Lignin biosynthesis in wheat (Triticum aestivum L.): its response to waterlogging and association with hormonal levels

Transcriptomic Profiling of Quinoa Reveals Distinct Defense Responses to Exogenous Methyl Jasmonate and Salicylic Acid

Plant defense responses are mediated by hormones such as jasmonic acid (JA) and salicylic acid (SA). JA and SA are known to trigger a range of different defense responses in model plants but little is described in crops like quinoa. Here, we present the first molecular description of JA and SA signaling at the transcriptomic level in quinoa. The transcriptomes of quinoa cv. Kurmi seedlings treated with 100 µM methyl JA or 1 mM SA for 4 h were analyzed, using on average 4.1 million paired-end reads per sample. Quinoa plants treated with JA showed 1246 differentially expressed (DE) genes and plants treated with SA showed 590 DE genes. The response to JA included the induction of genes for the biosynthesis of JA (8/8 genes) and lignin (10/11 genes), and displayed a strong association with treatments with Trichoderma biocontrol agents. The SA treatment triggered the upregulation of genes for the biosynthesis of monoterpenoids and glucosinolates, both having defense properties. Overall, this suggest that JA and SA promotes the biosynthesis of lignin polymers and chemical defense compounds, respectively. Overall, the DE genes identified can be used as molecular markers in quinoa for tracking plant-hormone pathway involvements in defense responses.

Multi-omics analysis reveals insights into hypoxia-tolerant rice growth and identifies the 1-Cys peroxiredoxin B-like protease

The rapid-growth ability of rice seedlings under flooded and hypoxic conditions is a crucial determinant for seedling establishment, survival and crop yield under direct-seeded rice cultivation systems. However, the molecular mechanisms underlying rice germination and seedling growth in flooded soil remains unclear. In this study, we used hypoxia-tolerant (Ht) and hypoxia-sensitive (nHt) rice varieties to analyze the response mechanisms of rice seedlings under hypoxic stress through integrated transcriptome, proteome, metabolome sequencing, and physiological analysis. The Ht variety showed higher antioxidant enzyme activity, osmoregulatory capacity, α-amylase activity, and levels of salicylic acid (SA) and indoleacetic acid (IAA). We detected 8096 differentially transcribed genes, 1886 differentially expressed proteins, and 588 differential metabolites between Ht and nHt. KEGG enrichment analysis revealed that key metabolic pathways such as phenylpropanoid biosynthesis, glutathione metabolism, and starch and sucrose metabolism are involved in the rice adaptive response to hypoxic stress. We hypothesized that Ht activates the SA synthesis pathway for rapid elongation and growth under hypoxic stress by inhibiting the phenylpropanoid biosynthetic pathway, thereby redirecting phenylalanine flux towards SA. Exogenous application of SA and IAA increased the flooding survival rate of nHt, suggesting that nHt has a deficiency in activating SA synthesis pathway under hypoxic stress. Additionally, the upregulation of glutathione S-transferase genes in the glutathione metabolism pathway may play critical roles in ROS scavenging and maintaining redox balance under hypoxic conditions. Moreover, a strong correlation was found between 28 DEGs and 4 DAMs (glucose-6-phosphate, sucrose, fumaric acid, and 2,5-dihydroxybenzoic acid) associated with starch and sucrose metabolism and tyrosine metabolism pathways, suggesting their potential pivotal roles in mediating rice response to flooding and hypoxia. These results elucidate the mechanisms underlying rice emergence and growth under flooding and hypoxic conditions.

Trans-zeatin modulates shade stress adaptation in soybean through transcription associated metabolic network

This study explores the molecular mechanisms by which trans-zeatin (tZ), a cytokinin, influences shade stress responses in shade-sensitive and shade-tolerant recombinant inbred lines (RILs) 160 and 165 of soybean (Glycine max) under varied light conditions. Using an integrative multi-omics approach combining metabolomics and transcriptomics, we elucidate the regulatory networks underlying soybean adaptation to shade stress. Using an integrative multi-omics approach that combines metabolomics and transcriptomics, we dissect the complex regulatory networks that enable soybean plants to adapt to shade stress. Our results demonstrate that tZ significantly affects growth, biomass accumulation, photosynthetic efficiency, and yield in soybean plants. Metabolomic analysis revealed that shade stress impacts key metabolic pathways, including phenylpropanoids, flavonoids, flavone and flavonol, anthocyanin, and brassinosteroid biosynthesis, with tZ treatment enhances the adaptive responses of soybean plants. Transcriptomic data further identified differential gene expression in these pathways, alongside those related to hormone-mediated signaling pathway, cell wall biogenesis, and defence response pathways underlining the molecular adjustments to tZ and shade stress. Importantly, the integration of metabolomics and transcriptomics data revealed key KEGG pathways and genes regulated by tZ treatment in RIL 160 under shade stress, including significant alterations in phenylpropanoids, flavonoids, hormone-mediated signaling pathway, cell wall biogenesis and defence response, anthocyanin biosynthesis, and fatty acid degradation pathways as well key responsive transcription factors. This study provides insights into the role of tZ in mediating soybean responses to shade stress at the molecular level, offering insights into improving soybean resilience to low light conditions and informing future agricultural practices for optimizing crop yield.

A precise and high-throughput assay for stem structural characteristics deepens understanding of lodging resistance in sorghum

BACKGROUND

Plant stem structural characteristics are crucial factors determining plant lodging resistance, while high throughput methods for rapid surveys of these traits are still lacking in sorghum.

RESULTS

Among 103 sorghum accessions, two kinds of stem powders (dry and water-washed) were subject to visible and near-infrared spectra acquisition, and 16 models (combinations) for stem structural characteristics were generated, revealing that the support vector machine regression model has significant positive effects on the prediction of stem structural characteristics while powder type and pretreatment of spectra has minor effects on the prediction of stem structural characteristics. In addition, we found that stem structure characteristics were positively correlated with agronomic traits but negatively correlated with lodging index which is the criterion that negatively accounts for plant lodging resistance.

CONCLUSION

This study for the first time provided a precise and high throughput method for the prediction of sorghum stem structural characteristics based on spectra, which could facilitate the improvement of lodging resistance in crop breeding.

Functional characterization of WsPR-1 reveals its interplay with cytokinin and gibberellin signaling pathways

Pathogenesis-related protein 1 (PR-1) is an antimicrobial protein involved in systemic acquired resistance (SAR) in plants, but its regulatory role and interactions with other pathways remain unclear. In this study, we functionally characterize WsPR-1 gene of Withania somnifera in Nicotiana tabacum to elucidate its role in plant defense, growth, and development. Interestingly, transgenic tobacco plants with increased levels of cytokinin (CK) and decreased gibberellins (GAs) exhibited stunted shoot growth, an underdeveloped root system, modified leaf morphology, reduced seed pod production, and delayed leaf senescence. Transcriptional analysis revealed that WsPR-1 overexpression downregulated the GA 20-oxidase (GA20ox) gene involved in GA biosynthesis while upregulating GA 2-oxidase (GA2ox), a GA catabolic enzyme. Moreover, transcript levels of FRUITFULL (FUL) and LEAFY (NFL2) flowering genes exhibited a decrease in WsPR-1 plants, which could explain the delayed flowering and reduced seed pod development in transgenic plants. Confocal microscopy confirmed increased lignin deposition in stem cross-sections of WsPR-1 transgenic plants, supported by gene expression analysis and lignin content quantification. Additionally, our findings also suggest the involvement of Knotted1-like homeobox (KNOX) gene in enhancing cytokinin levels. This study highlights PR-1's regulatory role in plant growth and development, with potential to boost crop yields and enhance resilience.

A fungal endophyte induces local cell wall-mediated resistance in wheat roots against take-all disease

Take-all disease, caused by the Ascomycete fungus Gaeumannomyces tritici, is one of the most important root diseases of wheat worldwide. The fungus invades the roots and destroys the vascular tissue, hindering the uptake of water and nutrients. Closely related non-pathogenic species in the Magnaporthaceae family, such as Gaeumannomyces hyphopodioides, occur naturally in arable and grassland soils and have previously been reported to reduce take-all disease in field studies. However, the mechanism of take-all protection has remained unknown. Here, we demonstrate that take-all control is achieved via local but not systemic host changes in response to prior G. hyphopodioides root colonisation. A time-course wheat RNA sequencing analysis revealed extensive transcriptional reprogramming in G. hyphopodioides-colonised tissues, characterised by a striking downregulation of key cell wall-related genes, including genes encoding cellulose synthases (CESA), and xyloglucan endotransglucosylase/hydrolases (XTH). In addition, we characterise the root infection biologies of G. tritici and G. hyphopodioides in wheat. We investigate the ultrastructure of previously described "subepidermal vesicles" (SEVs), dark swollen fungal cells produced in wheat roots by non-pathogenic G. hyphopodioides, but not by pathogenic G. tritici. We show that G. hyphopodioides SEVs share key characteristics of fungal resting structures, containing a greater number of putative lipid bodies and a significantly thickened cell wall compared to infection hyphae. We hypothesise that SEVs are fungal resting structures formed due to halted hyphal growth in the root cortex, perhaps as a stress response to locally induced wheat defence responses. In the absence of take-all resistant wheat cultivars or non-virulent G. tritici strains, studying closely related non-pathogenic G. hyphopodioides provides a much needed avenue to elucidate take-all resistance mechanisms in wheat.

Augmenting the basis of lodging tolerance in wheat (Triticum aestivum) under natural and simulated conditions

In wheat (Triticum aestivum ), canopy architecture, culm diameter and stem strength are the key providers of lodging tolerance. To better understand the lodging phenomenon and determine the best linked trait to lodging, a study of lodging resistance was conducted in both artificially-induced and natural lodging conditions. Various morphological, phenological and biochemical traits, such as acid detergent fibre, acid detergent lignin, cellulose and activity of lignin-synthesising enzymes (phenylalanine ammonia lyase and tyrosine ammonia lyase) were recorded. Anatomical features were also examined by light microscopy, using the Wiesner reaction. Genotype C306 demonstrated the highest susceptibility to lodging compared to other varieties due to its limited production of lignin-synthesising enzymes, as well as its taller plant height and narrower culms. The dwarf mutants (DM6 and DM7) have a stronger resistance against lodging because they have thick stems and a short plant canopy structure. The most suitable donors for lodging are semidwarf varieties (HD2967, DPW621-50, DBW88) because they have higher production of lignin and lignin-synthesising enzymes. Grey correlation analysis also confirmed the ability of these three genotypes to tolerate lodging. The genotypes studied were comprehensively ranked. The study also includes an effort towards the standardisation of lodging methodology under artificial conditions.

6-BA Reduced Yield Loss under Waterlogging Stress by Regulating the Phenylpropanoid Pathway in Wheat

Waterlogging stress causes substantial destruction to plant growth and production under climatic fluctuations globally. Plants hormones have been widely explored in numerous crops, displaying an imperative role in crop defense and growth mechanism. However, there is a paucity of research on the subject of plant hormones regulating waterlogging stress responses in wheat crop. In this study, we clarified the role of 6-BA in waterlogging stress through inducing phenylpropanoid biosynthesis in wheat. The application of 6-BA (6-benzyladenine) enhanced the growth and development of wheat plants under waterlogging stress, which was accompanied by reduced electrolyte leakage, high chlorophyll, and soluble sugar content. ROS scavenging was also enhanced by 6-BA, resulting in reduced MDA and H2O2 accumulation and amplified antioxidant enzyme activities. Additionally, under the effect of 6-BA, the acceleration of lignin content and accumulation in the cell walls of wheat tissues, along with the activation of PAL (phenylalanine ammonia lyase), TAL (tyrosine ammonia lyase), and 4CL (4-hydroxycinnamate CoA ligase) activities and the increase in the level of transcription of the TaPAL and Ta4CL genes, were observed under waterlogging stress. Also, 6-BA improved the root growth system under waterlogging stress conditions. Further qPCR analysis revealed increased auxin signaling (TaPR1) in 6-BA-treated plants under waterlogging stress that was consistent with the induction of endogenous IAA hormone content under waterlogging stress conditions. Here, 6-BA also reduced yield loss, as compared to control plants. Thus, the obtained data suggested that, under the application of 6-BA, phenylpropanoid metabolism (i.e., lignin) was stimulated, playing a significant role in reducing the negative effects of waterlogging stress on yield, as evinced by the improved plant growth parameters.

Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages

Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.

Integrated transcriptomic and metabolomic analysis reveals the potential mechanisms underlying indium-induced inhibition of root elongation in wheat plants

Soil contamination by indium, an emerging contaminant from electronics, has a negative impact on crop growth. Inhibition of root growth serves as a valuable biomarker for predicting indium phytotoxicity. Therefore, elucidating the molecular mechanisms underlying indium-induced root damage is essential for developing strategies to mitigate its harmful effects. Our transcriptomic findings revealed that indium affects the expression of numerous genes related to cell wall composition and metabolism in wheat roots. Morphological and compositional analysis revealed that indium induced a 2.9-fold thickening and a 17.5 % increase in the content of cell walls in wheat roots. Untargeted metabolomics indicated a substantial upregulation of the phenylpropanoid biosynthesis pathway. As the major end product of phenylpropanoid metabolism, lignin significantly accumulated in root cell walls after indium exposure. Together with increased lignin precursors, enhanced activity of lignin biosynthesis-related enzymes was observed. Moreover, analysis of the monomeric content and composition of lignin revealed a significant enrichment of p-hydroxyphenyl (H) and syringyl (S) units in root cell walls under indium stress. The present study contributes to the existing knowledge of indium toxicity. It provides valuable insights for developing sustainable solutions to address the challenges posed by electronic waste and indium contamination on agroecosystems.

Dual RNA-sequencing of Fusarium head blight resistance in winter wheat

Fusarium head blight (FHB) is a devastating fungal disease responsible for significant yield losses in wheat and other cereal crops across the globe. FHB infection of wheat spikes results in grain contamination with mycotoxins, reducing both grain quality and yield. Breeding strategies have resulted in the production of FHB-resistant cultivars, however, the underlying molecular mechanisms of resistance in the majority of these cultivars are still poorly understood. To improve our understanding of FHB-resistance, we performed a transcriptomic analysis of FHB-resistant AC Emerson, FHB-moderately resistant AC Morley, and FHB-susceptible CDC Falcon in response to Fusarium graminearum. Wheat spikelets located directly below the point of inoculation were collected at 7-days post inoculation (dpi), where dual RNA-sequencing was performed to explore differential expression patterns between wheat cultivars in addition to the challenging pathogen. Differential expression analysis revealed distinct defense responses within FHB-resistant cultivars including the enrichment of physical defense through the lignin biosynthesis pathway, and DON detoxification through the activity of UDP-glycosyltransferases. Nucleotide sequence variants were also identified broadly between these cultivars with several variants being identified within differentially expressed putative defense genes. Further, F. graminearum demonstrated differential expression of mycotoxin biosynthesis pathways during infection, leading to the identification of putative pathogenicity factors.

Singlet oxygen induces cell wall thickening and stomatal density reducing by transcriptome reprogramming

Singlet oxygen (1O2) has a very short half-life of 10-5 s; however, it is a strong oxidant that causes growth arrest and necrotic lesions on plants. Its signaling pathway remains largely unknown. The Arabidopsis flu (fluorescent) mutant accumulates a high level of 1O2 and shows drastic changes in nuclear gene expression. Only two plastid proteins, EX1 (executer 1) and EX2 (executer 2), have been identified in the singlet oxygen signaling. Here, we found that the transcription factor abscisic acid insensitive 4 (ABI4) binds the promoters of genes responsive to 1O2-signals. Inactivation of the ABI4 protein in the flu/abi4 double mutant was sufficient to compromise the changes of almost all 1O2-responsive-genes and rescued the lethal phenotype of flu grown under light/dark cycles, similar to the flu/ex1/ex2 triple mutant. In addition to cell death, we reported for the first time that 1O2 also induces cell wall thickening and stomatal development defect. Contrastingly, no apparent growth arrest was observed for the flu mutant under normal light/dim light cycles, but the cell wall thickening (doubled) and stomatal density reduction (by two-thirds) still occurred. These results offer a new idea for breeding stress tolerant plants.

Physiological, Epigenetic, and Transcriptome Analyses Provide Insights into the Responses of Wheat Seedling Leaves to Different Water Depths under Flooding Conditions

Flooding stress, including waterlogging and submergence, is one of the major abiotic stresses that seriously affects the growth and development of plants. In the present study, physiological, epigenetic, and transcriptomic analyses were performed in wheat seedling leaves under waterlogging (WL), half submergence (HS), and full submergence (FS) treatments. The results demonstrate that FS increased the leaves' hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents and reduced their chlorophyll contents (SPAD), photosynthetic efficiency (Fv/Fm), and shoot dry weight more than HS and WL. In addition, FS increased catalase (CAT) and peroxidase (POD) activities more than HS and WL. However, there were no significant differences in the contents of H2O2, MDA, SPAD, and Fv/Fm, and the activities of superoxide dismutase (SOD) and POD between the HS and WL treatments. The changes in DNA methylation were related to stress types, increasing under the WL and HS treatments and decreasing under the FS treatment. Additionally, a total of 9996, 10,619, and 24,949 genes were differentially expressed under the WL, HS, and FS treatments, respectively, among which the 'photosynthesis', 'phenylpropanoid biosynthesis', and 'plant hormone signal transduction' pathways were extensively enriched under the three flooding treatments. The genes involved in these pathways showed flooding-type-specific expression. Moreover, flooding-type-specific responses were observed in the three conditions, including the enrichment of specific TFs and response pathways. These results will contribute to a better understanding of the molecular mechanisms underlying the responses of wheat seedling leaves to flooding stress and provide valuable genetic and epigenetic information for breeding flood-tolerant varieties of wheat.

Comparative transcriptome profiling of potato cultivars infected by late blight pathogen Phytophthora infestans: Diversity of quantitative and qualitative responses

The Estonia potato cultivar Ando has shown elevated field resistance to Phytophthora infestans, even after being widely grown for over 40 years. A comprehensive transcriptional analysis was performed using RNA-seq from plant leaf tissues to gain insight into the mechanisms activated for the defense after infection. Pathogen infection in Ando resulted in about 5927 differentially expressed genes (DEGs) compared to 1161 DEGs in the susceptible cultivar Arielle. The expression levels of genes related to plant disease resistance such as serine/threonine kinase activity, signal transduction, plant-pathogen interaction, endocytosis, autophagy, mitogen-activated protein kinase (MAPK), and others were significantly enriched in the upregulated DEGs in Ando, whereas in the susceptible cultivar, only the pathway related to phenylpropanoid biosynthesis was enriched in the upregulated DEGs. However, in response to infection, photosynthesis was deregulated in Ando. Multi-signaling pathways of the salicylic-jasmonic-ethylene biosynthesis pathway were also activated in response to Phytophthora infestans infection.

Elucidating the molecular responses to waterlogging stress in onion (Allium cepa L.) leaf by comparative transcriptome profiling

Introduction

Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown.

Methods

This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress.

Results

Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666.

Discussion

The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.

Aspergillus nomiae and fumigatus Ameliorating the Hypoxic Stress Induced by Waterlogging through Ethylene Metabolism in Zea mays L

Transient and prolonged waterlogging stress (WS) stimulates ethylene (ET) generation in plants, but their reprogramming is critical in determining the plants' fate under WS, which can be combated by the application of symbiotically associated beneficial microbes that induce resistance to WS. The present research was rationalized to explore the potential of the newly isolated 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing fungal endophytic consortium of Aspergillus nomiae (MA1) and Aspergillus fumigatus (MA4) on maize growth promotion under WS. MA1 and MA4 were isolated from the seeds of Moringa oleifera L., which ably produced a sufficient amount of IAA, proline, phenols, and flavonoids. MA1 and MA4 proficiently colonized the root zone of maize (Zea mays L.). The symbiotic association of MA1 and MA4 promoted the growth response of maize compared with the non-inoculated plants under WS stress. Moreover, MA1- and MA4-inoculated maize plants enhanced the production of total soluble protein, sugar, lipids, phenolics, and flavonoids, with a reduction in proline content and H2O2 production. MA1- and MA4-inoculated maize plants showed an increase in the DPPH activity and antioxidant enzyme activities of CAT and POD, along with an increased level of hormonal content (GA3 and IAA) and decreased ABA and ACC contents. Optimal stomatal activity in leaf tissue and adventitious root formation at the root/stem junction was increased in MA1- and MA4-inoculated maize plants, with reduced lysigenous aerenchyma formation, ratio of cortex-to-stele, water-filled cells, and cell gaps within roots; increased tight and round cells; and intact cortical cells without damage. MA1 and MA4 induced a reduction in deformed mesophyll cells, and deteriorated epidermal and vascular bundle cells, as well as swollen metaxylem, phloem, pith, and cortical area, in maize plants under WS compared with control. Moreover, the transcript abundance of ethylene-responsive gene ZmEREB180, responsible for the induction of the WS tolerance in maize, showed optimally reduced expression sufficient for induction in WS tolerance, in MA1- and MA4-inoculated maize plants under WS compared with the non-inoculated control. The existing research supported the use of MA1 and MA4 isolates for establishing the bipartite mutualistic symbiosis in maize to assuage the adverse effects of WS by optimizing ethylene production.

Transcriptomic and physiological analyses reveal changes in secondary metabolite and endogenous hormone in ginger (Zingiber officinale Rosc.) in response to postharvest chilling stress

Storing postharvest ginger at low temperatures can extend its shelf life, but can also lead to chilling injury, loss of flavor, and excessive water loss. To investigate the effects of chilling stress on ginger quality, morphological, physiological, and transcriptomic changes were examined after storage at 26 °C, 10 °C, and 2 °C for 24 h. Compared to 26 °C and 10 °C, storage at 2 °C significantly increased the concentrations of lignin, soluble sugar, flavonoids, and phenolics, as well as the accumulation of H2O2, O2-, and thiobarbituric acid reactive substances (TBARS). Additionally, chilling stress inhibited the levels of indoleacetic acid, while enhancing gibberellin, abscisic acid, and jasmonic acid, which may have increased postharvest ginger's adaptation to chilling. Storage at 10 °C decreased lignin concentration and oxidative damage, and induced less fluctuant changes in enzymes and hormones than storage at 2 °C. RNA-seq revealed that the number of differentially expressed genes (DEGs) increased with decreasing temperature. Functional enrichment analysis of the 523 DEGs that exhibited similar expression patterns between all treatments indicated that they were primarily enriched in phytohormone signaling, biosynthesis of secondary metabolites, and cold-associated MAPK signaling pathways. Key enzymes related to 6-gingerol and curcumin biosynthesis were downregulated at 2 °C, suggesting that cold storage may negatively impact ginger quality. Additionally, 2 °C activated the MKK4/5-MPK3/6-related protein kinase pathway, indicating that chilling may increase the risk of ginger pathogenesis.

Transcriptomic, Physiological, and Metabolomic Response of an Alpine Plant, Rhododendron delavayi, to Waterlogging Stress and Post-Waterlogging Recovery

Climate change has resulted in frequent heavy and prolonged rainfall events that exacerbate waterlogging stress, leading to the death of certain alpine Rhododendron trees. To shed light on the physiological and molecular mechanisms behind waterlogging stress in woody Rhododendron trees, we conducted a study of Rhododendron delavayi, a well-known alpine flower species. Specifically, we investigated the physiological and molecular changes that occurred in leaves of R. delavayi subjected to 30 days of waterlogging stress (WS30d), as well as subsequent post-waterlogging recovery period of 10 days (WS30d-R10d). Our findings reveal that waterlogging stress causes a significant reduction in CO₂ assimilation rate, stomatal conductance, transpiration rate, and maximum photochemical efficiency of PSII (Fv/Fm) in the WS30d leaves, by 91.2%, 95.3%, 93.3%, and 8.4%, respectively, when compared to the control leaves. Furthermore, the chlorophyll a and total chlorophyll content in the WS30d leaves decreased by 13.5% and 16.6%, respectively. Both WS30d and WS30d-R10d leaves exhibited excessive H₂O₂ accumulation, with a corresponding decrease in lignin content in the WS30d-R10d leaves. At the molecular level, purine metabolism, glutathione metabolism, photosynthesis, and photosynthesis-antenna protein pathways were found to be primarily involved in WS30d leaves, whereas phenylpropanoid biosynthesis, fatty acid metabolism, fatty acid biosynthesis, fatty acid elongation, and cutin, suberin, and wax biosynthesis pathways were significantly enriched in WS30d-R10d leaves. Additionally, both WS30d and WS30d-R10d leaves displayed a build-up of sugars. Overall, our integrated transcriptomic, physiological, and metabolomic analysis demonstrated that R. delavayi is susceptible to waterlogging stress, which causes irreversible detrimental effects on both its physiological and molecular aspects, hence compromising the tree's ability to fully recover, even under normal growth conditions.

Components of the Phenylpropanoid Pathway in the Implementation of the Protective Effect of Sodium Nitroprusside on Wheat under Salinity

Nitric oxide (NO) is a multifunctional, gaseous signaling molecule implicated in both physiological and protective responses to biotic and abiotic stresses, including salinity. In this work, we studied the effects of 200 µM exogenous sodium nitroprusside (SNP, a donor of NO) on the components of the phenylpropanoid pathway, such as lignin and salicylic acid (SA), and its relationship with wheat seedling growth under normal and salinity (2% NaCl) conditions. It was established that exogenous SNP contributed to the accumulation of endogenous SA and increased the level of transcription of the pathogenesis-related protein 1 (PR1) gene. It was found that endogenous SA played an important role in the growth-stimulating effect of SNP, as evidenced by the growth parameters. In addition, under the influence of SNP, the activation of phenylalanine ammonia lyase (PAL), tyrosine ammonia lyase (TAL), and peroxidase (POD), an increase in the level of transcription of the TaPAL and TaPRX genes, and the acceleration of lignin accumulation in the cell walls of roots were revealed. Such an increase in the barrier properties of the cell walls during the period of preadaptation played an important role in protection against salinity stress. Salinity led to significant SA accumulation and lignin deposition in the roots, strong activation of TAL, PAL, and POD, and suppression of seedling growth. Pretreatment with SNP under salinity conditions resulted in additional lignification of the root cell walls, decreased stress-induced endogenous SA generation, and lower PAL, TAL, and POD activities in comparison to untreated stressed plants. Thus, the obtained data suggested that during pretreatment with SNP, phenylpropanoid metabolism was activated (i.e., lignin and SA), which contributed to reducing the negative effects of salinity stress, as evidenced by the improved plant growth parameters.

Optimum nitrogen improved stem breaking resistance of intercropped soybean by modifying the stem anatomical structure and lignin metabolism

Excessive use of nitrogen fertilizers enhanced the stem lodging, leading to serious threats to environmental sustainability. As the maize-soybean intercropping system is eco-friendly, however, soybean micro-climate hinders soybean growth and caused lodging. Since the relationship between nitrogen and lodging resistance under the intercropping system is not widely studied. Therefore, a pot experiment was conducted with the application of different nitrogen concentrations referring to low nitrogen (LN) = 0 mg/kg, optimum nitrogen (OpN) = 100 mg/kg, and high nitrogen (HN) = 300 mg/kg. To evaluate the optimum nitrogen fertilization under the maize-soybean intercropping system, two soybean cultivars were selected Tianlong 1 (TL-1), (lodging resistant) and Chuandou 16 (CD-16), (lodging susceptible). The results revealed that under the intercropping system, the OpN concentration significantly improved the lodging resistance of soybean cultivars by reducing the plant height of TL-1 and CD-16 by 4 and 28% as compared to LN, respectively. Following OpN, the lodging resistance index for CD-16 was also increased by 67% and 59% under the respective cropping systems. In addition, we found that OpN concentration prompted the lignin biosynthesis by stimulating the enzymatic activities of lignin biosynthetic enzymes (PAL, 4CL, CAD, and POD), which was reflected at the transcriptional levels (GmPAL, GmPOD, GmCAD, Gm4CL), too. Henceforth, we proposed that optimum nitrogen fertilization boosts soybean stem lodging resistance by modulating the lignin metabolism in the maize-soybean intercropping system.

In-silico identification and characterization of O-methyltransferase gene family in peanut (Arachis hypogaea L.) reveals their putative roles in development and stress tolerance

Cultivated peanut (Arachis hypogaea) is a leading protein and oil-providing crop and food source in many countries. At the same time, it is affected by a number of biotic and abiotic stresses. O-methyltransferases (OMTs) play important roles in secondary metabolism, biotic and abiotic stress tolerance. However, the OMT genes have not been comprehensively analyzed in peanut. In this study, we performed a genome-wide investigation of A. hypogaea OMT genes (AhOMTs). Gene structure, motifs distribution, phylogenetic history, genome collinearity and duplication of AhOMTs were studied in detail. Promoter cis-elements, protein-protein interactions, and micro-RNAs targeting AhOMTs were also predicted. We also comprehensively studied their expression in different tissues and under different stresses. We identified 116 OMT genes in the genome of cultivated peanut. Phylogenetically, AhOMTs were divided into three groups. Tandem and segmental duplication events played a role in the evolution of AhOMTs, and purifying selection pressure drove the duplication process. AhOMT promoters were enriched in several key cis-elements involved in growth and development, hormones, light, and defense-related activities. Micro-RNAs from 12 different families targeted 35 AhOMTs. GO enrichment analysis indicated that AhOMTs are highly enriched in transferase and catalytic activities, cellular metabolic and biosynthesis processes. Transcriptome datasets revealed that AhOMTs possessed varying expression levels in different tissues and under hormones, water, and temperature stress. Expression profiling based on qRT-PCR results also supported the transcriptome results. This study provides the theoretical basis for further work on the biological roles of AhOMT genes for developmental and stress responses.

Ethylene and Jasmonates Signaling Network Mediating Secondary Metabolites under Abiotic Stress

Plants are sessile organisms that face environmental threats throughout their life cycle, but increasing global warming poses an even more existential threat. Despite these unfavorable circumstances, plants try to adapt by developing a variety of strategies coordinated by plant hormones, resulting in a stress-specific phenotype. In this context, ethylene and jasmonates (JAs) present a fascinating case of synergism and antagonism. Here, Ethylene Insensitive 3/Ethylene Insensitive-Like Protein1 (EIN3/EIL1) and Jasmonate-Zim Domain (JAZs)-MYC2 of the ethylene and JAs signaling pathways, respectively, appear to act as nodes connecting multiple networks to regulate stress responses, including secondary metabolites. Secondary metabolites are multifunctional organic compounds that play crucial roles in stress acclimation of plants. Plants that exhibit high plasticity in their secondary metabolism, which allows them to generate near-infinite chemical diversity through structural and chemical modifications, are likely to have a selective and adaptive advantage, especially in the face of climate change challenges. In contrast, domestication of crop plants has resulted in change or even loss in diversity of phytochemicals, making them significantly more vulnerable to environmental stresses over time. For this reason, there is a need to advance our understanding of the underlying mechanisms by which plant hormones and secondary metabolites respond to abiotic stress. This knowledge may help to improve the adaptability and resilience of plants to changing climatic conditions without compromising yield and productivity. Our aim in this review was to provide a detailed overview of abiotic stress responses mediated by ethylene and JAs and their impact on secondary metabolites.

Molecular cloning and functional characterization of the promoter of a novel Aspergillus flavus inducible gene (AhOMT1) from peanut

Peanut is an important oil and food legume crop grown in more than one hundred countries, but the yield and quality are often impaired by different pathogens and diseases, especially aflatoxins jeopardizing human health and causing global concerns. For better management of aflatoxin contamination, we report the cloning and characterization of a novel A. flavus inducible promoter of the O-methyltransferase gene (AhOMT1) from peanut. The AhOMT1 gene was identified as the highest inducible gene by A. flavus infection through genome-wide microarray analysis and verified by qRT-PCR analysis. AhOMT1 gene was studied in detail, and its promoter, fussed with the GUS gene, was introduced into Arabidopsis to generate homozygous transgenic lines. Expression of GUS gene was studied in transgenic plants under the infection of A. flavus. The analysis of AhOMT1 gene characterized by in silico assay, RNAseq, and qRT-PCR revealed minute expression in different organs and tissues with trace or no response to low temperature, drought, hormones, Ca2+, and bacterial stresses, but highly induced by A. flavus infection. It contains four exons encoding 297 aa predicted to transfer the methyl group of S-adenosyl-L-methionine (SAM). The promoter contains different cis-elements responsible for its expression characteristics. Functional characterization of AhOMT1P in transgenic Arabidopsis plants demonstrated highly inducible behavior only under A. flavus infection. The transgenic plants did not show GUS expression in any tissue(s) without inoculation of A. flavus spores. However, GUS activity increased significantly after inoculation of A. flavus and maintained a high level of expression after 48 hours of infection. These results provided a novel way for future management of peanut aflatoxins contamination through driving resistance genes in A. flavus inducible manner.

Association studies of genes in a Pb response-associated network in maize (Zea mays L.) reveal that ZmPIP2;5 is involved in Pb tolerance

Lead (Pb) in the soil affects the growth and development of plants and causes damages to the human body through the food chain. Here, we identified and cloned a Pb-tolerance gene ZmPIP2;5 based on a weighted gene co-expression network analysis and gene-based association studies. We showed that ZmPIP2;5 encodes a plasma membrane aquaporin and positively regulated Pb tolerance and accumulation in Arabidopsis and yeast. Overexpression of ZmPIP2;5 increased root length and fresh weight of Arabidopsis seedlings under Pb stress. Heterologous expression of ZmPIP2;5 in yeast caused the enhanced growth speed under Pb treatment and Pb accumulation in yeast cells. A (T/A) SNP in the ZmPIP2;5 promoter affected the expression abundance of ZmPIP2;5 and thereby led to the difference in Pb tolerance among different maize lines. Our study helps to understand the mechanism underlying plant tolerance to Pb stress and provides new ideas for breeding Pb-tolerance maize varieties via molecular marker-assisted selection.

Genome-Wide Identification and Expression Analysis of the 4-Coumarate: CoA Ligase Gene Family in Solanum tuberosum

4-coumarate: CoA ligase (4CL) is not only involved in the biosynthetic processes of flavonoids and lignin in plants but is also closely related to plant tolerance to abiotic stress. UV irradiation can activate the expression of 4CL genes in plants, and the expression of 4CL genes changed significantly in response to different phytohormone treatments. Although the 4CL gene has been cloned in potatoes, there have been fewer related studies of the 4CL gene family on the potato genome-wide scale. In this study, a total of 10 potato 4CL genes were identified in the potato whole genome. Through multiple sequence alignment, phylogenetic analysis as well as gene structure analysis indicated that the potato 4CL gene family could be divided into two subgroups. Combined with promoter cis-acting element analysis, transcriptome data, and RT-qPCR results indicated that potato 4CL gene family was involved in potato response to white light, UV irradiation, ABA treatment, MeJA treatment, and PEG simulated drought stress. Abiotic stresses such as UV, ABA, MeJA, and PEG could promote the up-regulated expression of St4CL6 and St4CL8 but inhibits the expression of St4CL5. The above results will increase our understanding of the evolution and expression regulation of the potato 4CL gene family and provide reference value for further research on the molecular biological mechanism of 4CL participating in response to diverse environmental signals in potatoes.

Blue Light Regulates Cell Wall Structure and Carbohydrate Metabolism of Soybean Hypocotyl

Soybean stem elongation and thickening are related to cell wall composition. Plant morphogenesis can be influenced by blue light, which can regulate cell wall structure and composition, and affect stem growth and development. Here, using proteomics and metabolomics, differentially expressed proteins and metabolites of hypocotyls grown in the dark and under blue light were studied to clarify the effects of blue light on the cell wall structure and carbohydrate metabolism pathway of soybean hypocotyls. Results showed that 1120 differential proteins were upregulated and 797 differential proteins were downregulated under blue light treatment, while 63 differential metabolites were upregulated and 36 differential metabolites were downregulated. Blue light promoted the establishment of cell wall structure and composition by regulating the expression of both the enzymes and metabolites related to cell wall structural composition and nonstructural carbohydrates. Thus, under blue light, the cross-sectional area of the hypocotyl and xylem were larger, the longitudinal length of pith cells was smaller, elongation of the soybean hypocotyl was inhibited, and diameter was increased.

Soiltesting formula fertilization with organic fertilizer addition for target yield cannot stand long due to stem lodging of rice

INTRODUCTION

Soil testing formula fertilization using organic fertilizer (STFFOF)could increase grain yields and protect the ecological environment but the potential risks of STFFOF remains unclear.

METHODS

In order to assess the risk on rice stem lodging, a STFFOF field experiment is conducted continuously for 11 years.

RESULTS

After 11 years of continuous STFFOF treatment, the stem lodging rate of rice substantially increases by 81.1%*, which completely overweigh its increase in yield. Further research found that STFFOF greatly decreases the concentration of Ca, SiO2, K, Mg, and non-structural carbohydrates in basal internodes, dramatically increases that of N, P, and weight per ear, but slightly affects the structural carbohydrates. The strong correlations imply the increasement in weight per ear, N, and P concentrations, and the significant decrease in starch in the basal internodes might directly increase the brittleness of stem internodes and further cause severe stem lodging and yield loss of rice.

DISCUSSION

Results suggest that the potential risks of rice production including stem lodging must be considered when adopting the excessive exploration mode of productivity technology of paddy fields.

Defense responses induced by ulvan in wheat against powdery mildew caused by Blumeria graminis f. sp. tritici

Ulvan is a water-soluble sulfated heteropolysaccharide extracted from the cell walls of the green seaweeds Ulva spp. This polysaccharide is known to induce resistance and protect plants against a broad range of plant pathogenic fungi, such as Blumeria graminis f. sp. tritici (Bgt), the causal agent of powdery mildew in wheat. We aimed to study the defense mechanisms induced by ulvan against Bgt in susceptible wheat by investigating the defense-related gene expression, enzymes activity, accumulation of phenolic compounds and hydrogen peroxide (H₂O₂), as well as the development of Bgt infection structures in vitro and in planta. Symptoms were reduced by 42% in ulvan-treated plants. In vitro, ulvan did not inhibit conidial germination of Bgt but in planta, increased the appressorial germ tubes without haustorium. Ulvan increased the presence of fluorescent papillae and accumulation of H₂O₂ at the penetration sites of Bgt, as well as the content of phenolic compounds. POX, PAL and LOX activities were stimulated in ulvan-treated plants during the first 48 h after inoculation. However, few of defense-related genes studied were differentially expressed in infected plants after ulvan treatment. By contrast, in non-infected conditions, ulvan up-regulated the expression of genes involved in phenylpropanoid metabolism, i.e. PAL, CHS, COMT, ANS and FLS, genes encoding pathogenesis-related proteins, i.e. PR1, PR9, PR15, and LOX during the first 96 h after treatment. This study provides new insights about the multiple ulvan effects on wheat defense responses, and especially the elicitation of the phenylpropanoid pathway leading to phenolic compounds accumulation, which could be involved in cell wall reinforcement.

Characterization and Fine Mapping of qRPR1-3 and qRPR3-1, Two Major QTLs for Rind Penetrometer Resistance in Maize

Stalk strength is one of the most important traits in maize, which affects stalk lodging resistance and, consequently, maize harvestable yield. Rind penetrometer resistance (RPR) as an effective and reliable measurement for evaluating maize stalk strength is positively correlated with stalk lodging resistance. In this study, one F₂ and three F_2:3 populations derived from the cross of inbred lines 3705I (the low RPR line) and LH277 (the high RPR line) were constructed for mapping quantitative trait loci (QTL), conferring RPR in maize. Fourteen RPR QTLs were identified in four environments and explained the phenotypic variation of RPR from 4.14 to 15.89%. By using a sequential fine-mapping strategy based on the progeny test, two major QTLs, qRPR1-3 and qRPR3-1, were narrowed down to 4-Mb and 550-kb genomic interval, respectively. The quantitative real-time PCR (qRT-PCR) assay was adopted to identify 12 candidate genes responsible for QTL qRPR3-1. These findings should facilitate the identification of the polymorphism loci underlying QTL qRPR3-1 and molecular breeding for RPR in maize.

Genome-Wide Analysis and Expression Profiling of the Phenylalanine Ammonia-Lyase Gene Family in Solanum tuberosum

Phenylalanine ammonia-lyase is one of the most widely studied enzymes in the plant kingdom. It is a crucial pathway from primary metabolism to significant secondary phenylpropanoid metabolism in plants, and plays an essential role in plant growth, development, and stress defense. Although PAL has been studied in many actual plants, only one report has been reported on potato, one of the five primary staple foods in the world. In this study, 14 StPAL genes were identified in potato for the first time using a genome-wide bioinformatics analysis, and the expression patterns of these genes were further investigated using qRT-PCR. The results showed that the expressions of StPAL1, StPAL6, StPAL8, StPAL12, and StPAL13 were significantly up-regulated under drought and high temperature stress, indicating that they may be involved in the stress defense of potato against high temperature and drought. The expressions of StPAL1, StPAL2, and StPAL6 were significantly up-regulated after MeJa hormone treatment, indicating that these genes are involved in potato chemical defense mechanisms. These three stresses significantly inhibited the expression of StPAL7, StPAL10, and StPAL11, again proving that PAL is a multifunctional gene family, which may give plants resistance to multiple and different stresses. In the future, people may improve critical agronomic traits of crops by introducing other PAL genes. This study aims to deepen the understanding of the versatility of the PAL gene family and provide a valuable reference for further genetic improvement of the potato.

The Role of Phytohormones in Plant Response to Flooding

Climatic variations influence the morphological, physiological, biological, and biochemical states of plants. Plant responses to abiotic stress include biochemical adjustments, regulation of proteins, molecular mechanisms, and alteration of post-translational modifications, as well as signal transduction. Among the various abiotic stresses, flooding stress adversely affects the growth of plants, including various economically important crops. Biochemical and biological techniques, including proteomic techniques, provide a thorough understanding of the molecular mechanisms during flooding conditions. In particular, plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by an elaborate hormonal signaling network. With the help of these findings, the main objective is to identify plant responses to flooding and utilize that information for the development of flood-tolerant plants. This review provides an insight into the role of phytohormones in plant response mechanisms to flooding stress, as well as different mitigation strategies that can be successfully administered to improve plant growth during stress exposure. Ultimately, this review will expedite marker-assisted genetic enhancement studies in crops for developing high-yield lines or varieties with flood tolerance.

Hydrogen sulphide and nitric oxide mitigate the negative impacts of waterlogging stress on wheat (Triticum aestivum L.)

Nitric oxide (NO) and hydrogen sulphide (H₂ S) are important gaseous signalling molecules that regulate key physiochemical mechanisms of plants under environmental stresses. A number of attempts have been made to improve waterlogging tolerance in plants, but with limited success. Having said that, NO and H₂ S are vital signalling molecules, but their role in mitigating waterlogging effects on crop plants is not well established. We investigated the efficacy of exogenous NO and H₂ S to alleviate waterlogging effects in two wheat cultivars (Galaxy-2013 and FSD-2008). Waterlogging produced a noticeable reduction in plant growth, yield, chlorophyll, soluble sugars and free amino acids. Besides, waterlogging induced severe oxidative damage seen as higher cellular TBARS and H₂ O₂ content. Antioxidant enzyme activity increased together with a notable rise in Fe²⁺ and Mn²⁺ content. Proline content was higher in waterlogged plants compared with non-waterlogged plants. In contrast, waterlogging caused a substantial decline in endogenous levels of essential nutrients (K⁺ , Ca²⁺ and Mg²⁺ ). Waterlogged conditions led to Fe²⁺ and Mn²⁺ toxicity due to rapid reduction of Fe³⁺ and Mn³⁺ in the soil. Exogenous NO and H₂ S significantly protected plants from waterlogging effects by enhancing the oxidative defence and regulating nutritional status. Besides, the protective effects of exogenous NO were more prominent as compared with effects of H₂ S. Further, we did not study the effect of H₂ S and NO on photosynthetic attributes and expression of stress-related genes. Therefore, future studies should examine the effects of H₂ S and NO on wheat physiology and gene expression under waterlogging.

Salicylic Acid Enhances Adventitious Root and Aerenchyma Formation in Wheat under Waterlogged Conditions

The present study investigated the role of salicylic acid (SA) in regulating morpho-anatomical adaptive responses of a wheat plant to waterlogging. Our pharmacological study showed that treatment of waterlogged wheat plants with exogenous SA promotes the formation axile roots and surface adventitious roots that originate from basal stem nodes, but inhibits their elongation, leading to the formation of a shallow root system. The treatment also enhanced axile root formation in non-waterlogged plants but with only slight reductions in their length and branch root formation. Exogenous SA enhanced the formation of root aerenchyma, a key anatomical adaptive response of plants to waterlogging. Consistent with these results, waterlogging enhanced SA content in the root via expression of specific isochorismate synthase (ICS; ICS1 and ICS2) and phenylalanine ammonia lyase (PAL; PAL4, PAL5 and PAL6) genes and in the stem nodes via expression of specific PAL (PAL5 and PAL6) genes. Although not to the same level observed in waterlogged plants, exogenous SA also induced aerenchyma formation in non-waterlogged plants. The findings of this study furthermore indicated that inhibition of ethylene synthesis in SA treated non-waterlogged and waterlogged plants does not have any effect on SA-induced emergence of axile and/or surface adventitious roots but represses SA-mediated induction of aerenchyma formation. These results highlight that the role of SA in promoting the development of axile and surface adventitious roots in waterlogged wheat plants is ethylene independent while the induction of aerenchyma formation by SA requires the presence of ethylene.

Tolerance of Hymenaea courbaril L. to glyphosate

The objective was to evaluate the effect of the glyphosate on Hymenaea courbaril L. A randomized block design with five replications was implemented. Each experimental unit was composed of one plant in a 5 L container. The treatments were 0 "control"; 96; 240; 480; and 960 g ha-1 "corresponding to 10, 25, 50, and 100% of the commercial dose of glyphosate recommended for Caryocar brasiliense crop, respectively". The evaluations were performed at 24 h and 60 days after application. Visual and anatomical evaluations did not change regardless of the dose, while the histochemical evaluation showed an accumulation of starch grains in leaf tissues. There was an increase in the photosynthetic rate, in the electron transport rate, and in the effective quantum yield of photosystem II at 24 h after application. At 60 days after the application of the treatments, the photosynthetic rate showed a slight decrease and the transpiratory rate showed quadratic behavior. An increase in plant height was observed up to the dose of 480 g ha-1, a linear increase in stem diameter and a decrease in the number of leaves with increasing glyphosate doses. These results show that the cuticle protected the plant, and that the little absorbed glyphosate increased photosynthesis and transpiration to favor the plants. We can conclude that the H. courbaril species is able to survive after contact with glyphosate during the evaluated time, with no visual and/or anatomical damage, showing increases in growth and physiological characteristics for the tested doses.

iTRAQ Proteomic Analysis of Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance

Transient and chronic waterlogging constrains crop production in many regions of the world. Here, we invoke a novel iTRAQ-based proteomic strategy to elicit protein synthesis and regulation responses to waterlogging in tolerant (XM 55) and sensitive genotypes (YM 158). Of the 7,710 proteins identified, 16 were distinct between the two genotypes under waterlogging, partially defining a proteomic basis for waterlogging tolerance (and sensitivity). We found that 11 proteins were up-regulated and 5 proteins were down-regulated; the former included an Fe-S cluster assembly factor, heat shock cognate 70, GTP-binding protein SAR1A-like and CBS domain-containing protein. Down-regulated proteins contained photosystem II reaction center protein H, carotenoid 9, 10 (9', 10')-cleavage dioxygenase-like, psbP-like protein 1 and mitochondrial ATPase inhibitor. We showed that nine proteins responded to waterlogging with non-cultivar specificity: these included 3-isopropylmalate dehydratase large subunit, solanesyl-diphosphate synthase 2, DEAD-box ATP-dependent RNA helicase 3, and 3 predicted or uncharacterized proteins. Sixteen of the 28 selected proteins showed consistent expression patterns between mRNA and protein levels. We conclude that waterlogging stress may redirect protein synthesis, reduce chlorophyll synthesis and enzyme abundance involved in photorespiration, thus influencing synthesis of other metabolic enzymes. Collectively, these factors accelerate the accumulation of harmful metabolites in leaves in waterlogging-susceptible genotypes. The differentially expressed proteins enumerated here could be used as biological markers for enhancing waterlogging tolerance as part of future crop breeding programs.

Response of Lignin Metabolism to Light Quality in Wheat Population

The low red/far-red (R/FR) light proportion at the base of the high-density wheat population leads to poor stem quality and increases lodging risk. We used Shannong 23 and Shannong 16 as the test materials. By setting three-light quality treatments: normal light (CK), red light (RL), and far-red light (FRL), we irradiated the base internodes of the stem with RL and FRL for 7h. Our results showed that RL irradiation enhanced stem quality, as revealed by increased breaking strength, stem diameter, wall thickness and, dry weight per unit length, and the total amount of lignin and related gene expression increased, at the same time. The composition of lignin subunits was related to the lodging resistance of wheat. The proportion of S+G subunits and H subunits played a key role in wheat lodging resistance. RL could increase the content of S subunits and G subunits and the proportion of S+G subunits, reduce the proportion of H subunits. We described here, to the best of our knowledge, the systematic study of the mechanism involved in the regulation of stem breaking strength by light quality, particularly the effect of light quality on lignin biosynthesis and its relationship with lodging resistance in wheat.

Assessment of the Role of PAL in Lignin Accumulation in Wheat (Tríticum aestívum L.) at the Early Stage of Ontogenesis

The current study evaluates the role of phenylalanine ammonia-lyase (PAL) and the associated metabolic complex in the accumulation of lignin in common wheat plants (Tríticum aestívum L.) at the early stages of ontogenesis. The data analysis was performed using plant samples that had reached Phases 4 and 5 on the Feekes scale—these phases are characterized by a transition to the formation of axial (stem) structures in cereal plants. We have shown that the substrate stimulation of PAL with key substrates, such as L-phenylalanine and L-tyrosine, leads to a significant increase in lignin by an average of 20% in experimental plants compared to control plants. In addition, the presence of these compounds in the nutrient medium led to an increase in the number of gene transcripts associated with lignin synthesis (PAL6, C4H1, 4CL1, C3H1). Inhibition was the main tool of the study. Potential competitive inhibitors of PAL were used: the optical isomer of L-phenylalanine—D-phenylalanine—and the hydroxylamine equivalent of phenylalanine—O-Benzylhydroxylamine. As a result, plants incubated on a medium supplemented with O-Benzylhydroxylamine were characterized by reduced PAL activity (almost one third). The lignin content of the cell wall in plants treated with O-Benzylhydroxylamine was almost halved. In contrast, D-phenylalanine did not lead to significant changes in the lignin-associated metabolic complex, and its effect was similar to that of specific substrates.

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat

Background

Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood.

Results

Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data.

Conclusions

This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07849-y.

Cloning, expression analysis and molecular marker development of cinnamyl alcohol dehydrogenase gene in common wheat

In common wheat, stem strength is one of the key factors for lodging resistance, which is influenced by lignin content. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme in the pathway of lignin biosynthesis. Cloning and marker development of the CAD gene could be helpful for lodging resistance breeding. In this study, the full-length genomic DNA sequence of CAD gene in wheat was cloned by using homologous strategy. A marker 5-f2r2 was developed based on CAD sequence and used to genotype 258 wheat lines. Four haplotype combinations of CAD genes were identified in 258 wheat lines. Correction analyses among the CAD gene expression, CAD activity, and stem strength indicated significant positive correlation between CAD gene expression and CAD activity, between wheat CAD activity and wheat stem strength. The haplotype combination B is significantly associated with the lower enzyme activity and weak stem strength, which was supported by the level of CAD gene expression. The CAD activity and stem strength of wheat could be distinguished to some extent using this pair of specific primer 5-f2r2 designed in this study, indicating that the sequence targeted site (STS) marker 5-f2r2 could be used in marker assistant selection (MAS) breeding.

Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin

Wheat (Triticum aestivum L.), the most widely cultivated crop, is affected by waterlogging that limited the wheat production. Given the incompleteness of its genome annotation, PacBio SMRT plus Illumina short-read sequencing strategy provided an efficient approach to investigate the genetic regulation of waterlogging stress in wheat. A total of 947,505 full-length non-chimetric (FLNC) sequences were obtained with two wheat cultivars (XM55 and YM158) with PacBio sequencing. Of these, 5,309 long-non-coding RNAs, 1,574 fusion genes and 739 transcription factors were identified with the FLNC sequences. These full-length transcripts were derived from 49,368 genes, including 47.28% of the genes annotated in IWGSC RefSeq v1.0 and 40.86% genes encoded two or more isoforms, while 27.31% genes in the genome annotation of IWGSC RefSeq v1.0 were multiple-exon genes encoding two or more isoforms. Meanwhile, the individuals with waterlogging treatments (WL) and control group (CK) were selected for Illumina sequencing. Totally, 6,829 differentially expressed genes (DEGs) were detected from four pairwise comparisons. Notably, 942 DEGs were overlapped in the two comparisons (i.e., XM55-WL vs. YM158-WL and YM158-WL vs. YM158-CK). Undoubtedly, the genes involved in photosynthesis were downregulated after waterlogging treatment in two cultivars. Notably, the genes related to steroid biosynthesis, steroid hormone biosynthesis, and downstream plant hormone signal transduction were significantly upregulated after the waterlogging treatment, and the YM158 variety revealed different genetic regulation patterns compared with XM55. The findings provided valuable insights into unveiling regulation mechanisms of waterlogging stress in wheat at anthesis and contributed to molecular selective breeding of new wheat cultivars in future.

Increasing Lignification in Translucent Disorder Aril of Mangosteen Related to the ROS Defensive Function

Mangosteen fruit has a high potential on the global fruit market, but some disorders, including translucent flesh, are major problems of fruit quality, limiting the marketability. The present study was conducted to compare physiological changes of reactive oxygen species (ROS), cellular lignification between translucent and normal aril, and elucidate the relation. Mangosteen fruits at purple peel color were collected from eastern Thailand during the middle of the rainy season of 2019. Translucent aril accumulated higher lignin content in the tissues, expressing firmer texture ten times higher than normal aril. Lignification was increased in translucent aril by 740% and 25% higher coniferyl alcohol dehydrogenase (CAD) and peroxidase (POD) activity, respectively, induced by high H2O2. Healthy aril performed higher activities of superoxide dismutase (SOD) (8.5 times) and ascorbate peroxidase (APX) (1.3 times) to those in translucent aril. Furthermore, the higher flavonoid content, ascorbic acid content, and antioxidant capacities detected in normal aril could significantly reduce oxidative stress. Although containing high antioxidant systems, healthy aril was found to accumulate higher malonaldehyde content (MDA). This study provides intensive evidence of oxidative stress and the defensive systems between normal and translucent tissues.

Hormesis in plants: Physiological and biochemical responses

Hormesis is a favorable response to low level exposures to substance or to adverse conditions. This phenomenon has become a target to achieve greater crop productivity. This review aimed to address the physiological mechanisms for the induction of hormesis in plants. Some herbicides present a hormetic dose response. Among them, those with active ingredients glyphosate, 2,4-D and paraquat. The application of glyphosate as a hormesis promoter is therefore showing promess . Glyphosate has prominent role in shikimic acid pathway, decreasing lignin synthesis resulting in improved growth and productivity of several crops. Further studies are still needed to estimate optimal doses for other herbicides of crops or agricultural interest. Biostimulants are also important, since they promote effects on secondary metabolic pathways and production of reactive oxygen species (ROS). When ROS are produced, hydrogen peroxide act as a signaling molecule that promote cell walls malleability allowing inward water transport causing cell expansion. . Plants'ability to overcome several abiotic stress conditions is desirable to avoid losses in crop productivity and economic losses. This review compiles information on how hormesis in plants can be used to achieve new production levels.

Agro-Techniques for Lodging Stress Management in Maize-Soybean Intercropping System-A Review

Lodging is one of the most chronic restraints of the maize-soybean intercropping system, which causes a serious threat to agriculture development and sustainability. In the maize-soybean intercropping system, shade is a major causative agent that is triggered by the higher stem length of a maize plant. Many morphological and anatomical characteristics are involved in the lodging phenomenon, along with the chemical configuration of the stem. Due to maize shading, soybean stem evolves the shade avoidance response and resulting in the stem elongation that leads to severe lodging stress. However, the major agro-techniques that are required to explore the lodging stress in the maize-soybean intercropping system for sustainable agriculture have not been precisely elucidated yet. Therefore, the present review is tempted to compare the conceptual insights with preceding published researches and proposed the important techniques which could be applied to overcome the devastating effects of lodging. We further explored that, lodging stress management is dependent on multiple approaches such as agronomical, chemical and genetics which could be helpful to reduce the lodging threats in the maize-soybean intercropping system. Nonetheless, many queries needed to explicate the complex phenomenon of lodging. Henceforth, the agronomists, physiologists, molecular actors and breeders require further exploration to fix this challenging problem.

Stem lodging resistance in hulless barley: Transcriptome and metabolome analysis of lignin biosynthesis pathways in contrasting genotypes

Hulless barley is an important economic and food crop for local population in the Qinghai-Tibet plateau. However, due to extreme weather conditions, its production suffers from stem lodging stress, inflicting significant yield losses. Herein, we selected five lodging resistant and five non-resistant genotypes to investigate changes in concentration of lignin related metabolites and expression levels of related genes in node samples. The lodging resistant genotypes displayed high content of lignin intermediate metabolites. 57% of the expressed genes were differentially expressed (DEG) between the two groups. 31 DEGs participate in the lignin pathways and we found that 65% of these DEGs were strongly up-regulated in the lodging resistant group, indicating a mechanism towards high lignin synthesis within said group. The candidate structural genes as well as the co-expressed TFs identified in this study represent important molecular tools for functional characterization and exploitation in molecular breeding programmes.

Polyamine-Mediated Transcriptional Regulation of Enzymatic Antioxidative Response to Excess Soil Moisture during Early Seedling Growth in Soybean

This study examined the expression patterns of antioxidative genes and the activity of the corresponding enzymes in the excess moisture-stressed seedlings of soybean in response to seed treatment with polyamines, spermine (Spm) and spermidine (Spd). At the 4 day after planting (DAP) stage, the excess moisture impaired the embryo axis growth, and this effect is associated with the downregulation of superoxide dismutase (GmSOD1) expression and SOD activity in the cotyledon. Seed treatment with Spm reversed the effects of excess moisture on embryo axis growth partly through enhancing glutathione reductase (GR) activity, in both the cotyledon and embryo axis, although no effect on the GmGR expression level was evident. Excess moisture inhibited the shoot and root growth in 7 DAP seedlings, and this is associated with decreased activities of GR in the shoot and SOD in the root. The effect of excess moisture on shoot and root growth was reversed by seed treatment with Spd, and this was mediated by the increased activities of ascorbate peroxidase (APX), catalase (CAT) and GR in the shoot, and APX in the root, however, only GR in the shoot appears to be regulated transcriptionally. Root growth was also reversed by seed treatment with Spm with no positive effect on gene expression and enzyme activity.

Phenylalanine and Tyrosine as Exogenous Precursors of Wheat (Triticum aestivum L.) Secondary Metabolism through PAL-Associated Pathways

Reacting to environmental exposure, most higher plants activate secondary metabolic pathways, such as the metabolism of phenylpropanoids. This pathway results in the formation of lignin, one of the most important polymers of the plant cell, as well as a wide range of phenolic secondary metabolites. Aromatic amino acids, such as phenylalanine and tyrosine, largely stimulate this process, determining two ways of lignification in plant tissues, varying in their efficiency. The current study analyzed the effect of phenylalanine and tyrosine, involved in plant metabolism through the phenylalanine ammonia-lyase (PAL) pathway, on the synthesis and accumulation of phenolic compounds, as well as lignin by means of the expression of a number of genes responsible for its biosynthesis, based on the example of common wheat (Triticum aestivum L.).

Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we used Illumina RNA-sequencing (RNA-seq) to perform large-scale transcriptome sequencing of two sugarcane cultivars to contrast gene expression patterns of plants between Aaa and mock inoculations, and identify key genes and pathways involved in sugarcane defense responses to Aaa infection. At 0–72 hours post-inoculation (hpi) of the red stripe disease-resistant cultivar ROC22, a total of 18,689 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples. Of these, 8498 and 10,196 genes were up- and downregulated, respectively. In MT11-610, which is susceptible to red stripe disease, 15,782 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples and 8807 and 6984 genes were up- and downregulated, respectively. The genes that were differentially expressed following Aaa inoculation were mainly involved in photosynthesis and carbon metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction pathways. Further, qRT-PCR and RNA-seq used for additional validation of 12 differentially expressed genes (DEGs) showed that eight genes in particular were highly expressed in ROC22. These eight genes participated in the biosynthesis of lignin and coumarin, as well as signal transduction by salicylic acid, jasmonic acid, ethylene, and mitogen-activated protein kinase (MAPK), suggesting that they play essential roles in sugarcane resistance to Aaa. Collectively, our results characterized the sugarcane transcriptome during early infection with Aaa, thereby providing insights into the molecular mechanisms responsible for bacterial tolerance.

Improving Lodging Resistance: Using Wheat and Rice as Classical Examples

One of the most chronic constraints to crop production is the grain yield reduction near the crop harvest stage by lodging worldwide. This is more prevalent in cereal crops, particularly in wheat and rice. Major factors associated with lodging involve morphological and anatomical traits along with the chemical composition of the stem. These traits have built up the remarkable relationship in wheat and rice genotypes either prone to lodging or displaying lodging resistance. In this review, we have made a comparison of our conceptual perceptions with foregoing published reports and proposed the fundamental controlling techniques that could be practiced to control the devastating effects of lodging stress. The management of lodging stress is, however, reliant on chemical, agronomical, and genetic factors that are reducing the risk of lodging threat in wheat and rice. But, still, there are many questions remain to be answered to elucidate the complex lodging phenomenon, so agronomists, breeders, physiologists, and molecular biologists require further investigation to address this challenging problem.

Transcriptomics of cytokinin and auxin metabolism and signaling genes during seed maturation in dormant and non-dormant wheat genotypes

To gain insights into the roles of cytokinin (CK) and auxin in regulating dormancy during seed maturation in wheat, we examined changes in the levels of CK and indole-3-acetic acid (IAA) and expression patterns of their metabolism and signaling genes in embryonic and endospermic tissues of dormant and non-dormant genotypes. Seed maturation was associated with a decrease in the levels of isopentenyladenine in both tissues mainly via repression of the CK biosynthetic TaLOG genes. Differential embryonic trans-zeatin content and expression patterns of the CK related genes including TacZOG, TaGLU and TaARR12 between maturing seeds of the two genotypes implicate CK in the control of seed dormancy induction and maintenance. Seed maturation induced a decrease of IAA level in both tissues irrespective of genotype, and this appeared to be mediated by repression of specific IAA biosynthesis, transport and IAA-conjugate hydrolysis genes. The differential embryonic IAA content and expression pattern of the IAA biosynthetic gene TaAO during the early stage of seed maturation between the two genotypes imply the role of IAA in dormancy induction. It appears from our data that the expression of specific auxin signaling genes including TaRUB, TaAXR and TaARF mediate the role of auxin signaling in dormancy induction and maintenance during seed maturation in wheat.