide (20 g·L-1, 30 g·L-1, and 40 g·L-1) as a seed potato dressing on sprouting, seedling growth, and biomass were investigated. The phytohormone content, respiratory intensity, and starch metabolism enzyme activity were analyzed to elucidate the physiological mechanisms involved. The sprouting rate significantly increased after 20 g·L-1 and 30 g·L-1 treatments by 40.63% and 15.63%, respectively. The sprouting energy was the highest (52.0%) at 20 g·L-1, 7.67 times higher than the control. The 20 g·L-1 and 30 g·L-1 treatments also promoted emergence and growth, with the emergence rate increasing by 18.18% and 27.27% and growth increasing by over 8.1% and 11.9%, respectively. These effects were related to changes in phytohormone content and accelerated starch conversion. After treatment, the auxin and cytokinin contents in the apical buds increased significantly at the germination initiation stage, and during the germination and vigorous growth phases, the auxin, cytokinin, and gibberellin contents increased. Polyacrylamide treatment activated α-amylase and promoted starch degradation, increasing soluble sugar content to provide nutrients and energy for sprouting. This study provides a promising approach for promoting potato tuber sprouting and seedling growth.

The molecular dynamics between reactive oxygen species (ROS), reactive nitrogen species (RNS) and phytohormones in plant's response to biotic stress.

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are critical for plant development as well as for its stress response. They can function as signaling molecules to orchestrate a well-defined response of plants to biotic stress. These responses are further fine-tuned by phytohormones, such as salicylic acid, jasmonic acid, and ethylene, to modulate immune response. In the past decades, the intricacies of redox and phytohormonal signaling have been uncovered during plant-pathogen interactions. This review explores the dynamic interplay of these components, elucidating their roles in perceiving biotic threats and shaping the plant's defense strategy. Molecular regulators and sites of oxidative burst have been explored during pathogen perception. Further, the interplay between various components of redox and phytohormonal signaling has been explored during bacterial, fungal, viral, and nematode infections as well as during insect pest infestation. Understanding these interactions highlights gaps in the current knowledge and provides insights into engineering crop varieties with enhanced resistance to pathogens and pests. This review also highlights potential applications of manipulating regulators of redox signaling to bolster plant immunity and ensure global food security. Future research should explore regulators of these signaling pathways as potential target to develop biotic stress-tolerant crops. Further insights are also needed into roles of endophytes and host microbiome modulating host ROS and RNS pool for exploiting them as biocontrol agents imparting resistance against pathogens in plants.

Genome-wide identification, characterization and expression pattern analysis of TIFY family members in Artemisia argyi.

BACKGROUND: Plant-specific TIFY proteins play crucial roles in regulating plant growth, development, and various stress responses. However, there is no information available about this family in Artemisia argyi, a well-known traditional medicinal plant with great economic value. RESULTS: A total of 34 AaTIFY genes were identified, including 4 TIFY, 22 JAZ, 5 PPD, and 3 ZML genes. Structural, motif scanning, and phylogenetic relationships analysis of these genes revealed that members within the same group or subgroup exhibit similar exon-intron structures and conserved motif compositions. The TIFY genes were unevenly distributed across the 15 chromosomes. Tandem duplication events and segmental duplication events have been identified in the TIFY family in A. argyi. These events have played a crucial role in the gene multiplication and compression of different subfamilies within the TIFY family. Promoter analysis revealed that most AaTIFY genes contain multiple cis-elements associated with stress response, phytohormone signal transduction, and plant growth and development. Expression analysis of roots and leaves using RNA-seq data revealed that certain AaTIFY genes showed tissue-specific expression patterns, and some AaTIFY genes, such as AaTIFY19/29, were found to be involved in regulating salt and saline-alkali stresses. In addition, RT-qPCR analysis showed that TIFY genes, especially AaTIFY19/23/27/29, respond to a variety of hormonal treatments, such as MeJA, ABA, SA, and IAA. This suggested that TIFY genes in A. argyi regulate plant growth and respond to different stresses by following different hormone signaling pathways. CONCLUSION: Taken together, our study conducted a comprehensive identification and analysis of the TIFY gene family in A. argyi. These findings suggested that TIFY might play an important role in plant development and stress responses, which laid a valuable foundation for further understanding the function of TIFY genes in multiple stress responses and phytohormone crosstalk in A. argyi.

Physiological Basis of Plant Growth Promotion in Rice by Rhizosphere and Endosphere Associated Streptomyces Isolates from India.

This study demonstrated the plant growth-promoting capabilities of native actinobacterial strains obtained from different regions of the rice plant, including the rhizosphere (FT1, FTSA2, FB2, and FH7) and endosphere (EB6). We delved into the molecular mechanisms underlying the beneficial effects of these plant-microbe interactions by conducting a transcriptional analysis of a select group of key genes involved in phytohormone pathways. Through in vitro screening for various plant growth-promoting (PGP) traits, all tested isolates exhibited positive traits for indole-3-acetic acid synthesis and siderophore production, with FT1 being the sole producer of hydrogen cyanide (HCN). All isolates were identified as members of the Streptomyces genus through 16S rRNA amplification. In pot culture experiments, rice seeds inoculated with strains FB2 and FTSA2 exhibited significant increases in shoot dry mass by 7% and 34%, respectively, and total biomass by 8% and 30%, respectively. All strains led to increased leaf nitrogen levels, with FTSA2 demonstrating the highest increase (4.3%). On the contrary, strains FB2 and FT1 increased root length, root weight ratio, root volume, and root surface area, leading to higher root nitrogen content. All isolates, except for FB2, enhanced total chlorophyll and carotenoid levels. Additionally, qRT-PCR analysis supported these findings, revealing differential gene expression in auxin (OsAUX1, OsIAA1, OsYUCCA1, OsYUCCA3), gibberellin (OsGID1, OsGA20ox-1), and cytokinin (OsIPT3, OsIPT5) pathways in response to specific actinobacterial treatments. These actinobacterial strains, which enhance both aboveground and belowground crop characteristics, warrant further evaluation in field trials, either as individual strains or in consortia. This could lead to the development of commercial bioinoculants for use in integrated nutrient management practices.

Gamma-aminobutyric acid as a regulator of astaxanthin production in Haematococcus lacustris under salinity: Exploring physiology, signaling, autophagy, and multi-omics landscape.

Haematococcus lacustris-derived natural astaxanthin has significant commercial value, but stressful conditions alone impair cell growth and reduce the total productivity of astaxanthin in industrial settings. This study used gamma-aminobutyric acid (GABA) to increase biomass, astaxanthin productivity, and tolerance to salinity. GABA under NaCl stress enhanced the biomass to 1.76 g/L, astaxanthin content to 30.37 mg g-1, and productivity to 4.10 mg/L d-1, outperforming the control. Further analysis showed GABA enhanced nitrogen assimilation, Ca2+ level, and cellular GABA content, boosting substrate synthesis, energy metabolism, osmoregulation, autophagy, and antioxidant defenses. GABA also activated signaling pathways involving phytohormones, cAMP, cGMP, and MAPK, aiding astaxanthin synthesis. The application of biomarkers (ethylene, salicylic acid, trans-zeatin) and an autophagy inhibitor cooperated with GABA to further enhance the total astaxanthin productivity under NaCl stress. Combining GABA with 25 µM salicylic acid maximized astaxanthin yield at 4.79 mg/L d-1, offering new strategies for industrial astaxanthin production.

Master Regulatory Transcription Factors in ß-Aminobutyric Acid-Induced Resistance (BABA-IR): A Perspective on Phytohormone Biosynthesis and Signaling in Arabidopsis thaliana and Hordeum vulgare.

The endogenous stress metabolite ß-aminobutyric acid (BABA) primes plants for enhanced resistance against abiotic and biotic stress by activating a complex phytohormone signaling network that includes abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and ethylene (ET). In this study, through stringent filtering, we identify 14 master regulatory transcription factors (TFs) from the DOF, AHL, and ERF families that potentially regulate the biosynthesis and signaling of these phytohormones. Transcriptional analysis of BABA-treated Arabidopsis thaliana and Hordeum vulgare suggests that DOF family TFs play a crucial role in stress response regulation in both species. BABA treatment in A. thaliana upregulates the TFs MNB1A and PBF and enhances the expression of the genes ICS1, EDS5, and WIN3 in the SA biosynthesis pathway, potentially boosting NPR1 and PR1 in the SA signaling pathway. Conversely, in H. vulgare, the BABA-induced upregulation of TF DOF5.8 may negatively regulate SA biosynthesis by downregulating ICS1, EDS5, and PR1. Additionally, in A. thaliana, BABA triggers the expression of TF PBF, which may result in the decreased expression of MYC2, a key gene in JA signaling. In contrast, H. vulgare exhibits increased expression of ERF2 TF, which could positively regulate the JA biosynthesis genes LOX and Tify9, along with the COI1 and JAZ genes involved in the JA signaling pathway. These findings offer new perspectives on the transcriptional regulation of phytohormones during plant priming.

Fermentation broth of a novel endophytic fungus enhanced maize salt tolerance by regulating sugar metabolism and phytohormone biosynthesis or signaling.

Soil salinization is a major environmental factor that severely affects global agriculture. Root endophytes can enter root cells, and offer various ecological benefits, such as promoting plant growth, improving soil conditions, and enhancing plant resistance. Su100 is a novel strain of endophytic fungus that was characterized from blueberry roots. In this study, we focused on evaluating the effects of Su100 secretion on maize growth. The results demonstrated that maize treated with Su100 fermentation broth (SFB) exhibited significantly stronger salt tolerance than the control. It is worth mentioning that the treated root system not only had an advantage in terms of biomass but also a change in root structure with a significant increase in lateral roots (LRs) compared to the control. Transcriptome analysis combined with hormone content measurements indicated that SFB upregulated the auxin signaling pathway, and also caused alterations in brassinosteroids (BR) and jasmonic acid (JA) biosynthesis and signaling pathways. Transcriptome analyses also indicated that SFB caused significant changes in the sugar metabolism of maize roots. The major changes included: enhancing the conversion and utilization of sucrose in roots; increasing carbon flow to uridine diphosphate glucose (UDPG), which acted as a precursor for producing more cell wall polysaccharides, mainly pectin and lignin; accelerating the tricarboxylic acid cycle, which were further supported by sugar content determinations. Taken together, our results indicated that the enhanced salt tolerance of maize treated with SFB was due to the modulation of sugar metabolism and phytohormone biosynthesis or signaling pathways. This study provided new insights into the mechanisms of action of endophytic fungi and highlighted the potential application of fungal preparations in agriculture.

Ectopic Expression of AetPGL from Aegilops tauschii Enhances Cadmium Tolerance and Accumulation Capacity in Arabidopsis thaliana.

Cadmium (Cd) is a toxic heavy metal that accumulates in plants, negatively affecting their physiological processes, growth, and development, and poses a threat to human health through the food chain. 6-phosphogluconolactonase (PGL) is a key enzyme in the Oxidative Pentose Phosphate Pathway(OPPP) in plant cells, essential for cellular metabolism. The OPPP pathway provides energy and raw materials for organisms and is involved in antioxidant reactions, lipid metabolism, and DNA synthesis. This study describes the Cd responsive gene AetPGL from Aegilops tauschii. Overexpression of AetPGL under Cd stress increased main root length and germination rate in Arabidopsis. Transgenic lines showed higher antioxidant enzyme activities and lower malondialdehyde (MDA) content compared to the wild type. The transgenic Arabidopsis accumulated more Cd in the aboveground part but not in the underground part. Expression levels of AtHMA3, AtNRAMP5, and AtZIP1 in the roots of transgenic plants increased under Cd stress, suggesting AetPGL may enhance Cd transport from root to shoot. Transcriptome analysis revealed enrichment of differentially expressed genes (DEGs) in the plant hormone signal transduction pathway in AetPGL-overexpressing plants. Brassinosteroids (BR), Gibbenellin acid (GA), and Jasmonic acid (JA) contents significantly increased after Cd treatment. These results indicate that AetPGL may enhance Arabidopsis' tolerance to Cd by modulating plant hormone content. In conclusion, AetPGL plays a critical role in improving cadmium tolerance and accumulation and mitigating oxidative stress by regulating plant hormones, providing insights into the molecular mechanisms of plant Cd tolerance.

Buckwheat: An Underutilized Himalayan Crop with Multifaceted Nutraceutical Benefits.

The human population is growing and alternate food options are needed to provide food and nutritional security to mankind. Reduced agricultural output as a result of climate change and increased demand for grains because of continuous population growth have created a gap between demand and supply of food. Buckwheat is a pseudocereal crop plant with high nutritional value that can be included as an alternate food in our diet. It is a traditional crop plant grown in the high mountains of the Himalayas for food as well as fodder. It completes its life cycle in 3-4 months, so is mostly grown as a second crop in between main crops like maize and barley. It also acts as a green manure by improving the phosphorus content of the soil. Buck-wheat has high nutritional value as it is rich in essential amino acids, vitamin B, trace elements, and other nutrients. The main bioactive compounds identified in buckwheat are rutin, quercetin, isoquercetin, d-chiroinositol, resveratol, and vitexin, which are responsible for its pharmacolog-ical properties. Research focused on value addition by exploring its nutritional, pharmaceutical, and other alternative uses of commercial importance, is needed for reviving buckwheat cultiva-tion practices and its conservation. Considering the multifarious applications of buckwheat, this review summarizes the currently available knowledge on the agronomic and nutraceutical sig-nificance of buckwheat to project its value as a future crop in the avenue of agriculture and functional food.

Revisiting Citrus Rootstocks Polyploidy as a Means to Improve Drought Resilience: Sometimes Less Is More.

Polyploid varieties have been suggested as an alternative approach to promote drought tolerance in citrus crops. In this study, we compared the responses of diploid and tetraploid Sunki 'Tropical' rootstocks to water deficit when grafted onto 'Valencia' sweet orange trees and subjected to water withholding in isolation or competition experiments under potted conditions. Our results revealed that, when grown in isolation, tetraploid rootstocks took longer to show drought symptoms, but this advantage disappeared when grown in competition under the same soil moisture conditions. The differences in drought responses were mainly associated with variations in endogenous leaf levels of abscisic acid (ABA), hydrogen peroxide (H2O2) and carbohydrates among treatments. Overall, tetraploids were more affected by drought in individual experiments, showing higher H2O2 production, and in competition experiments, rapidly increasing ABA production to regulate stomatal closure and reduce water loss through transpiration. Therefore, our results highlight the crucial importance of evaluating diploid and tetraploid rootstocks under the same soil moisture conditions to better simulate field conditions, providing important insights to improve selection strategies for more resilient citrus rootstocks.

Gamma-aminobutyric acid elicits H2O2 signalling and promotes wheat seed germination under combined salt and heat stress.

Background: In the realm of wheat seed germination, abiotic stresses such as salinity and high temperature have been shown to hinder the process. These stresses can lead to the production of reactive oxygen species, which, within a certain concentration range, may actually facilitate seed germination. γ-aminobutyric acid (GABA), a non-protein amino acid, serves as a crucial signaling molecule in the promotion of seed germination. Nevertheless, the potential of GABA to regulate seed germination under the simultaneous stress of heat and salinity remains unexplored in current literature. Methods: This study employed observational methods to assess seed germination rate (GR), physiological methods to measure H2O2 content, and the activities of glutamate decarboxylase (GAD), NADPH oxidase (NOX), superoxide dismutase (SOD), and catalase (CAT). The levels of ABA and GABA were quantified using high-performance liquid chromatography technology. Furthermore, quantitative real-time PCR technology was utilized to analyze the expression levels of two genes encoding antioxidant enzymes, MnSOD and CAT. Results: The findings indicated that combined stress (30 °C + 50 mM NaCl) decreased the GR of wheat seeds to about 21%, while treatment with 2 mM GABA increased the GR to about 48%. However, the stimulatory effect of GABA was mitigated by the presence of ABA, dimethylthiourea, and NOX inhibitor, but was strengthened by H2O2, antioxidant enzyme inhibitor, fluridone, and gibberellin. In comparison to the control group (20 °C + 0 mM NaCl), this combined stress led to elevated levels of ABA, reduced GAD and NOX activity, and a decrease in H2O2 and GABA content. Further investigation revealed that this combined stress significantly suppressed the activity of superoxide dismutase (SOD) and catalase (CAT), as well as downregulated the gene expression levels of MnSOD and CAT. However, the study demonstrates that exogenous GABA effectively reversed the inhibitory effects of combined stress on wheat seed germination. These findings suggest that GABA-induced NOX-mediated H2O2 signalling plays a crucial role in mitigating the adverse impact of combined stress on wheat seed germination. This research holds significant theoretical and practical implications for the regulation of crop seed germination by GABA under conditions of combined stress.

The Diterpene Isopimaric Acid Modulates the Phytohormone Pathway to Promote Oryza sativa L. Rice Seedling Growth.

Many plant secondary metabolites are active and important in the regulation of plant growth. Certain plant-derived diterpenes are known to promote plant growth, but the pathways by which this promotion occurs are still unknown. Activity screening revealed that the plant-derived diterpene isopimaric acid exhibits growth-promoting activity in rice (Oryza sativa L.) seedlings. Furthermore, 25 µg/mL of isopimaric acid promoted the growth of 15 self-incompatible associated populations from different rice lineages to different extents. Quantitative analyses revealed a significant decrease in the concentration of the defense-related phytohormone abscisic acid (ABA) following treatment with isopimaric acid. Correlation analysis of the phytohormone concentrations with growth characteristics revealed that the length of seedling shoots was significantly negatively correlated with concentrations of 3-indole-butyric acid (IBA). Moreover, the total root weight was not only negatively correlated with ABA concentrations but also negatively correlated with concentrations of isopentenyl adenine (iP). These data suggest that isopimaric acid is able to influence the phytohormone pathway to balance energy allocation between growth and defense in rice seedlings and also alter the correlation between the concentrations of phytohormones and traits such as shoot and root length and weight. We provide a theoretical basis for the development and utilization of isopimaric acid as a plant growth regulator for rice.

Combined Metabolome and Transcriptome Analyses of Maize Leaves Reveal Global Effect of Biochar on Mechanisms Involved in Anti-Herbivory to Spodoptera frugiperda.

Fall armyworm (FAW, Spodoptera frugiperda) has now spread to more than 26 Chinese provinces. The government is working with farmers and researchers to find ways to prevent and control this pest. The use of biochar is one of the economic and environmentally friendly strategies to increase plant growth and improve pest resistance. We tested four v/v combinations of bamboo charcoal with coconut bran [BC1 (10:1), BC2(30:1), BC3(50:1)] against a control (CK) in maize. We found that plant height, stem thickness, fresh weight and chlorophyll content were significantly higher in BC2, in addition to the lowest FAW survival %. We then compared the metabolome and transcriptome profiles of BC2 and CK maize plants under FAW herbivory. Our results show that the levels of flavonoids, amino acids and derivatives, nucleotides and derivatives and most phenolic acids decreased, while terpenoids, organic acids, lipids and defense-related hormones increased in BC-grown maize leaves. Transcriptome sequencing revealed consistent expression profiles of genes enriched in these pathways. We also observed the increased expression of genes related to abscisic acid, jasmonic acid, auxin and MAPK signaling. Based on these observations, we discussed the possible pathways involved in maize against FAW herbivory. We conclude that bamboo charcoal induces anti-herbivory responses in maize leaves.

Comprehensive Identification and Expression Analysis of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Brachypodium distachyon.

The Multidrug and Toxic Compound Extrusion (MATE) proteins serve as pivotal transporters responsible for the extrusion of metabolites, thereby playing a significant role in both plant development and the detoxification of toxins. The MATE gene family within the Brachypodium distachyon, which is an important model organism of the Poaceae family, remains largely unexplored. Here, a comprehensive identification and analysis of MATE genes that complement B. distachyon were conducted. The BdMATE genes were systematically categorized into five distinct groups, predicated on an assessment of their phylogenetic affinities and protein structure. Furthermore, our investigation revealed that dispersed duplication has significantly contributed to the expansion of the BdMATE genes, with tandem and segmental duplications showing important roles, suggesting that the MATE genes in Poaceae species have embarked on divergent evolutionary trajectories. Examination of ω values demonstrated that BdMATE genes underwent purifying selection throughout the evolutionary process. Furthermore, collinearity analysis has confirmed a high conservation of MATE genes between B. distachyon and rice. The cis-regulatory elements analysis within BdMATEs promoters, coupled with expression patterns, suggests that BdMATEs play important roles during plant development and in response to phytohormones. Collectively, the findings presented establish a foundational basis for the subsequent detailed characterization of the MATE gene family members in B. distachyon.

Transcriptomic network underlying physiological alterations in the stem of Myricaria laxiflora in response to waterlogging stress.

Myricaria laxiflora is an endangered shrub plant with remarkable tolerance to waterlogging stress, however, little attention has been paid to understanding the underlying mechanisms. Here, physiological and transcriptomic approaches were applied to uncover the physiological and molecular reconfigurations in the stem of M. laxiflora in response to waterlogging stress. The accumulation of the contents of H2O2 and malonaldehyde (MDA) alongside increased activities of enzymes for scavenging the reactive oxygen species (ROS) in the stem of M. laxiflora were observed under waterlogging stress. The principal component analysis (PCA) of transcriptomes from five different timepoints uncovered PC1 counted for 17.3 % of total variations and separated the treated and non-treated samples. A total of 8714 genes in the stem of M. laxiflora were identified as differentially expressed genes (DEGs) under waterlogging stress, which could be assigned into two different subgroups with distinct gene expression patterns and biological functions. The DEGs involved in glycolysis were generally upregulated, whereas opposite results were observed for nitrogen uptake and the assimilation pathway. The contents of abscisic acid (ABA) and jasmonic acid (JA) were sharply decreased alongside the decreased mRNA levels of the genes involved in corresponding synthesis pathways upon waterlogging stress. A network centered by eight key transcription factors has been constructed, which uncovered the inhibited cell division processes in the stem of M. laxiflora upon waterlogging stress. Taken together, the obtained results showed that glycolysis, nitrogen metabolism and meristem activities played an important role in the stem of M. laxiflora in response to waterlogging stress.

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 our aim was to understand how phytochemical signals 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. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs. CONCLUSIONS: We highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial 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, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics 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. Video Abstract.