Manipulation of arginase expression modulates abiotic stress tolerance in Arabidopsis: effect on arginine metabolism and ROS accumulation

Gaseous exchange-dependent in vitro culture extensively alters plant growth and metabolic landscape revealed by comprehensive metabolomics

A complex interplay of environmental factors profoundly influences plant cellular metabolism, with gaseous exchange serving as a fundamental physiological process critical to growth and survival. While well-characterized in natural environments, the role of gaseous exchange in plant in-vitro culture remains underexplored. Plant in-vitro culture offers a versatile platform for studying metabolism, where metabolic networks are highly flexible and sensitive to environmental factors. Despite advancements in understanding these dynamics, there has been relatively little investigation into how gaseous exchange within tissue culture systems affects cellular metabolism. In the present study, we investigated the effects of gaseous exchange on plant growth and metabolism by comparing traditional Parafilm- and micropore-tape-based cultures designed to facilitate different levels of gaseous exchange. A comprehensive metabolomics approach using liquid chromatography-high-resolution mass spectrometry and gas chromatography-mass spectrometry was employed to delineate the metabolic changes in Arabidopsis under Parafilm- and micropore-tape-sealed culture conditions at two and three weeks of growth. Metabolic profiling identified increased levels of oxidized glutathione, arginine, ornithine, and aspartic acid, and decreased levels of TCA cycle intermediates and phenylpropanoid metabolites, indicating that restricted gas exchange alters the redox status and reprograms primary and secondary metabolism. This reprogramming affected amino acid metabolism, arginine metabolism, energy metabolism, as well as phenylpropanoid and flavonoid biosynthetic pathways. Restricted gaseous exchange in Parafilm-wrapped cultures also led to altered accumulation of several essential macro- and microelements in Arabidopsis seedlings. The present study demonstrated that restricted gaseous exchange inhibits plant growth and disrupts metabolism.

Trimethylamine-N-oxide enhances drought tolerance in Eucalyptus by increasing photosynthesis

Drought stress significantly reduces agricultural productivity, threatening global food security and timber production. Although trimethylamine-N-oxide (TMAO) has been shown to enhance drought tolerance in plants such as Arabidopsis thaliana and tomato, the physiological and molecular mechanisms by which it regulates drought tolerance in plants remain unclear. In this study, we investigated the physiological and transcriptomic changes in Eucalyptus under drought stress following exogenous TMAO treatment. Physiological analyses showed that TMAO treatment improved the drought resistance of Eucalyptus, and the optimal application concentration was 10 mM. Under drought stress, exogenous TMAO reduced the malondialdehyde content and electrolyte leakage in Eucalyptus leaves, and maintained the stability of the cell membrane. At the same time, TMAO maintained the stability of the photosynthetic electron transport chain and regulates stomatal aperture, which results in a 59% increase in the net photosynthetic efficiency of Eucalyptus under drought. Transcriptomic analysis revealed that TMAO activated pathways for phenylpropanoid biosynthesis, photosynthesis, and carbon metabolism, and influenced the drought resistance of Eucalyptus by regulating the expression of genes such as Phenylalanine ammonia-lyase (PAL), photosystem II reaction center PSB28 protein (Psb28), and FTSH protease 1 (FTSH1), thereby mediating the growth and development of Eucalyptus and its adaptation to adverse conditions. The findings of this study provide an important theoretical basis for using exogenous substances to alleviate plant stress under drought conditions and lay the foundation for exploring the use of exogenous substances in forestry and agriculture.

Transcriptomic analysis reveals the molecular mechanisms of heterosis in low-temperature tolerance in the hybrids of Argopecten scallops

The F1 hybrid of Argopecten irradians irradians (♀) × A. purpuratus (♂) exhibits significant heterosis in growth performance and mid-parent heterosis in low-temperature tolerance. This study presents a comparative transcriptomic analysis of A. irradians irradians (Ai), A. purpuratus (Ap), and the hybrid A. irradians irradians♀ × A. purpuratus♂ (Aip) to explore the mechanisms underlying low-temperature tolerance heterosis in Aip. A total of 33,376 differentially expressed genes (DEGs) were identified between F1 hybrids and purebreds under cold stress. In Aip, 80.32 % of DEGs exhibited non-additive expression patterns, with over-dominant expression observed in 30.65 % of these genes. Pairwise comparisons among the transcriptomes of Ai, Ap, and Aip revealed 14,959 alternative splicing events, affecting 8169 genes. KEGG pathway analysis indicated substantial enrichment of overlapping genes from common DEGs and non-additively expressed genes (NAGs) in apoptosis, longevity regulation, ABC transporters, and spliceosome pathways. Furthermore, analysis of DEGs, DAGs (Differentially Alternative Splicing genes), and NAGs identified 6 genes undergoing alternative splicing. These pathways and genes may be crucial in Aip's response to low-temperature stress and offer insights for advancing scallop cross-breeding strategies.

Combined transcriptomic and metabolomic analysis revealed the salt tolerance mechanism of Populus talassica × Populus euphratica

BACKGROUND

To investigate the salt tolerance of Populus talassica × Populus euphratica, morphological and physiological parameters were measured on the second day after the 15th, 30th and 45th days of NaCl treatment, revealing significant effects of NaCl on growth. To further elucidate the mechanisms underlying salt tolerance, transcriptomic and metabolomic analysis were conducted under different NaCl treatments.

RESULTS

The results of morphological and physiological indexes showed that under low salt treatment, P. talassica × P. euphratica was able to coordinate the growth of aboveground and belowground parts. Under high salt concentration, the growth and water balance of P. talassica × P. euphratica were markedly inhibited. The most significant differences between treatments were observed on the second day after the 45th day of NaCl treatment. Transcriptomic analysis showed that the pathways of gene enrichment in the roots and stems of P. talassica × P. euphratica were different in the salt resistance response. And it involves several core pathways such as plant hormone signal transduction, phenylpropanoid biosynthesis, MAPK signaling pathway-plant, plant- pathogen interaction, carbon metabolism, biosynthesis of amino acids, and several key Transcription factors (TFs) such as AP2/ERF, NAC, WRKY and bZIP. Metabolomic analysis revealed that KEGG pathway enrichment analysis showed unique metabolic pathways were enriched in P. talassica × P. euphratica under both 200 mM and 400 mM NaCl treatments. Additionally, while there were some differences in the metabolic pathways enriched in the roots and stems, both tissues commonly enriched pathways related to the biosynthesis of secondary metabolites, biosynthesis of cofactors, biosynthesis of amino acids, flavonoid biosynthesis, and ABC transporters. Association analysis further indicated that biosynthesis of amino acids and plant hormone signal transduction pathway play key roles in the response of P. talassica × P. euphratica to salt stress. The interactions between the differentially expressed genes (DEGs) and several differentially accumulated metabolites (DAMs), especially the strong association between LOC105124002 and Jasmonoyl-L-Isoleucine (pme2074), were again revealed by the interactions analysis.

CONCLUSIONS

In this study, we resolved the changes of metabolic pathways in roots and stems of P. talassica × P. euphratica under different NaCl treatments and explored the associations between characteristic DEGs and DAMs, which provided insights into the mechanisms of P. talassica × P. euphratica in response to salt stress.

Lead toxicity in Nicotiana tabacum L.: Damage antioxidant system and disturb plant metabolism

In this study, we treated tobacco seedlings with 0, 200, 400, and 800 mg/kg Pb2 +, and explored the response mechanism of tobacco under Pb stress through a combination of growth physiology and metabolomics analysis. The physiological results showed that compared with CK, with the increase of Pb concentration, Pb treatment inhibited tobacco growth, reduced the biomass and photosynthetic pigment content of tobacco seedlings, and severely damaged the chloroplast structure. In addition, compared with CK, the pore conductivity and pore density of Pb800 treatment decreased by 45.77 % and 93.55 %, respectively. Pb treatment disrupted the cell membrane system, and Pb800 treatment increased the content of malondialdehyde (MDA) in leaves and roots by 67.65 % and 31.90 %, respectively. Meanwhile, Pb treatment increased the activity of tobacco SOD and POD enzymes. Metabolomics results showed that Pb stress enhanced tryptophan metabolism, glutathione metabolism, alanine, aspartate, and glutamate metabolism, as well as cysteine and methionine metabolism pathways. These results indicate that increasing the content of photosynthetic pigments and hormones, clearing reactive oxygen species by enhancing antioxidant enzyme activity, and improving amino acid metabolism may play an important role in reducing the toxicity of Pb to tobacco.

Jingfang Granule promotes the tricarboxylic acid cycle to improve chronic fatigue syndrome by increasing the expression of Idh1 and Idh2

ETHNOPHARMACOLOGICAL RELEVANCE

Chronic fatigue syndrome (CFS), as a complex, multisystemic, and multisystemic disorder affecting multiple organs and systems, often accompanies by symptoms such as post-exercise discomfort, sleep disorders, cognitive difficulties, and orthostatic intolerance. Jingfang Granule (JFG) is a traditional Chinese medicine that have significant protective effects on CFS, but the mechanism is still vague.

AIM OF STUDY

This study was designed to evaluate the protective mechanism of JFG on mice with CFS.

MATERIALS AND METHODS

The combined stimuli method was used to establish the mice CFS model, and JFG was orally administered. The body weight, exhaustion swimming training and tail suspension test were assayed every 7 days to evaluate the improvement of JFG on CFS. Lactic acid, adenosine triphosphate (ATP), malondialdehyde (MDA), superoxide dismutase (SOD), reactive oxygen species (ROS), IL-1β, TNF-α, IL-6 in serum and liver glycogen, muscle glycogen in muscle were analyzed. Transmission electron microscopy was used to detect mitochondrial morphology. The regulatory networks were investigated by proteomics and central carbon metabolomics, which were verified by Western blot.

RESULTS

JFG reversed the loss of weight and reduce of exhaust swimming time (P < 0.05) induced by CFS in mice, and increased the tail suspension time (P < 0.05), indicating that JFG has an improving effect on CFS. Meanwhile, JFG increased the spleen index (P < 0.05), decreased the thymus index (P < 0.05) and cardiac index (P < 0.05), inhibited the secretion of Lactic acid (P < 0.05), and increased the content of liver glycogen (P < 0.05), muscle glycogen (P < 0.05), and ATP (P < 0.05), and improved mitochondrial morphology in mice with CFS. JFG also inhibited the release of TNF-α (P < 0.05), IL-1β (P < 0.05) and IL-6 (P < 0.05) in serum by inhibiting TLR4/NF-κB signaling pathway and NLRP3 inflammasome signaling pathway, and inhibited oxidative stress by activating Nrf2/HO-1/NQO1 axis. Integrated central carbon metabolomics, proteomics and Western blot showed that JFG intervened in CFS by increasing the expression of Idh1 (P < 0.05) and Idh2 (P < 0.01) to promote tricarboxylic acid (TCA) cycle.

CONCLUSIONS

This study confirmed that JFG promoted the TCA cycle by increasing the expression of Idh1 and Idh2, and then inhibited inflammation and oxidative stress to prevent CFS injury, which provided a potential drug candidate for CFS treatment.

Genome assembly and population analysis of tetraploid marama bean reveal two distinct genome types

Tylosema esculentum (marama bean), an underutilized orphan legume native to southern Africa, holds significant potential for domestication as a rescue crop to enhance local food security. Well-adapted to harsh desert environments, it offers valuable insights into plant resilience to extreme drought and high temperatures. In this study, k-mer analysis indicated marama as an ancient allotetraploid legume. Using 21.5 Gb of PacBio HiFi data, the genome was assembled with two assemblers, HiCanu and Hifiasm, followed by scaffolding with Omni-C data from Dovetail Genomics (Cantata Bio) using HiRise, resulting in a 558.78 Mb assembly with near chromosome-level continuity (N50 = 22.68 Mb, L50 = 8). Repeats accounted for 58.43% of the genome. Phylogenetic analysis indicated a close relationship with Bauhinia variegata and Cercis canadensis, diverging approximately 27.22 and 31.68 million years ago (Ma), respectively. Whole-genome duplication (WGD) analysis revealed an ancient duplication event in marama. Gene family analysis revealed expanded families enriched in pathways related to stress adaptation, energy metabolism, and environmental signaling, including the spliceosome, citrate cycle, and carbon fixation pathways. These findings highlight marama's resilience to arid environments. In contrast, contracted gene families associated with secondary metabolite biosynthesis and defense pathways suggest a trade-off, potentially due to reduced pathogen pressure. Marama-specific genes were enriched in amino acid catabolism pathways, potentially playing roles in stress signaling and energy regulation. Core gene families shared with other legumes were enriched in conserved pathways, such as photosynthesis and hormone signaling, which are fundamental for plant growth and survival. Population analysis of geographically diverse samples revealed two distinct clusters, though phenotypic differences remain unclear. Overall, this study presents the first high-quality genome assembly of marama bean, offering a valuable genomic reference for understanding its unique biology and highlighting its potential for crop improvement in challenging environments.

Rhizophagus irregularis regulates RiCPSI and RiCARI expression to influence plant drought tolerance

Arbuscular mycorrhizal fungi (AMF) can transfer inorganic nitrogen (N) from the soil to host plants to cope with drought stress, with arginine synthesis and NH4+ transport being pivotal processes. However, the regulatory mechanism underlying these processes remains unclear. Here, we found that drought stress upregulated expression of genes involved in the N transfer pathway and putrescine and glutathione synthesis in the mycorrhizal structures of Rhizophagus irregularis within alfalfa (Medicago sativa) roots, i.e. carbamoyl phosphate synthase (RiCPSI), arginase (RiCARI), urease (RiURE), ornithine decarboxylase (RiODC), and glutamate-cysteine ligase (RiGCL). Furthermore, we confirmed that RiCPSI is a carbamoyl phosphate synthase. Silencing RiCARI via host-induced gene silencing inhibited arbuscule formation, suppressed putrescine and glutathione synthesis, and altered arginine metabolism within R. irregularis-plant symbiosis, leading to a substantial reduction in the drought tolerance of M. sativa. Conversely, silencing RiCPSI decreased arginine, putrescine, and glutathione synthesis in R. irregularis but did not adversely affect NH4+ transfer from fungi to the host plant and drought tolerance of M. sativa. Interestingly, overexpressing RiCPSI via our host-induced gene overexpressing system enhanced arginine, putrescine, and glutathione synthesis in R. irregularis, reduced arbuscule abundance, and improved drought tolerance of M. sativa. Our findings demonstrate that under drought stress, the nitrogen transfer from AMF to the host plant was improved. This is accompanied by increased arginine, putrescine, and glutathione synthesis within R. irregularis, driven by the upregulation of RiCPSI and RiCARI expression in mycorrhizal structures within the roots. These molecular adjustments collectively contribute to enhanced drought tolerance in R. irregularis-plant symbiosis.

Integrated transcriptomic, proteomic and metabolomic analyses revealing the roles of amino acid and sucrose metabolism in augmenting drought tolerance in Agropyron mongolicum

Drought, a major consequence of climate change, initiates molecular interactions among genes, proteins, and metabolites. Agropyron mongolicum a high-quality perennial grass species, exhibits robust drought resistance. However, the molecular mechanism underlying this resistance remaining largely unexplored. In this study, we performed an integrated analysis of the transcriptome, proteome, and metabolome of A. mongolicum under optimal and drought stress conditions. This combined analysis highlighted the pivotal role of transporters in responding to drought stress. Moreover, metabolite profiling indicated that arginine and proline metabolism, as well as the pentose phosphate pathway, are significantly involved in the drought response of A. mongolicum. Additionally, the integrated analysis suggested that proline metabolism and the pentose phosphate pathway are key elements of the drought resistance strategy in A. mongolicum plants. In summary, our research elucidates the drought adaptation mechanisms of A. mongolicum and identifies potential candidate genes for further study.

Spatial organization of putrescine synthesis in plants

Three plant pathways for the synthesis of putrescine have been described to date. These are the synthesis of putrescine from ornithine, by ornithine decarboxylase (ODC); the synthesis of putrescine from arginine by arginine decarboxylase, agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (NLP1); and arginine decarboxylase and agmatinase. To address how these pathways are organized in plants, we have used transient expression analysis of these genes in the leaves of Nicotiana benthamiana. Brassicas do not have ODC, but the single ODC gene from rice and one of the soybean genes, were localized to the ER. Transient expression of the rice agmatinase gene showed that it was localized to the mitochondria. In A. thaliana there are five isoforms of AIH and three isoforms of NLP1. Stable GFP-tagged transformants of the longest isoforms of AIH and NLP1 showed that both proteins were localized to the ER, but in tissues with chloroplasts, the localization was concentrated to lamellae adjacent to chloroplasts. Transient expression analyses showed that four of the isoforms of AIH and all of the isoforms of NLP1 were localized to the ER. However, AIH.4 was localized to the chloroplast. Combining these results with other published data, reveal that putrescine synthesis is excluded from the cytoplasm and is spatially localized to the chloroplast, ER, and likely the mitochondria. Synthesis of putrescine in the ER may facilitate cell to cell transport via plasmodesmata, or secretion via vesicles. Differential expression of these pathways may enable putrescine-mediated activation of hormone-responsive genes.

Zinc Oxide Nanoparticle-Mediated Root Metabolic Reprogramming for Arsenic Tolerance in Soybean

Arsenate (AsV) is absorbed and accumulated by plants, which can affect their physiological activities, disrupt gene expression, alter metabolite content, and influence growth. Despite the potential of zinc oxide nanoparticles (ZnONPs) to mitigate the adverse effects of arsenic stress in plants, the underlying mechanisms of ZnONPs-mediated detoxification of AsV, as well as the specific metabolites and metabolic pathways involved, remain largely unexplored. In this study, we demonstrated root metabolomic profiling of soybean germinating seedlings subjected to 25 μmol L-1 arsenate (Na2HAsO4) and ZnONPs at concentrations of 25 μmol L-1 (ZnO25) and 50 μmol L-1 (ZnO50). The objective of this study was to examine the effects on soybean root metabolomics under AsV toxicity. Metabolomic analysis indicated that 453, 501, and 460 metabolites were significantly regulated in response to AsV, ZnO25, and ZnO50 treatments, respectively, compared to the control. Pathway analysis of the differentially regulated metabolites (DRMs) revealed that the tricarboxylic acid (TCA) cycle, glutathione metabolism, proline and aldarate metabolism, and arginine and proline metabolism were the most statistically enriched pathways in ZnONPs-supplemented plants. These findings suggest that ZnONPs enhance the tolerance response to AsV. Collectively, our results support the hypothesis that ZnONPs fertilization could be a potential strategy for improving soybean crop resilience under AsV stress.

Transcriptome analysis to identify genes related to programmed cell death resulted from manipulating of BnaFAH ortholog by CRISPR/Cas9 in Brassica napus

Fumarylacetoacetate hydrolase (FAH) catalyzes the final step of the tyrosine degradation pathway. In this study, we isolated and characterized two homologous BnaFAH genes in Brassica napus L. variant Westar, and then used CRISPR/Cas9-mediated targeted mutagenesis to generate a series of transgene-free mutant lines either with single or double-null bnafah alleles. Among these mutant lines, the aacc (bnafah) double-null mutant line, rather than the aaCC (bnaa06fah) mutant line, exhibited programmed cell death (PCD) under short days (SD). Histochemical staining and content measurement confirmed that the accumulation of reactive oxygen species (ROS) in bnafah was significantly higher than that in bnaa06fah. To further elucidate the mechanism of PCD, we performed transcriptomic analyses of bnaa06fah and bnafah at different SD stages. A heatmap cluster of differentially expressed genes (DEGs) revealed that PCD may be related to various redox regulatory genes involved in antioxidant activity, ROS-responsive regulation and calcium signaling. Combined with the results of previous studies, our work revealed that the expression levels of BnaC04CAT2, BnaA09/C09SAL1, BnaA08/C08ACO2, BnaA07/C06ERO1, BnaA08ACA1, BnaC04BIK1, BnaA09CRK36 and BnaA03CPK4 were significantly different and that these genes might be candidate hub genes for PCD. Together, our results underscore the ability of different PCD phenotypes to alter BnaFAH orthologs through gene editing and further elucidated the molecular mechanisms of oxidative stress-induced PCD in plants.

Knockdown of β-conglycinin α' and α subunits alters seed protein composition and improves salt tolerance in soybean

Soybean is an important plant source of protein worldwide. Increasing demands for soybean can be met by improving the quality of its seed protein. In this study, GmCG-1, which encodes the β-conglycinin α' subunit, was identified via combined genome-wide association study and transcriptome analysis. We subsequently knocked down GmCG-1 and its paralogues GmCG-2 and GmCG-3 with CRISPR-Cas9 technology and generated two stable multigene knockdown mutants. As a result, the β-conglycinin content decreased, whereas the 11S/7S ratio, total protein content and sulfur-containing amino acid content significantly increased. Surprisingly, the globulin mutant exhibited salt tolerance in both the germination and seedling stages. Little is known about the relationship between seed protein composition and the salt stress response in soybean. Metabonomics and RNA-seq analysis indicated that compared with the WT, the mutant was formed through a pathway that was more similar to that of active salicylic acid biosynthesis; however, the synthesis of cytokinin exhibited greater defects, which could lead to increased expression of plant dehydrin-related salt tolerance proteins and cell membrane ion transporters. Population evolution analysis suggested that GmCG-1, GmCG-2, and GmCG-3 were selected during soybean domestication. The soybean accessions harboring GmCG-1Hap1 presented relatively high 11S/7S ratios and relatively high salt tolerance. In conclusion, knockdown of the β-conglycinin α and α' subunits can improve the nutritional quality of soybean seeds and increase the salt tolerance of soybean plants, providing a strategy for designing soybean varieties with high nutritional value and high salt tolerance.

Physiological and metabolomic analyses reveal the mechanism by which exogenous spermine improves drought resistance in alfalfa leaves (Medicago sativa L.)

Introduction

Alfalfa (Medicago sativa L.) is a globally important legume crop with high nutritional and ecological value. Drought poses a serious threat to alfalfa acreage and yields. Spermine (Spm) has been shown to protect plants from drought damage. The aim of this study was to clarify the mechanism of exogenous Spm to improve drought resistance of alfalfa.

Methods

In this study, we root applied 0.1, 0.5, and 1 mM Spm to Gannong No. 3 (G3) alfalfa under drought stress, and then determined their physiological and metabolic changes.

Results

The results showed that exogenous Spm increased chlorophyll content, chlorophyll fluorescence parameters and gas exchange parameters, enhanced antioxidant enzymes activity, improved ascorbic acid-glutathione (AsA-GSH) cycle, increased osmoregulatory substances content, reduced hydrogen peroxide and superoxide anion levels, and inhibited malondialdehyde accumulation in alfalfa under drought stress, thereby increasing plant height and leaf relative water content and enhancing drought tolerance of alfalfa. The redundancy analysis of the above physiological indicators showed that the addition of the optimal Spm to improve drought tolerance of alfalfa under drought stress was mainly achieved by increasing catalase activity and improving the ASA-GSH cycle. In addition, metabolomics analysis revealed that exogenous Spm increased the content of oxobutanedioic acid, citric acid, fumaric acid and malic acid to enhance the tricarboxylic acid cycle. Meanwhile, exogenous Spm increased endogenous Spm and proline (Pro) content to resist drought stress by enhancing Spm and Pro metabolism. Moreover, exogenous Spm increased the accumulation of the signaling substance abscisic acid.

Discussion

In conclusion, exogenous Spm enhanced drought resistance of alfalfa leaves under drought stress.

Root exudates facilitate the regulation of soil microbial community function in the genus Haloxylon

Introduction

Root exudates act as the "language" of plant-soil communication, facilitating crucial interactions, information exchange, and energy transfer between plants and soil. The interactions facilitated by root exudates between plants and microorganisms in the rhizosphere are crucial for nutrient uptake and stress resilience in plants. However, the mechanism underlying the interaction between root exudates and rhizosphere microorganisms in desert plants under drought conditions remains unclear, especially among closely related species.

Methods

To reveal the ecological strategies employed by the genus Haloxylon in different habitats. Using DNA extraction and sequencing and UPLC-Q-Tof/MS methods, we studied root exudates and soil microorganisms from two closely related species, Haloxylon ammodendron (HA) and Haloxylon persicum (HP), to assess differences in their root exudates, soil microbial composition, and interactions.

Results

Significant differences were found in soil properties and root traits between the two species, among which soil water content (SWC) and soil organic carbon (SOC) in rhizosphere and bulk soils (P < 0.05). While the metabolite classification of root exudates was similar, their components varied, with terpenoids being the main differential metabolites. Soil microbial structure and diversity also exhibited significant differences, with distinct key species in the network and differential functional processes mainly related to nitrogen and carbon cycles. Strong correlations were observed between root exudate-mediated root traits, soil microorganisms, and soil properties, although the complex interactions differed between the two closely relative species. The primary metabolites found in the network of HA include sugars and fatty acids, while HP relies on secondary metabolites, steroids and terpenoids.

Discussion

These findings suggest that root exudates are key in shaping rhizosphere microbial communities, increasing microbial functionality, fostering symbiotic relationships with hosts, and bolstering the resilience of plants to environmental stress.

Oxidative stress and metabolic process responses of Chlorella pyrenoidosa to nanoplastic exposure: Insights from integrated analysis of transcriptomics and metabolomics

Oxidative stress is a universal interpretation for the toxicity mechanism of nanoplastics to microalgae. However, there is a lack of deeper insight into the regulation mechanism in microalgae response to oxidative stress, thus affecting the prevention and control for nanoplastics hazard. The integrated analysis of transcriptomics and metabolomics was employed to investigate the mechanism for the oxidative stress response of Chlorella pyrenoidosa to nanoplastics and subsequently lock the according core pathways and driver genes induced. Results indicated that the linoleic acid metabolism, glycine (Gly)-serine (Ser)-threonine (Thr) metabolism, and arginine and proline metabolism pathways of C. pyrenoidosa were collectively involved in oxidative stress. The analysis of linoleic acid metabolism suggested that nanoplastics prompted algal cells to secrete more allelochemicals, thereby leading to destroy the immune system of cells. Gly-Ser-Thr metabolism and arginine and proline metabolism pathways were core pathways involved in algal regulation of cell membrane function and antioxidant system. Key genes, such as LOX2.3, SHM1, TRPA1, and proC1, are drivers of regulating the oxidative stress of algae cells. This investigation lays the foundation for future applications of gene editing technology to limit the hazards of nanoplastics on aquatic organism.

Unraveling the role of urea hydrolysis in salt stress response during seed germination and seedling growth in Arabidopsis thaliana

Urea is intensively utilized as a nitrogen fertilizer in agriculture, originating either from root uptake or from catabolism of arginine by arginase. Despite its extensive use, the underlying physiological mechanisms of urea, particularly its adverse effects on seed germination and seedling growth under salt stress, remain unclear. In this study, we demonstrate that salt stress induces excessive hydrolysis of arginine-derived urea, leading to an increase in cytoplasmic pH within seed radical cells, which, in turn, triggers salt-induced inhibition of seed germination (SISG) and hampers seedling growth. Our findings challenge the long-held belief that ammonium accumulation and toxicity are the primary causes of SISG, offering a novel perspective on the mechanism underlying these processes. This study provides significant insights into the physiological impact of urea hydrolysis under salt stress, contributing to a better understanding of SISG.

Bao Yuan decoction alleviates fatigue by restraining inflammation and oxidative stress via the AMPK/CRY2/PER1 signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Baoyuan Decoction (BYD) was initially recorded in the classic of "Bo Ai Xin Jian" in the Ming dynasty. It is traditionally used for treating weakness and cowardice, and deficiency of vital energy. In researches related to anti-fatigue effects, the reciprocal regulation of AMPK and circadian clocks likely plays an important role in anti-fatigue mechanism, while it has not yet been revealed. Therefore, we elucidated the anti-fatigue mechanism of BYD through AMPK/CRY2/PER1 pathway.

AIM OF THE STUDY

To investigate the effect and mechanism of BYD in reducing fatigue, using pharmacodynamics, network pharmacology and transcriptomics through the AMPK/CRY2/PER1 signaling pathway.

MATERIALS AND METHODS

Firstly, the chemical constituents of BYD were qualitatively identified by UHPLC-Q-Exactive Orbitrap/MS, establishing a comprehensive strategy with an in-house library, Xcalibur software and Pubchem combined. Secondly, a Na2SO3-induced fatigue model and 2,2'-Azobis (2-methylpropionamidine) dihydrochloride (AAPH)-induced oxidative stress model were developed to evaluate the anti-fatigue and anti-oxidant activities of BYD using AB zebrafish. The anti-inflammatory activity of BYD was evaluated using CuSO4-induced and tail cutting-induced Tg (lyz: dsRed) transgenic zebrafish inflammation models. Then, target screening was performed by Swiss ADME, GeneCards, OMIM and DrugBank databases, the network was constructed using Cytoscape 3.9.0. Transcriptome and network pharmacology technology were used to investigate the related signaling pathways and potential mechanisms after treatment with BYD, which were verified by real-time quantitative PCR (RT-qPCR).

RESULTS

In total, 114 compounds from the water extract of BYD were identified as major compounds. Na₂SO₃-induced fatigue model and AAPH-induced oxidative stress model indicated that BYD has significant anti-fatigue and antioxidant effects. Meanwhile, BYD showed significant anti-inflammatory effects on CuSO4-induced and tail cutting-induced zebrafish inflammation models. The KEGG result of network pharmacology showed that the anti-fatigue function of BYD was mainly effected through AMPK signaling pathway. Besides, transcriptome analysis indicated that the circadian rhythm, AMPK and IL-17 signaling pathways were recommended as the main pathways related to the anti-fatigue effect of BYD. The RT-qPCR results showed that compared with a model control group, the treatment of BYD significantly elevated the expression mRNA of AMPK, CRY2 and PER1.

CONCLUSION

Herein, we identified 114 chemical constituents of BYD, performed zebrafish activity validation, while demonstrated that BYD can relieve fatigue by AMPK/CRY2/PER1 signaling pathway through network pharmacology and transcriptome.

Biochemistry of microwave controlled Heracleum sosnowskyi (Manden.) roots with an ecotoxicological aspect

Sosnowski hogweed is an invasive weed in eastern-middle Europe that is dangerous to human health and the environment. The efficacy of its control using chemical and mechanical methods is limited. Electromagnetic radiation (microwaves) could be an environmentally friendly alternative for controlling this species. This study aims to: (1) Determine the effect of varying microwave treatment (MWT) durations on the control of S. hogweed using a device emitting microwaves at 2.45 GHz, 32.8 kW/m2; (2) Evaluate the impact of MWT on soil by an ecotoxicological bioassays; (3) Analyze biochemical changes occurring in the roots during the process. A field study was performed to assess the efficacy of S. hogweed control using MWT in times from 2.5 to 15 min. The MWT-treated soil was collected immediately after treatment (AT) and tested using bioassays (Phytotoxkit, Ostracodtoxkit, and Microtox). Fourteen days AT, the MWT hogweed roots were dug out, air-dried, and analyzed for the content and composition of essential oil, sugars, and fatty acids. According to the ecotoxicological biotests, the MWT soils were classified as non-toxic or low-toxic. The regeneration of hogweed was observed only in non-treated plants (control). Hogweed MWT for 2.5-15 min did not regenerate up to 14 days AT. The average weight of roots in hogweed MWT for 15.0 min was ca. two times smaller than the control plants. Those roots contained significantly higher amounts of sugars and saturated fatty acids than the control. We did not find a correlation between S. hogweed root essential oil content and composition and MWT time. The main compounds of essential oil were p‑cymene and myristicin. No highly photosensitizing compounds were identified in the tested root oil. We conclude that MWT of S. hogweed could be an environmentally safe and prospective control method, but more studies are needed.

Cloning and Functional Analysis of CsROP5 and CsROP10 Genes Involved in Cucumber Resistance to Corynespora cassiicola

The cloning of resistance-related genes CsROP5/CsROP10 and the analysis of their mechanism of action provide a theoretical basis for the development of molecular breeding of disease-resistant cucumbers. The structure domains of two Rho-related guanosine triphosphatases from plant (ROP) genes were systematically analyzed using the bioinformatics method in cucumber plants, and the genes CsROP5 (Cucsa.322750) and CsROP10 (Cucsa.197080) were cloned. The functions of the two genes were analyzed using reverse-transcription quantitative PCR (RT-qPCR), virus-induced gene silencing (VIGS), transient overexpression, cucumber genetic transformation, and histochemical staining technology. The conserved elements of the CsROP5/CsROP10 proteins include five sequence motifs (G1-G5), a recognition site for serine/threonine kinases, and a hypervariable region (HVR). The knockdown of CsROP10 through VIGS affected the transcript levels of ABA-signaling-pathway-related genes (CsPYL, CsPP2Cs, CsSnRK2s, and CsABI5), ROS-signaling-pathway-related genes (CsRBOHD and CsRBOHF), and defense-related genes (CsPR2 and CsPR3), thereby improving cucumber resistance to Corynespora cassiicola. Meanwhile, inhibiting the expression of CsROP5 regulated the expression levels of ROS-signaling-pathway-related genes (CsRBOHD and CsRBOHF) and defense-related genes (CsPR2 and CsPR3), thereby enhancing the resistance of cucumber to C. cassiicola. Overall, CsROP5 and CsROP10 may participate in cucumber resistance to C. cassiicola through the ROS and ABA signaling pathways.

Grafting seedling rootstock strengthens tolerance to drought stress in polyploid mulberry (Morus alba L.)

The economically adaptable mulberry (Morus alba L.) has a long history of grafting in China, yet the physiological mechanisms and advantages in drought tolerance remain unexplored. In our study, we investigated the responses of self-rooted 2X (diploid), 3X (triploid), and 4X (tetraploid) plants, as well as polyploid plants grafted onto diploid seedling rootstocks (2X/2X, 3X/2X, and 4X/2X) under drought stress. We found that self-rooted diploid plants exhibited the most severe phenotypic damage, lowest water retention, photosynthetic capacity, and the least effective osmotic stress adjustment compared to tetraploid and triploid plants. However, grafted diploid and triploid plants showed effective mitigation of drought-induced damage, with higher relative water content and improved soil water retention. Grafted plants also improved the photosystem response to drought stress through elevated photosynthetic potential, closed stomatal aperture, and faster recovery of chlorophyll biosynthesis in the leaves. Additionally, grafted plants altered osmotic protective compound levels, including starch, soluble sugar, and proline content, thereby enhancing drought resistance. Absolute quantification PCR indicated that the expression levels of proline synthesis-related genes in grafted plants were not influenced after drought stress, whereas they were significantly increased in self-rooted plants. Consequently, our findings support that self-rooted triploid and tetraploid mulberries exhibited superior drought resistance compared to diploid plants. Moreover, grafting onto seedling rootstocks enhanced tolerance against drought stress in diploid and triploid mulberry, but not in tetraploid. Our study provides valuable insights for a comprehensive analysis of physiological effects in response to drought stress between stem-roots and seedling rootstocks.

PbrWRKY62-PbrADC1 module involves in superficial scald development of Pyrus bretschneideri Rehd.fruit via regulating putrescine biosynthesis

Putrescine plays a role in superficial scald development during the cold storage of pear fruit. However, the molecular mechanism behind this phenomenon has not been un-fully clarified until recently. In this study, a conjoint analysis of metabolites and gene expression profiles in the putrescine-metabolic pathway of P. bretschneideri Rehd. fruit followed by experimental validation revealed that PbrADC1, forming a homodimer in the chloroplast, was involved in putrescine biosynthesis and thus fruit chilling resistance. Additionally, the substrate-binding residue Cys546 in PbrADC1, whose activity was modified by H2O2, played a crucial role in arginine decarboxylation into agmatine. Through a combined analysis of the distribution of cis-acting elements in the PbrADC1 promoter as well as the expression profiles of related transcription factors (TFs), several TFs were identified as upstream regulators of PbrADC1 gene. Further investigation revealed that the nuclear PbrWRKY62 could directly bind to the W-box elements in the PbrADC1 promoter, activate its expression, enhance putrescine accumulation, and thus increase fruit chilling tolerance. In conclusion, our results suggest that the PbrWRKY62-PbrADC1 module is involved in the development of superficial scald in P. bretschneideri Rehd. fruit via regulating putrescine biosynthesis. Consequently, these findings could serve as valuable genetic resources for breeding scald-resistant pear fruit.

Enhanced azadirachtin production in neem (Azadirachta indica) callus through NaCl elicitation: Insights into differential protein regulation via shotgun proteomics

With their remarkable bioactivity and evolving commercial importance, plant secondary metabolites (PSMs) have gained significant research interest in recent years. Plant tissue culture serves as a credible tool to examine how abiotic stresses modulate the production of PSMs, enabling clear insights into plant stress responses and the prospects for controlled synthesis of bioactive compounds. Azadirachta indica, or neem has been recognized as a repository of secondary metabolites for centuries, particularly for the compound named azadirachtin, due to its bio-pesticidal and high antioxidant properties. Introducing salt stress as an elicitor makes it possible to enhance the synthesis of secondary metabolites, specifically azadirachtin. Thus, in this research, in vitro callus cultures of neem were micro-propagated and induced with salinity stress to explore their effects on the production of azadirachtin and identify potential proteins associated with salinity stress through comparative shotgun proteomics (LCMS/MS). To induce salinity stress, 2-month-old calli were subjected to various concentrations of NaCl (0.05-1.5%) for 4 weeks. The results showed that the callus cultures were able to adapt and survive in the salinity treatments, but displayed a reduction in fresh weight as the NaCl concentration increased. Notably, azadirachtin production was significantly enhanced in the salinity treatment compared to control, where 1.5% NaCl-treated calli produced the highest azadirachtin amount (10.847 ± 0.037 mg/g DW). The proteomics analysis showed that key proteins related to primary metabolism, such as defence, energy, cell structure, redox, transcriptional and photosynthesis, were predominantly differentially regulated (36 upregulated and 93 downregulated). While a few proteins were identified as being regulated in secondary metabolism, they were not directly involved in the synthesis of azadirachtin. In conjunction with azadirachtin elicitation, salinity stress treatment could therefore be successfully applied in commercial settings for the controlled synthesis of azadirachtin and other plant-based compounds. Further complementary omics approaches can be employed to enhance molecular-level modifications, to facilitate large-scale production of bioactive compounds in the future.

Cucumis sativus CsbZIP90 suppresses Podosphaera xanthii resistance by modulating reactive oxygen species

Resistance to disease in plants requires the coordinated action of multiple functionally related genes, as it is difficult to improve disease resistance with a single functional gene. Therefore, the use of transcription factors to regulate the expression of multiple resistance genes to improve disease resistance has become a recent focus in the field of gene research. The basic leucine zipper (bZIP) transcription factor family plays vital regulatory roles in processes, such as plant growth and development and the stress response. In our previous study, CsbZIP90 (Cucsa.134370) was involved in the defense response of cucumber to Podosphaera xanthii, but the relationship between cucumber and resistance to powdery mildew remained unclear. Herein, we detected the function of CsbZIP90 in response to P. xanthii. CsbZIP90 was localized to the cytoplasm and nucleus, and its expression was significantly induced during P. xanthii attack. Transient overexpression of CsbZIP90 in cucumber cotyledons resulted in decreased resistance to P. xanthii, while silencing CsbZIP90 increased resistance to P. xanthii. CsbZIP90 negatively regulated the expression of reactive oxygen species (ROS)-related genes and activities of ROS-related kinases. Taken together, our results show that CsbZIP90 suppresses P. xanthi resistance by modulating ROS. This study will provide target genes for breeding cucumbers resistant to P. xanthii.

Sheng Mai Yin shows anti-fatigue, anti-hypoxia and cardioprotective potential in an experimental joint model of fatigue and acute myocardial infarction

ETHNOPHARMACOLOGICAL RELEVANCE

Cardiovascular disease (CVD) and fatigue are two common diseases endangering human life and health that may interact and reinforce one another. Myocardial infarction survivors frequently experience fatigue, and acute myocardial infarction (AMI) is one of the most common cardiovascular diseases that cause fatigue-induced sudden death. Sheng Mai Yin (SMY), a Chinese medicine prescription, is traditionally used for the treatment of diabetes and cardiovascular disease, and has been demonstrated to reduce fatigue and safeguard cardiac function.

AIM OF THE STUDY

This study aims to investigate the effects and underlying mechanisms of SMY in treating fatigue and AMI.

MATERIALS AND METHODS

The pharmacological mechanisms of SMY in treating fatigue and AMI were predicted by bioinformatics and network pharmacology methods. After administering SMY at high, medium and low doses, the swimming time to exhaustion, hemoglobin level, serological parameters and hypoxia tolerance time were detected in C57BL/6N mice, and the left ventricular ejection fractions (LVEF), left ventricular fractional shortening (LVFS), grasp strength, cardiac histopathology, serological parameters and the expression of PINK1 and Parkin proteins were examined in Wistar rats.

RESULTS

371 core targets for SMY and 282 disease targets for fatigue and AMI were obtained using bioinformatics and network pharmacology methods. Enrichment analysis of target genes revealed that SMY might interfere with fatigue and AMI through biological processes such as mitochondrial autophagy, apoptosis, and oxidative stress. For in vivo experiments, SMY showed significant anti-fatigue and hypoxia tolerance effects in mice; It also improved the cardiac function and grasp strength, decreased their cardiac index, myocardial injury and fibrosis degree, and induced serological parameters levels and the expression of PTEN-induced putative kinase 1 (PINK1) and Parkin proteins in myocardium, suggesting that SMY may exert cardioprotective effects in a joint rat model of fatigue and AMI by inhibiting excessive mitochondrial autophagy.

CONCLUSION

This study revealed the anti-fatigue, anti-hypoxia and cardioprotective effects of SMY in a joint model of fatigue-AMI, and the pharmacological mechanism may be related to the inhibition of mitochondrial autophagy in cardiomyocytes through the PINK1/Parkin pathway. The discoveries may provide new ideas for the mechanism study of traditional Chinese medicine, especially complex prescriptions, in treating fatigue and AMI.

BcaSOD1 enhances cadmium tolerance in transgenic Arabidopsis by regulating the expression of genes related to heavy metal detoxification and arginine synthesis

Cadmium (Cd), which is a nonessential heavy metal element for organisms, can have a severe impact on the growth and development of organisms that absorb excessive Cd. Studies have shown that Brassica carinata, a semiwild oil crop, has strong tolerance to various abiotic stresses, and RNA-seq has revealed that the B. carinata superoxide dismutase gene (BcaSOD1) likely responds to Cd stress. To elucidate the BcaSOD1 function involved in tolerance of Cd stress, we cloned the coding sequences of BcaSOD1 from a purple B. carinata accession and successfully transferred it into Arabidopsis thaliana. The subcellular localization results demonstrated that BcaSOD1 was primarily located in the plasma membrane, mitochondria and nucleus. Overexpression of BcaSOD1 in transgenic Arabidopsis (OE) effectively decreased the toxicity caused by Cd stress. Compared to the WT (wild type lines), the OE lines exhibited significantly increased activities of antioxidant enzymes (APX, CAT, POD, and SOD) after exposure to 2.5 mM CdCl2. The Cd content of underground (root) in the OE line was dominantly higher than that in the WT; however, the Cd content of aboveground (shoot) was comparable between the OE and WT types. Moreover, the qRT‒PCR results showed that several heavy metal detoxification-related genes (AtIREG2, AtMTP3, AtHMA3, and AtNAS4) were significantly upregulated in the roots of OE lines under Cd treatment, suggesting that these genes are likely involved in Cd absorption in the roots of OE lines. In addition, both comparable transcriptome and qRT-PCR analyses revealed that exogenous BcaSOD1 noticeably facilitates detoxification by stimulating the expression of two arginine (Arg) biosynthesis genes (AtGDH1 and AtGDH2) while inhibiting the expression of AtARGAH1, a negative regulator in biosynthesis of Arg. The Arg content was subsequently confirmed to be significantly enhanced in OE lines under Cd treatment, indicating that BcaSOD1 likely strengthened Cd tolerance by regulating the expression of Arg-related genes. This study demonstrates that BcaSOD1 can enhance Cd tolerance and reveals the molecular mechanism of this gene, providing valuable insights into the molecular mechanism of Cd tolerance in plants.

Genome-wide transcriptomic and functional analyses provide new insights into the response of spring barley to drought stress

Drought is a major abiotic stress that impairs the physiology and development of plants, ultimately leading to crop yield losses. Drought tolerance is a complex quantitative trait influenced by multiple genes and metabolic pathways. However, molecular intricacies and subsequent morphological and physiological changes in response to drought stress remain elusive. Herein, we combined morpho-physiological and comparative RNA-sequencing analyses to identify core drought-induced marker genes and regulatory networks in the barley cultivar 'Giza134'. Based on field trials, drought-induced declines occurred in crop growth rate, relative water content, leaf area duration, flag leaf area, concentration of chlorophyll (Chl) a, b and a + b, net photosynthesis, and yield components. In contrast, the Chl a/b ratio, stoma resistance, and proline concentration increased significantly. RNA-sequence analysis identified a total of 2462 differentially expressed genes (DEGs), of which 1555 were up-regulated and 907 were down-regulated in response to water-deficit stress (WD). Comparative transcriptomics analysis highlighted three unique metabolic pathways (carbohydrate metabolism, iron ion binding, and oxidoreductase activity) as containing genes differentially expressed that could mitigate water stress. Our results identified several drought-induced marker genes belonging to diverse physiochemical functions like chlorophyll concentration, photosynthesis, light harvesting, gibberellin biosynthetic, iron homeostasis as well as Cis-regulatory elements. These candidate genes can be utilized to identify gene-associated markers to develop drought-resilient barley cultivars over a short period of time. Our results provide new insights into the understanding of water stress response mechanisms in barley.

A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress

The main factor leading to a decrease in crop productivity is abiotic stresses, particularly drought. Plants with C4 and CAM photosynthesis are better adapted to drought-prone areas than C3 plants. Therefore, it is beneficial to compare the stress response of plants with different photosynthetic pathways. Since most crops are C3 and C4 plants, this study focused on conducting an RNA-seq meta-analysis to investigate and compare how C3 and C4 plants respond to drought stress at the gene expression level in their leaves. Additionally, the accuracy of the meta-analysis results was confirmed with RT-qPCR. Based on the functional enrichment and network analysis, hub genes related to ribosomal proteins and photosynthesis were found to play a potential role in stress response. Moreover, our findings suggest that the low abundant amino acid degradation pathway, possibly through providing ATP source for the TCA cycle, in both groups of plants and the activation of the OPPP pathway in C4 plants, through providing the electron source required by this plant, can help to improve drought stress tolerance.

SnRK2.4-mediated phosphorylation of ABF2 regulates ARGININE DECARBOXYLASE expression and putrescine accumulation under drought stress

Arginine decarboxylase (ADC)-mediated putrescine (Put) biosynthesis plays an important role in plant abiotic stress response. SNF1-related protein kinases 2s (SnRK2s) and abscisic acid (ABA)-response element (ABRE)-binding factors (ABFs), are core components of the ABA signaling pathway involved in drought stress response. We previously reported that ADC of Poncirus trifoliata (PtrADC) functions in drought tolerance. However, whether and how SnRK2 and ABF regulate PtrADC to modulate putrescine accumulation under drought stress remains largely unclear. Herein, we employed a set of physiological, biochemical, and molecular approaches to reveal that a protein complex composed of PtrSnRK2.4 and PtrABF2 modulates putrescine biosynthesis and drought tolerance by directly regulating PtrADC. PtrABF2 was upregulated by dehydration in an ABA-dependent manner. PtrABF2 activated PtrADC expression by directly and specifically binding to the ABRE core sequence within its promoter and positively regulated drought tolerance via modulating putrescine accumulation. PtrSnRK2.4 interacts with and phosphorylates PtrABF2 at Ser93. PtrSnRK2.4-mediated PtrABF2 phosphorylation is essential for the transcriptional regulation of PtrADC. Besides, PtrSnRK2.4 was shown to play a positive role in drought tolerance by facilitating putrescine synthesis. Taken together, this study sheds new light on the regulatory module SnRK2.4-ABF2-ADC responsible for fine-tuning putrescine accumulation under drought stress, which advances our understanding on transcriptional regulation of putrescine synthesis.

Comparative analyses of functional traits based on metabolome and economic traits variation of Bletilla striata: Contribution of intercropping

The intercropping practice has been regarded as a practical land-use selection to improve the management benefits of Bletilla striata plantations. The reports about the variety of economic and functional traits of Bletilla pseudobulb under intercropping systems were limited. The present study investigated the variation of economic and functional traits of Bletilla pseudobulb under different intercropping systems (the deep-rooted intercropping system: B. striata - Cyclocarya paliurus, CB; and the shallow-rooted intercropping system: B. striata - Phyllostachys edulis, PB). The functional traits were analyzed through non-targeted metabolomics based on GC-MS. The results indicated that the PB intercropping system significantly decreased the yield of Bletilla pseudobulb while significantly increasing the total phenol and flavonoids compared with the control (CK). However, there were no significant differences in all economic traits between CB and CK. The functional traits among CB, PB, and CK were separated and exhibited significant differences. Under different intercropping systems, B. striata may adopt different functional strategies in response to interspecific competition. The functional node metabolites (D-galactose, cellobiose, raffinose, D-fructose, maltose, and D-ribose) were up-regulated in CB, while the functional node metabolites (L-valine, L-leucine, L-isoleucine, methionine, L-lysine, serine, D-glucose, cellobiose, trehalose, maltose, D-ribose, palatinose, raffinose, xylobiose, L-rhamnose, melezitose, and maltotriose) were up-regulated in PB. The correlation between economic and functional traits depends on the degree of environmental stress. Artificial neural network models (ANNs) accurately predicted the variation in economic traits via the combination of functional node metabolites in PB. The correlation analysis of environmental factors indicated that Ns (including TN, NH₄ ⁺-, and NO₃ ^--), SRI (solar radiation intensity), and SOC were the main factors that affected the economic traits (yield, total phenol, and total flavonoids). TN, SRI, and SOC were the main factors affecting the functional traits of the Bletilla pseudobulb. These findings strengthen our understanding of the variation of economic and functional traits of Bletilla pseudobulb under intercropping and clarify the main limiting environmental factors under B. striata intercropping systems.

Integrated transcriptome and metabolome analyses shed light on the defense mechanisms in tomato plants after (E)-2-hexenal fumigation

Tomato is a widely cultivated fruit and vegetable and is valued for its flavor, colour, and nutritional value. C₆-aldehydes, such as (E)-2-hexenal, not only have antibacterial and antifungal properties but also function as signaling molecules that control the defense mechanisms of plants, including tomatoes. In this study, we used liquid chromatography-mass spectrometry (LC-MS) and RNA sequencing techniques to generate metabolome and transcriptome datasets that elucidate the molecular mechanisms regulating defense responses in tomato leaves exposed to (E)-2-hexenal. A total of 28.27 Gb of clean data were sequenced and assembled into 23,720 unigenes. In addition, a non-targeted metabolomics approach detected 739 metabolites. There were 233 significant differentially expressed genes (DEGs) (158 up-regulated, 75 down-regulated) and 154 differentially expressed metabolites (DEMs) (86 up-regulated, 69 down-regulated). Most nucleotides and amino acids (L-Phenylalanine, L-Asparagine, L-Histidine, L-Arginine, and L-Tyrosine) and their derivatives were enriched. The analyses revealed that mitogen-activated protein kinase (MPK), pathogenesis-related protein (PR), and endochitinase (CHIB) were primarily responsible for the adaptation of plant defense responses. Therefore, the extensive upregulation of these genes may be associated with the increased plant defense response. These findings help us comprehend the defense response of plants to (E)-2-hexenal and improve the resistance of horticultural plants.

PheLBD29, an LBD transcription factor from Moso bamboo, causes leaf curvature and enhances tolerance to drought stress in transgenic Arabidopsis

The lateral organ boundaries domain (LBD), a unique family of transcription factors in higher plants, plays a key role in plant growth and development, and stress response. Here, we report on the novel lateral organ boundaries domain (LBD) gene PheLBD29, a nuclear localization protein that can bind the conserved GCCCCG sequence, as determined by electrophoretic mobility shift assay (EMSA). PheLBD29 was highly expressed in blade leaf and significantly induced by polyethylene glycol (PEG). Overexpression of PheLBD29 leads to small and abaxially rolled leaves in Arabidopsis, and anatomically, 35S:PheLBD29 Arabidopsis leaves showed transformation of adaxial cells into abaxial cells. Moreover, overexpression of PheLBD29 in Arabidopsis increased plant tolerance to drought stress, by accumulation of more soluble sugars, less malondialdehyde (MDA), and had lower REL levels under drought stress. Transient expression assay revealed PheLBD29 directly bound to the promoter region of RAB18. In addition, 35S:PheLBD29 Arabidopsis showed higher sensitivity to abscisic acid (ABA) than the wild type. Therefore, we conclude that PheLBD29 may participate in the ABA-dependent signaling pathway to improve drought tolerance. Our study provides new evidence for a Moso bamboo LBD protein regulatory module in leaf curvature and drought resistance.

Conserved hierarchical gene regulatory networks for drought and cold stress response in Myrica rubra

Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (Myrica rubra). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses. Drought- and cold-responsive GRNs, which have been built according to the timing of transcription under both abiotic stresses, have a conserved trans-regulator and a common regulatory network. In both GRNs, basic helix-loop-helix family transcription factor (bHLH) serve as central nodes. MrbHLHp10 transcripts exhibited continuous increase in the two abiotic stresses and acts upstream regulator of ASCORBATE PEROXIDASE (APX) gene. To examine the potential biological functions of MrbHLH10, we generated a transgenic Arabidopsis plant that constitutively overexpresses the MrbHLH10 gene. Compared to wild-type (WT) plants, overexpressing transgenic Arabidopsis plants maintained higher APX activity and biomass accumulation under drought and cold stress. Consistently, RNAi plants had elevated susceptibility to both stresses. Taken together, these results suggested that MrbHLH10 mitigates abiotic stresses through the modulation of ROS scavenging.

Expanding roles for S-nitrosylation in the regulation of plant immunity

Following pathogen recognition, plant cells produce a nitrosative burst resulting in a striking increase in nitric oxide (NO), altering the redox state of the cell, which subsequently helps orchestrate a plethora of immune responses. NO is a potent redox cue, efficiently relayed between proteins through its co-valent attachment to highly specific, powerfully reactive protein cysteine (Cys) thiols, resulting in formation of protein S-nitrosothiols (SNOs). This process, known as S-nitrosylation, can modulate the function of target proteins, enabling responsiveness to cellular redox changes. Key targets of S-nitrosylation control the production of reactive oxygen species (ROS), the transcription of immune-response genes, the triggering of the hypersensitive response (HR) and the establishment of systemic acquired resistance (SAR). Here, we bring together recent advances in the control of plant immunity by S-nitrosylation, furthering our appreciation of how changes in cellular redox status reprogramme plant immune function.

Over-expression of spermidine synthase 2 (SlSPDS2) in tomato plants improves saline-alkali stress tolerance by increasing endogenous polyamines content to regulate antioxidant enzyme system and ionic homeostasis

Endogenous spermidine can improve the resistance of plants to saline-alkali stress. SlSPDS1 and SlSPDS2 are the main spermidine synthase (SPDS) genes in tomatoes. In comparison with SlSPDS1, SlSPDS2 plays an important role in wild-type tomato seedling under saline-alkali stress. However, limited research has focused on the role of SlSPDS2 in saline-alkali stress. Wild-type (WT) and SPDS gene (SlSPDS2) transgenic over-expression tomato seedlings were used to explore the function of endogenous spermidine on the saline-alkali resistance of tomato seedlings. The results show that SlSPDS2 overexpression under normal conditions and saline-alkali stress increased the content of endogenous free polyamines and the expression levels of polyamine synthesis-related genes in tomato seedlings. Under saline-alkali stress, SlSPDS2 overexpression significantly reduced Na+/K+ ratio, relative electrical conductivity, O2·-, H2O2, and malondialdehyde content, increased Seedling index, relative water content, antioxidant enzyme activities (peroxidase, superoxide dismutase, and catalase), and the contents of proline and soluble sugar in tomato leaf, and mitigated the adverse effect of saline-alkali stress on tomato seedlings. In summary, the overexpression of SlSPDS2 tomato seedlings regulated the ionic homeostasis, antioxidant enzyme system, and osmotic regulatory substances of tomato seedlings living in saline-alkali environment by increasing endogenous free polyamine content, thereby improving the resistance of tomato seedlings against saline-alkali stress.

The C2H2-type zinc finger protein PhZFP1 regulates cold stress tolerance by modulating galactinol synthesis in Petunia hybrida

The C2H2 zinc finger proteins (ZFPs) play essential roles in regulating cold stress responses. Similarly, raffinose accumulation contributes to freezing stress tolerance. However, the relationship between C2H2 functions and raffinose synthesis in cold tolerance remains uncertain. Here, we report the characterization of the cold-induced C2H2-type zinc finger protein PhZFP1 in Petunia hybrida. PhZFP1 was found to be predominantly localized in the nucleus. Overexpression of PhZFP1 conferred enhanced cold tolerance in transgenic petunia lines. In contrast, RNAi mediated suppression of PhZFP1 led to increased cold susceptibility. PhZFP1 regulated the expression of a range of abiotic stress responsive-genes including genes encoding proteins involved in reactive oxygen species (ROS) scavenging and raffinose metabolism. The accumulation of galactinol and raffinose, and the levels of PhGolS1-1 transcripts, were significantly increased in PhZFP1-overexpressing plants and decreased in PhZFP1-RNAi plants under cold stress. Moreover, the galactinol synthase (GolS)-encoding gene PhGolS1-1 was identified as a direct target of PhZFP1. Taken together, these results demonstrate that PhZFP1 functions in cold stress tolerance by modulation of galactinol synthesis via regulation of PhGolS1-1. This study also provides new insights into the mechanisms underlying C2H2 zinc finger protein-mediated cold stress tolerance, and has identified a candidate gene for improving cold stress tolerance.

Acidifiers Attenuate Diquat-Induced Oxidative Stress and Inflammatory Responses by Regulating NF-κB/MAPK/COX-2 Pathways in IPEC-J2 Cells

In this study, we evaluated the protective effects and potential mechanisms of acidifiers on intestinal epithelial cells exposure to oxidative stress (OS). IPEC-J2 cells were first pretreated with 5 × 10⁻⁵ acidifiers for 4 h before being exposed to the optimal dose of diquat to induce oxidative stress. The results showed that acidifiers attenuated diquat-induced oxidative stress, which manifests as the improvement of antioxidant capacity and the reduction in reactive oxygen species (ROS) accumulation. The acidifier treatment decreased cell permeability and enhanced intestinal epithelial barrier function through enhancing the expression of claudin-1 and occludin in diquat-induced cells. Moreover, acidifier treatment attenuated diquat-induced inflammatory responses, which was confirmed by the decreased secretion and gene expression of pro-inflammatory (TNF-α, IL-8) and upregulated anti-inflammatory factors (IL-10). In addition, acidifiers significantly reduced the diquat-induced gene and protein expression levels of COX-2, NF-κB, I-κB-β, ERK1/2, and JNK2, while they increased I-κB-α expression in IPEC-J2 cells. Furthermore, we discovered that acidifiers promoted epithelial cell proliferation (increased expression of PCNA and CCND1) and inhibited apoptosis (decreased expression of BAX, increased expression of BCL-2). Taken together, these results suggest that acidifiers are potent antioxidants that attenuate diquat-induced inflammation, apoptosis, and maintain cellular barrier integrity by regulating the NF-κB/MAPK/COX-2 signaling pathways.

Transcriptomics Using the Enriched Arabidopsis Shoot Apex Reveals Developmental Priming Genes Involved in Plastic Plant Growth under Salt Stress Conditions

In the shoot apical meristem (SAM), the homeostasis of the stem cell population supplying new cells for organ formation is likely a key mechanism of multicellular plant growth and development. As plants are sessile organisms and constantly encounter environmental abiotic stresses, postembryonic development from the shoot stem cell population must be considered with surrounding abiotic stresses for plant adaptation. However, the underlying molecular mechanisms for plant adaptation remain unclear. Previous studies found that the stem-cell-related mutant clv3-2 has the property of salt tolerance without the differential response of typical stress-responsive genes compared to those in WT Ler. Based on these facts, we hypothesized that shoot meristems contain developmental priming genes having comprehensively converged functions involved in abiotic stress response and development. To better understand the biological process of developmental priming genes in the SAM, we performed RNA sequencing (RNA-seq) and transcriptome analysis through comparing genome-wide gene expression profiles between enriched shoot apex and leaf tissues. As a result, 121 putative developmental priming genes differentially expressed in the shoot apex compared to the leaf were identified under normal and salt stress conditions. RNA-seq experiments also revealed the shoot apex-specific responsive genes for salt stress conditions. Based on combinatorial comparisons, 19 developmental priming genes were finally identified, including developmental genes related to cell division and abiotic/biotic-stress-responsive genes. Moreover, some priming genes showed CLV3-dependent responses under salt stress conditions in the clv3-2. These results presumably provide insight into how shoot meristem tissues have relatively high viability against stressful environmental conditions for the developmental plasticity of plants.

ZAT10 plays dual roles in cadmium uptake and detoxification in Arabidopsis

Cadmium (Cd) is a harmful heavy metal that is risky for plant growth and human health. The zinc-finger transcription factor ZAT10 is highly conserved with ZAT6 and ZAT12, which are involved in Cd tolerance in plants. However, the definite function of ZAT10 in Cd tolerance remains uncertain. Here, we demonstrated that ZAT10 negatively regulated Cd uptake and enhanced Cd detoxification in Arabidopsis. The expression of ZAT10 in plants is induced by Cd treatment. The zat10 mutant plants exhibited a greater sensitivity to Cd stress and accumulated more Cd in both shoot and root. Further investigations revealed that ZAT10 repressed the transcriptional activity of IRT1, which encodes a key metal transporter involved in Cd uptake. Meanwhile, ZAT10 positively regulated four heavy metal detoxification-related genes: NAS1, NAS2, IRT2, and MTP3. We further found that ZAT10 interacts with FIT, but their regulatory relationship is still unclear. In addition, ZAT10 directly bound to its own promoter and repressed its transcription as a negative feedback regulation. Collectively, our findings provided new insights into the dual functions of ZAT10 on Cd uptake and detoxification in plants and pointed to ZAT10 as a potential gene resource for Cd tolerance improvement in plants.

Phosphatidic acid binds to and stimulates the activity of ARGAH2 from Arabidopsis

Phosphatidic acid (PA) has emerged as an important lipid signal during abiotic and biotic stress conditions such as drought, salinity, freezing, nutrient starvation, wounding and microbial elicitation. PA acts during stress responses primarily via binding and translocating target proteins or through modulating their activity. Owing to the importance of PA during stress signaling and developmental stages, it is imperative to identify PA interacting proteins and decipher their specific roles. In the present study, we have identified PA binding proteins from the leaves of Arabidopsis thaliana. Mass spectroscopy analysis led to the identification of 21 PA binding proteins with known roles in various cellular processes. One of the PA-binding proteins identified during this study, AtARGAH2, was further studied to unravel the role of PA interaction. Recombinant AtARGAH2 binding with immobilized PA on a solid support validated PA-AtARGAH2 binding invitro. PA binding to AtARGAH2 leads to the enhancement of arginase enzymatic activity in a dose dependent manner. Enzyme kinetics of recombinant AtARGAH2 demonstrated a lower K_m value in presence of PA, suggesting role of PA in efficient enzyme-substrate binding. This simple approach could systematically be applied to perform an inclusive study on lipid binding proteins to elucidate their role in physiology of plants.

ELO2 Participates in the Regulation of Osmotic Stress Response by Modulating Nitric Oxide Accumulation in Arabidopsis

The ELO family is involved in synthesizing very-long-chain fatty acids (VLCFAs) and VLCFAs play a crucial role in plant development, protein transport, and disease resistance, but the physiological function of the plant ELO family is largely unknown. Further, while nitric oxide synthase (NOS)-like activity acts in various plant environmental responses by modulating nitric oxide (NO) accumulation, how the NOS-like activity is regulated in such different stress responses remains misty. Here, we report that the yeast mutant Δelo3 is defective in H₂O₂-triggered cell apoptosis with decreased NOS-like activity and NO accumulation, while its Arabidopsis homologous gene ELO2 (ELO HOMOLOG 2) could complement such defects in Δelo3. The expression of this gene is enhanced and required in plant osmotic stress response because the T-DNA insertion mutant elo2 is more sensitive to the stress than wild-type plants, and ELO2 expression could rescue the sensitivity phenotype of elo2. In addition, osmotic stress-promoted NOS-like activity and NO accumulation are significantly repressed in elo2, while exogenous application of NO donors can rescue this sensitivity of elo2 in terms of germination rate, fresh weight, chlorophyll content, and ion leakage. Furthermore, stress-responsive gene expression, proline accumulation, and catalase activity are also repressed in elo2 compared with the wild type under osmotic stress. In conclusion, our study identifies ELO2 as a pivotal factor involved in plant osmotic stress response and reveals its role in regulating NOS-like activity and NO accumulation.

Metabolite shift in Medicago truncatula occurs in phosphorus deprivation

Symbiotic nitrogen (N) fixation entails successful interaction between legume hosts and rhizobia that occur in specialized organs called nodules. N-fixing legumes have a higher demand for phosphorus (P) than legumes grown on mineral N. Medicago truncatula is an important model plant for characterization of effects of P deficiency at the molecular level. Hence, a study was carried out to address the alteration in metabolite levels of M. truncatula grown aeroponically and subjected to 4 weeks of P stress. First, GC-MS-based untargeted metabolomics initially revealed changes in the metabolic profile of nodules, with increased levels of amino acids and sugars and a decline in amounts of organic acids. Subsequently, LC-MS/MS was used to quantify these compounds including phosphorylated metabolites in the whole plant. Our results showed a drastic reduction in levels of organic acids and phosphorylated compounds in -P leaves, with a moderate reduction in -P roots and nodules. Additionally, sugars and amino acids were elevated in the whole plant under P deprivation. These findings provide evidence that N fixation in M. truncatula is mediated through a N feedback mechanism that in parallel is related to carbon and P metabolism.

Polyamines Metabolism Interacts with γ-Aminobutyric Acid, Proline and Nitrogen Metabolisms to Affect Drought Tolerance of Creeping Bentgrass

Due to increased global warming and climate change, drought has become a serious threat to horticultural crop cultivation and management. The purpose of this study was to investigate the effect of spermine (Spm) pretreatment on metabolic alterations of polyamine (PAs), γ-aminobutyric acid (GABA), proline (Pro), and nitrogen associated with drought tolerance in creeping bentgrass (Agrostis stolonifera). The results showed that drought tolerance of creeping bentgrass could be significantly improved by the Spm pretreatment, as demonstrated by the maintenance of less chlorophyll loss and higher photosynthesis, gas exchange, water use efficiency, and cell membrane stability. The Spm pretreatment further increased drought-induced accumulation of endogenous PAs, putrescine, spermidine, and Spm, and also enhanced PAs metabolism through improving arginine decarboxylases, ornithine decarboxylase, S-adenosylmethionine decarboxylase, and polyamine oxidase activities during drought stress. In addition, the Spm application not only significantly improved endogenous GABA content, glutamate content, activities of glutamate decarboxylase and α-ketoglutarase, but also alleviated decline in nitrite nitrogen content, nitrate reductase, glutamine synthetase, glutamate synthetase, and GABA aminotransferase activities under drought stress. The Spm-pretreated creeping bentgrass exhibited significantly lower ammonia nitrogen content and nitrite reductase activity as well as higher glutamate dehydrogenase activity than non-pretreated plants in response to drought stress. These results indicated beneficial roles of the Spm on regulating GABA and nitrogen metabolism contributing towards better maintenance of Tricarboxylic acid (TCA) cycle in creeping bentgrass. Interestingly, the Spm-enhanced Pro metabolism rather than more Pro accumulation could be the key regulatory mechanism for drought tolerance in creeping bentgrass. Current findings provide a comprehensive understanding of PAs interaction with other metabolic pathways to regulate drought tolerance in grass species.

HrTCP20 dramatically enhance drought tolerance of sea buckthorn (Hippophae rhamnoides L). by mediating the JA signaling pathway

Sea buckthorn, an important ecological and economical tree species, have remarkable drought and salt resistance. The plant-specific transcription factor TCPs play important roles in plant growth, development, and stress responses. However, in sea buckthorn, the molecular mechanism of TCP proteins and their involvement in drought stress are unknown. Here, we found that the expression of HrTCP20 was significantly up-regulated in sea buckthorn under drought stress. Overexpression of HrTCP20 in Arabidopsis thaliana showed that the superoxide dismutase (SOD), polyphenol oxidase (POD), and chlorophyll (SPAD) content was significantly increased by 1.37 and 1.35 times. However, the malondialdehyde (MDA) content decreased by 0.51 times. Our studies further confirmed that silencing HrTCP20 by virus-induced gene silencing (VIGS) led to a decrease in the content of defense enzymes, relative water content (RWC), and an increase of relative electrical conductivity (REC). Silencing HrTCP20 also caused the jasmonic acid (JA) content to decrease in the VIGS-treated tree. Interestingly, we found that JA accumulation content and the expression of HrLOX2, an essential enzyme for JA synthesis, was significantly inhibited in HrTCP20-silenced sea buckthorn under drought stress. Yeast two-hybrid analysis also showed that HrTCP20 is directly bound to HrLOX2. Taken together, the HrTCP20 transcription factor was a positive regulator in drought resistance of sea buckthorn. Further, our findings will provide comprehensive insights into the forest tree defence system of drought stress.

Arginine Increases Tolerance to Nitrogen Deficiency in Malus hupehensis via Alterations in Photosynthetic Capacity and Amino Acids Metabolism

Arginine plays an important role in the nitrogen (N) cycle because it has the highest ratio of N to carbon among amino acids. In recent years, there has been increased research interest in improving the N use of plants, reducing the use of N fertilizer, and enhancing the tolerance of plants to N deficiency. Here, the function of arginine in the growth of apple (Malus hupehensis) under N deficiency was explored. The application of 100 μmol L-1 arginine was effective for alleviating N-deficiency stress. Exogenous arginine promoted the absorption and use of N, phosphorus (P), and potassium (K) under low N stress. The net photosynthetic rate, maximal photochemical efficiency of photosystem II, and chlorophyll content were higher in treated plants than in control plants. Exogenous arginine affected the content of many metabolites, and the content of many amino acids with important functions was significantly increased, such as glutamate and ornithine, which play an important role in the urea cycle. Half of the metabolites were annotated to specialized metabolic pathways, including the synthesis of phenolic substances, flavonoids, and other substances with antioxidant activity. Our results indicate that arginine promotes the plant photosynthetic capacity and alters amino acid metabolism and some antioxidants including phenolic substances and flavonoids to improve the tolerance of apple to N deficiency, possibly through the improvement of arginine content, and the absorption of mineral.

Differential Physio-Biochemical and Metabolic Responses of Peanut (Arachis hypogaea L.) under Multiple Abiotic Stress Conditions

The frequency and severity of extreme climatic conditions such as drought, salinity, cold, and heat are increasing due to climate change. Moreover, in the field, plants are affected by multiple abiotic stresses simultaneously or sequentially. Thus, it is imperative to compare the effects of stress combinations on crop plants relative to individual stresses. This study investigated the differential regulation of physio-biochemical and metabolomics parameters in peanut (Arachis hypogaea L.) under individual (salt, drought, cold, and heat) and combined stress treatments using multivariate correlation analysis. The results showed that combined heat, salt, and drought stress compounds the stress effect of individual stresses. Combined stresses that included heat had the highest electrolyte leakage and lowest relative water content. Lipid peroxidation and chlorophyll contents did not significantly change under combined stresses. Biochemical parameters, such as free amino acids, polyphenol, starch, and sugars, significantly changed under combined stresses compared to individual stresses. Free amino acids increased under combined stresses that included heat; starch, sugars, and polyphenols increased under combined stresses that included drought; proline concentration increased under combined stresses that included salt. Metabolomics data that were obtained under different individual and combined stresses can be used to identify molecular phenotypes that are involved in the acclimation response of plants under changing abiotic stress conditions. Peanut metabolomics identified 160 metabolites, including amino acids, sugars, sugar alcohols, organic acids, fatty acids, sugar acids, and other organic compounds. Pathway enrichment analysis revealed that abiotic stresses significantly affected amino acid, amino sugar, and sugar metabolism. The stress treatments affected the metabolites that were associated with the tricarboxylic acid (TCA) and urea cycles and associated amino acid biosynthesis pathway intermediates. Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and heatmap analysis identified potential marker metabolites (pinitol, malic acid, and xylopyranose) that were associated with abiotic stress combinations, which could be used in breeding efforts to develop peanut cultivars that are resilient to climate change. The study will also facilitate researchers to explore different stress indicators to identify resistant cultivars for future crop improvement programs.

Genome-wide association analysis and pathway enrichment provide insights into the genetic basis of photosynthetic responses to drought stress in Persian walnut

Uncovering the genetic basis of photosynthetic trait variation under drought stress is essential for breeding climate-resilient walnut cultivars. To this end, we examined photosynthetic capacity in a diverse panel of 150 walnut families (1500 seedlings) from various agro-climatic zones in their habitats and grown in a common garden experiment. Photosynthetic traits were measured under well-watered (WW), water-stressed (WS) and recovery (WR) conditions. We performed genome-wide association studies (GWAS) using three genomic datasets: genotyping by sequencing data (∼43 K SNPs) on both mother trees (MGBS) and progeny (PGBS) and the Axiom™ Juglans regia 700 K SNP array data (∼295 K SNPs) on mother trees (MArray). We identified 578 unique genomic regions linked with at least one trait in a specific treatment, 874 predicted genes that fell within 20 kb of a significant or suggestive SNP in at least two of the three GWAS datasets (MArray, MGBS, and PGBS), and 67 genes that fell within 20 kb of a significant SNP in all three GWAS datasets. Functional annotation identified several candidate pathways and genes that play crucial roles in photosynthesis, amino acid and carbohydrate metabolism, and signal transduction. Further network analysis identified 15 hub genes under WW, WS and WR conditions including GAPB, PSAN, CRR1, NTRC, DGD1, CYP38, and PETC which are involved in the photosynthetic responses. These findings shed light on possible strategies for improving walnut productivity under drought stress.

The moso bamboo WRKY transcription factor, PheWRKY86, regulates drought tolerance in transgenic plants

PheWRKY86 is a member of the WRKY transcription factor family in moso bamboo (Phyllostachys edulis). Expression of PheWRKY86 is strongly induced by drought and abscisic acid (ABA) treatments. The PheWRKY86 protein localizes to the cell nucleus and is specifically able to bind to W-box elements. 35S:PheWRKY86 transgenic Arabidopsis and rice showed significantly improved tolerance to drought stress. 35S:PheWRKY86 transgenic plants exhibited better water retention and lower relative electrolyte leakage (REL) and malondialdehyde (MDA) compared to wild type plants. Moreover, 35S:PheWRKY86 transgenic lines showed higher sensitivity to ABA stress. The 35S:PheWRKY86 transgenic plants exhibited higher ABA levels relative to wild type, while also exhibiting a lower germination rate, root length and fresh weight compared to wild type. Further analysis showed that expression of some ABA-responsive genes was changed in the 35S:PheWRKY86 transgenic lines under drought conditions. Transient expression and yeast one-hybrid assays demonstrated that PheWRKY86 could bind to the W-box element in the promoter region of NCED1. Taken together, these results demonstrate that PheWRKY86 plays a positive role in drought tolerance by regulating NCED1 expression.

Integrated physiological and transcriptomic analyses of two warm- and cool-season turfgrass species in response to heat stress

Warm- and cool-season turfgrasses were originated from different locations with contrasting heat tolerance. The molecular mechanisms of heat tolerance have not been extensively studied in turfgrass species. In this study, transcriptomic analysis showed that bermudagrass was more tolerant to heat stress as evidenced by lower contents of H₂O₂, proline and glutathione than those in tall fescue after heat treatment. RNA sequencing analysis revealed that 32.7% and 17.7% more genes were changed in tall fescue than in bermudagrass after 2 and 12h heat treatment, respectively. GO terms of redox were enriched in bermudagrass whereas metabolite transportation ones were over-represented in tall fescue after 2h treatment. Ubiquitin dependent degradation pathways were commonly regulated in both grass species. CdF-box and FaF-box transgenic Arabidopsis exhibited improved tolerance to heat stress. Regulatory elements analysis revealed that four ABA-responsive elements present in CdF-box promoter, indicating CdF-box could be potentially regulated by ABRE binding factors (ABFs). All these findings provide evidences for understanding heat stress response in warm- and cool-season grass species.