Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase

Comparative transcriptomics of indica and japonica rice roots under heat stress reveals the crucial role of OsMAPK3 in heat response

Heat stress is one of the most critical environmental factors impacting rice cultivation, driven by the rising global temperatures. Therefore, understanding the differences in molecular mechanisms of heat stress tolerance between rice cultivars, particularly indica and japonica, is crucial for developing heat-tolerant varieties. In this study, high throughput RNA-sequencing technology was utilized to explore the transcriptomic changes in the root tissues of two rice varieties, 93-11 (indica) and ZH11 (japonica) under heat stress and during recovery. Differentially Expressed Genes (DEGs) analysis revealed that ZH11 had 14,719 DEGs after the two-day heat treatment, and 10,178 DEGs during the recovery process. In contrast, 93-11 had a lower number of DEGs than ZH11 in both the heat treatment and recovery phases, with 12,433 DEGs and 5986 DEGs, respectively. The GO and KEGG analyses showed that the two rice varieties shared several enriched pathways in response to heat stress. However, each cultivar also had its own uniquely enriched pathways, reflecting distinct responses to heat stress in ZH11 and 93-11. In addition, WGCNA analysis highlighted that the OsMAPK3 is novel hub gene in response to heat stress in rice. Knockout of OsMAPK3 compromises rice heat stress tolerance. These results provide new insights into the differences in molecular mechanisms of heat stress response in roots between indica and japonica rice cultivars, offering valuable targets for genetic improvement and breeding programs aimed at developing heat-tolerant rice varieties.

RPT: An integrated root phenotyping toolbox for segmenting and quantifying root system architecture

The dissection of genetic architecture for rice root system is largely dependent on phenotyping techniques, and high-throughput root phenotyping poses a great challenge. In this study, we established a cost-effective root phenotyping platform capable of analysing 1680 root samples within 2 h. To efficiently process a large number of root images, we developed the root phenotyping toolbox (RPT) with an enhanced SegFormer algorithm and used it for root segmentation and root phenotypic traits. Based on this root phenotyping platform and RPT, we screened 18 candidate (quantitative trait loci) QTL regions from 219 rice recombinant inbred lines under drought stress and validated the drought-resistant functions of gene OsIAA8 identified from these QTL regions. This study confirmed that RPT exhibited a great application potential for processing images with various sources and for mining stress-resistance genes of rice cultivars. Our developed root phenotyping platform and RPT software significantly improved high-throughput root phenotyping efficiency, allowing for large-scale root trait analysis, which will promote the genetic architecture improvement of drought-resistant cultivars and crop breeding research in the future.

The DnaJ1 heat shock protein interacts with the flavanone 3-hydroxylase-like protein F3HL to synergistically enhance drought tolerance by scavenging reactive oxygen species in tomato

The widely distributed heat shock protein DnaJ is renowned for its pivotal role in enhancing thermal tolerance in plants; however, its involvement in drought tolerance remains elusive. In this study, genes encoding DnaJ1 were cloned from drought-resistant wild tomato (Solanum pennellii) and drought-sensitive cultivated tomato (Solanum lycopersicum). SpDnaJ1 and SlDnaJ1 from both tomato species were localized in the chloroplast, and their gene expression was induced by various abiotic stresses. SpDnaJ1 was found to be a more potent regulator than SlDnaJ1 in oxidative stress tolerance when expressed in yeast cells. Overexpression of SpDnaJ1 was demonstrated to confer drought tolerance in transgenic plants of cultivated tomato. These transgenic plants exhibited reduced relative conductivity, leaf water loss rate, and malondialdehyde content as compared to the wild-type plants following drought treatment. RNA-seq analysis revealed that overexpression of SpDnaJ1 primarily affects the expression of genes associated with antioxidants, protease inhibitors, and MAPK signaling in response to drought stress. Screening of a tomato cDNA library in the yeast two-hybrid system identified a flavanone 3-hydroxylase-like protein (F3HL) as an interacting protein of DnaJ1. Subsequent findings revealed that F3HL enhances drought tolerance in tomato by increasing the activity of antioxidant enzymes and scavenging reactive oxygen species. These findings demonstrate a pivotal role of DnaJ1-F3HL interaction in enhancing drought tolerance, unveiling a novel molecular mechanism in drought tolerance in plants.

The OsMAPK5-OsWRKY72 module negatively regulates grain length and grain weight in rice

Grain size and grain weight are important determinants for grain yield. In this study, we identify a novel OsMAPK5-OsWRKY72 module that negatively regulates grain length and grain weight in rice. We found that loss-of-function of OsMAPK5 leads to larger cell size of the rice spikelet hulls and a significant increase in both grain length and grain weight in an indica variety Minghui 86 (MH86). OsMAPK5 interacts with OsMAPKK3/4/5 and OsWRKY72 and phosphorylates OsWRKY72 at T86 and S88. Similar to the osmapk5 MH86 mutants, the oswrky72 knockout MH86 mutants exhibited larger size of spikelet hull cells and increased grain length and grain weight, whereas the OsWRKY72-overexpression MH86 plants showed opposite phenotypes. OsWRKY72 targets the W-box motifs in the promoter of OsARF6, an auxin response factor involved in auxin signaling. Dual-luciferase reporter assays demonstrated that OsWRKY72 activates OsARF6 expression. The activation effect of the phosphorylation-mimicking OsWRKY72T86D/S88D on OsARF6 expression was significantly enhanced, whereas the effects of the OsWRKY72 phosphorylation-null mutants were significantly reduced. In addition, auxin levels in young panicles of the osmapk5 and oswrky72 mutants were significantly higher than that in the wild-type MH86. Collectively, our study uncovered novel connections of the OsMAPKK3/4/5-OsMAPK5-mediated MAPK signaling, OsWRKY72-mediated transcription regulation, and OsARF6-mediated auxin signaling pathways in regulating grain length and grain weight in an indica-type rice, providing promising targets for molecular breeding of rice varieties with high yield and quality.

Combined Physiological and Transcriptomic Analysis Reveals Key Regulatory Networks and Potential Hub Genes Controlling Chilling Tolerance During Soybean Germination

Chilling is an important limiting factor for seed germination of soybean (Glycine max [L.] Merr.). To reveal the regulatory mechanism of chilling tolerance during the soybean germination stage, based on previous studies, the chilling tolerance line R48 and chilling sensitive line R89 in chromosome segment substitution lines were selected for physiological index determination and transcriptome sequencing. It was found that reactive oxygen species (ROS) scavenging system related enzymes, ROS, and osmotic regulators were significantly different between the two lines. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes enrichment were performed on the differentially expressed genes obtained by transcriptome sequencing. It was found that terms or pathways related to flavonoids, unsaturated fatty acids, and abscisic acid were highly enriched. In addition, weighted gene coexpression network analysis (WGCNA) method was used to analyze the physiological index data and transcriptome sequencing data. Four main coexpression modules significantly related to physiological indicators were obtained, and the hub genes in each module were screened according to eigengene-based connectivity value. Haplotype analysis of important candidate genes using soybean germplasm resources showed that there were significant differences in germination indexes between different major haplotypes of Glyma.17G163200. Based on the results of enrichment analysis and WGCNA, the regulation model of low temperature tolerance during soybean germination was preliminarily drawn. This study will provide theoretical guidance for analyzing the molecular regulation mechanism of cold tolerance in soybean germination stage.

Advances in Understanding Drought Stress Responses in Rice: Molecular Mechanisms of ABA Signaling and Breeding Prospects

Drought stress is a pivotal environmental factor impacting rice production and presents a significant challenge to sustainable agriculture worldwide. This review synthesizes the latest research advancements in the regulatory mechanisms and signaling pathways that rice employs in response to drought stress. It elaborates on the adaptive changes and molecular regulatory mechanisms that occur in rice under drought conditions. The review highlights the perception and initial transmission of drought signals, key downstream signaling networks such as the MAPK and Ca2+ pathways, and their roles in modulating drought responses. Furthermore, the discussion extends to hormonal signaling, especially the crucial role of abscisic acid (ABA) in drought responses, alongside the identification of drought-resistant genes and the application of gene-editing technologies in enhancing rice drought resilience. Through an in-depth analysis of these drought stress regulatory signaling pathways, this review aims to offer valuable insights and guidance for future rice drought resistance breeding and agricultural production initiatives.

Comparative transcriptome and coexpression network analysis revealed the regulatory mechanism of Astragalus cicer L. in response to salt stress

BACKGROUND

Astragalus cicer L. is a perennial rhizomatous legume forage known for its quality, high biomass yield, and strong tolerance to saline-alkaline soils. Soil salinization is a widespread environmental pressure. To use A. cicer L. more scientifically and environmentally in agriculture and ecosystems, it is highly important to study the molecular response mechanism of A. cicer L. to salt stress.

RESULTS

In this study, we used RNA-seq technology and weighted gene coexpression network analysis (WGCNA) were performed. The results showed 4 key modules were closely related to the physiological response of A. cicer. L. to salt stress. The differentially expressed genes (DEGs) of key modules were mapped into the KEGG database, and found that the most abundant pathways were the plant hormone signal transduction pathway and carbon metabolism pathway. The potential regulatory networks of the cytokinin signal transduction pathway, the ethylene signal transduction pathway, and carbon metabolism related pathways were constructed according to the expression pathways of the DEGs. Seven hub genes in the key modules were selected and distributed among these pathways. They may involved in the positive regulation of cytokinin signaling and carbon metabolism in plant leaves, but limited the positive expression of ethylene signaling. Thus endowing the plant with salt tolerance in the early stage of salt stress.

CONCLUSIONS

Based on the phenotypic and physiological responses of A. cicer L. to salt stress, this study constructed the gene coexpression network of potential regulation to salt stress in key modules, which provided a new reference for exploring the response mechanism of legumes to abiotic stress.

Mutagenesis-Derived Resistance to Black Point in Wheat

Black point, a severe global wheat disease, necessitates deploying resistant cultivars for effective control. However, susceptibility remains prevalent among most wheat cultivars. Identifying new sources of resistance and understanding their mechanisms are crucial for breeding resistant cultivars. This study pinpointed black point resistance in an ethyl methane sulfonate (EMS)-mutagenized wheat population of Wanyuanbai 1 (WYB) and analyzed resistant mutants using RNA-Seq. The findings revealed the following: (i) wyb-18, among 10,008 EMS-mutagenized lines, exhibited robust resistance with significantly lower black point incidence under artificial Bipolaris sorokiniana inoculation in 2020 and 2021 (average incidence of 5.2% over 2 years), markedly reduced compared with WYB (50.9%). (ii) wyb-18 kernels displayed black point symptoms at 12 days after inoculation (dai), 3 days later than WYB. At 15 dai, wyb-18 kernels had isolated black spots, unlike WYB kernels, where the entire embryo turned black. (iii) wyb-18 showed heightened antioxidant enzyme activity, including peroxidase, catalase, and superoxide dismutase. (iv) Analysis of 543 differentially expressed genes between wyb-18 and WYB at 9 dai identified enrichment in the MAPK signaling pathway through KEGG analysis. Ten genes in this pathway exhibited upregulated expression, while one was downregulated in wyb-18. Among these genes, PR1, WRKY11, SAPK5, and TraesCS1A02G326800 (chitin recognition protein) consistently showed upregulation in wyb-18, making them potential candidates for black point resistance. These results offer valuable germplasm resources for breeding and novel insights into the mechanisms of black point resistance.

Comparison of Transcriptome Differences between Two Rice Cultivars Differing in Cadmium Translocation from Spike-Neck to Grain

At present, the mechanism of varietal differences in cadmium (Cd) accumulation in rice is not well understood. Two rice cultivars, ZZY (high translocation-high grain Cd) and SJ18 (low translocation-low grain Cd), were used to analyze transcriptome differences in the spike-neck tissue in field trials. The results showed that, compared with ZZY, 22,367 differentially expressed genes (DEGs) were identified in SJ18, including 2941 upregulated and 19,426 downregulated genes. GO analysis enriched 59 downregulated terms, concerning 24 terms enriched for more than 1000 DEGs, including cellular and metabolic processes, biological regulation, localization, catalytic activity, transporter activity, signaling, etc. KEGG enrichment identified 21 significant downregulated pathways, regarding the ribosome, metabolic pathways, biosynthesis of secondary metabolism, signaling transduction, cell membrane and cytoskeleton synthesis, genetic information transfer, amino acid synthesis, etc. Weighted gene co-expression network analysis (WGCNA) revealed that these DEGs could be clustered into five modules. Among them, the yellow module was significantly related to SJ18 with hub genes related to OsHMA and OsActin, whereas the brown module was significantly related to ZZY with hub genes related to mitogen-activated protein kinase (MAPK), CBS, and glutaredoxin. This suggests that different mechanisms are involved in the process of spike-neck-grain Cd translocation among varieties. This study provides new insights into the mechanisms underlying differences in Cd transport among rice varieties.

Nanopore Direct RNA Sequencing Reveals the Short-Term Salt Stress Response in Maize Roots

Transcriptome analysis, relying on the cutting-edge sequencing of cDNA libraries, has become increasingly prevalent within functional genome studies. However, the dependence on cDNA in most RNA sequencing technologies restricts their ability to detect RNA base modifications. To address this limitation, the latest Oxford Nanopore Direct RNA Sequencing (ONT DRS) technology was employed to investigate the transcriptome of maize seedling roots under salt stress. This approach aimed to unveil both the RNA transcriptional profiles and alterations in base modifications. The analysis of the differential expression revealed a total of 1398 genes and 2223 transcripts that exhibited significant variation within the maize root system following brief exposure to salt stress. Enrichment analyses, such as the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway assessments, highlighted the predominant involvement of these differentially expressed genes (DEGs) in regulating ion homeostasis, nitrogen metabolism, amino acid metabolism, and the phytohormone signaling pathways. The protein-protein interaction (PPI) analysis showed the participation of various proteins related to glycolytic metabolism, nitrogen metabolism, amino acid metabolism, abscisic acid signaling, and the jasmonate signaling pathways. It was through this intricate molecular network that these proteins collaborated to safeguard root cells against salt-induced damage. Moreover, under salt stress conditions, the occurrence of variable shear events (AS) in RNA modifications diminished, the average length of poly(A) tails underwent a slight decrease, and the number of genes at the majority of the variable polyadenylation (APA) sites decreased. Additionally, the levels of N5-methylcytosine (m5C) and N6-methyladenosine (m6A) showed a reduction. These results provide insights into the mechanisms of early salt tolerance in maize.

Genome-wide identification of MAPK family in papaya (Carica papaya) and their involvement in fruit postharvest ripening

BACKGROUND

Papaya (Carica papaya) is an economically important fruit cultivated in the tropical and subtropical regions of China. However, the rapid softening rate after postharvest leads to a short shelf-life and considerable economic losses. Accordingly, understanding the mechanisms underlying fruit postharvest softening will be a reasonable way to maintain fruit quality and extend its shelf-life.

RESULTS

Mitogen-activated protein kinases (MAPKs) are conserved and play essential roles in response to biotic and abiotic stresses. However, the MAPK family remain poorly studied in papaya. Here, a total of nine putative CpMAPK members were identified within papaya genome, and a comprehensive genome-wide characterization of the CpMAPKs was performed, including evolutionary relationships, conserved domains, gene structures, chromosomal locations, cis-regulatory elements and expression profiles in response to phytohormone and antioxidant organic compound treatments during fruit postharvest ripening. Our findings showed that nearly all CpMAPKs harbored the conserved P-loop, C-loop and activation loop domains. Phylogenetic analysis showed that CpMAPK members could be categorized into four groups (A-D), with the members within the same groups displaying high similarity in protein domains and intron-exon organizations. Moreover, a number of cis-acting elements related to hormone signaling, circadian rhythm, or low-temperature stresses were identified in the promoters of CpMAPKs. Notably, gene expression profiles demonstrated that CpMAPKs exhibited various responses to 2-chloroethylphosphonic acid (ethephon), 1-methylcyclopropene (1-MCP) and the combined ascorbic acid (AsA) and chitosan (CTS) treatments during papaya postharvest ripening. Among them, both CpMAPK9 and CpMAPK20 displayed significant induction in papaya flesh by ethephon treatment, and were pronounced inhibition after AsA and CTS treatments at 16 d compared to those of natural ripening control, suggesting that they potentially involve in fruit postharvest ripening through ethylene signaling pathway or modulating cell wall metabolism.

CONCLUSION

This study will provide some valuable insights into future functional characterization of CpMAPKs, and hold great potential for further understanding the molecular mechanisms underlying papaya fruit postharvest ripening.

Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice

Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.

R-loops act as regulatory switches modulating transcription of COLD-responsive genes in rice

COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R-loops function in various cellular processes, including development and stress responses, in plants. However, how R-loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.). We conducted DRIP-Seq along with other omics data (RNA-Seq, DNase-Seq and ChIP-Seq) in rice with or without COLD treatment. COLD treatment caused R-loop reprogramming across the genome. COLD-biased R-loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R-loops can directly/indirectly modulate the transcription of a subset of COLD-responsive genes, which can be mediated by R-loop overlapping TF-centered or cis-regulatory element-related regulatory networks and lncRNAs, accounting for c. 60% of COLD-induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R-loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD-responsive gene expression, as potential targets for enhanced COLD resistance. Our study provides detailed evidence showing functions of R-loop reprogramming during COLD responses and provides some potential R-loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.

Identification and expression analysis of MAPK cascade gene family in foxtail millet (Setaria italica)

The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including Arabidopsis thaliana, Oryza sativa, and Triticum aestivum, but have not been identified in foxtail millet (Setaria italica). In this study, a total of 93 MAPK cascade genes, including 15 SiMAPKs, 10 SiMAPKKs and 68 SiMAPKKKs genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the SiMAPKs and SiMAPKKs into four subgroups, respectively, and the SiMAPKKKs into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most SiMAPKs and SiMAPKKs were changed under both exogenous hormone and abiotic stress treatments, with SiMAPK3 and SiMAPKK4-2 being induced under almost all treatments, while the expression of SiMAPKK5 was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (Setaria italica).

OsMAPK6 positively regulates rice cold tolerance at seedling stage via phosphorylating and stabilizing OsICE1 and OsIPA1

Rice is a chilling-sensitive plant, and extremely low temperatures seriously decrease rice production. Several genes involved in chilling stress have been reported in rice; however, the chilling signaling in rice remains largely unknown. Here, we investigated the chilling tolerance phenotype of overexpression of constitutive active OsMAPK6 (CAMAPK6-OE) and OsMAPK6 mutant dsg1, and demonstrated that OsMAPK6 positively regulated rice chilling tolerance. It was shown that, under cold stress, the survival rate of dsg1 was significantly lower than that of WT, whereas CAMAPK6-OE display higher survival rate than WT. Physiological assays indicate that ion leakage and dead cell in dsg1 was much more severe than those in WT and CAMAPK6-OE. Consistently, expression of chilling responsive genes in dsg1, including OsCBFs and OsTPP1, was significantly lower than that of in WT and CAMAPK6-OE. Biochemical analyses revealed that chilling stress promotes phosphorylation of OsMAPK6. Besides, we found that OsMAPK6 interacts with and phosphorylates two key regulators in rice cold signaling, OsIPA1 and OsICE1, and then enhance their protein stability. Overall, our results revealed a cold-induced OsMAPK6-OsICE1/OsIPA1 signaling cascade by which OsMAPK6 was involved in rice chilling tolerance, which provides novel insights to understand rice cold response at seedling stage.

Genome-wide identification of the mitogen-activated kinase gene family from Limonium bicolor and functional characterization of LbMAPK2 under salt stress

BACKGROUND

Mitogen-activated protein kinases (MAPKs) are ubiquitous signal transduction components in eukaryotes. In plants, MAPKs play an essential role in growth and development, phytohormone regulation, and abiotic stress responses. The typical recretohalophyte Limonium bicolor (Bunge) Kuntze has multicellular salt glands on its stems and leaves; these glands secrete excess salt ions from its cells to mitigate salt damage. The number, type, and biological function of L. bicolor MAPK genes are unknown.

RESULTS

We identified 20 candidate L. bicolor MAPK genes, which can be divided into four groups. Of these 20 genes, 17 were anchored to 7 chromosomes, while LbMAPK18, LbMAPK19, and LbMAPK20 mapped to distinct scaffolds. Structure analysis showed that the predicted protein LbMAPK19 contains the special structural motif TNY in its activation loop, whereas the other LbMAPK members harbor the conserved TEY or TDY motif. The promoters of most LbMAPK genes carry cis-acting elements related to growth and development, phytohormones, and abiotic stress. LbMAPK1, LbMAPK2, LbMAPK16, and LbMAPK20 are highly expressed in the early stages of salt gland development, whereas LbMAPK4, LbMAPK5, LbMAPK6, LbMAPK7, LbMAPK11, LbMAPK14, and LbMAPK15 are highly expressed during the late stages. These 20 LbMAPK genes all responded to salt, drought and ABA stress. We explored the function of LbMAPK2 via virus-induced gene silencing: knocking down LbMAPK2 transcript levels in L. bicolor resulted in fewer salt glands, lower salt secretion ability from leaves, and decreased salt tolerance. The expression of several genes [LbTTG1 (TRANSPARENT TESTA OF GL1), LbCPC (CAPRICE), and LbGL2 (GLABRA2)] related to salt gland development was significantly upregulated in LbMAPK2 knockdown lines, while the expression of LbEGL3 (ENHANCER OF GL3) was significantly downregulated.

CONCLUSION

These findings increase our understanding of the LbMAPK gene family and will be useful for in-depth studies of the molecular mechanisms behind salt gland development and salt secretion in L. bicolor. In addition, our analysis lays the foundation for exploring the biological functions of MAPKs in an extreme halophyte.

Deciphering the mechanisms, hormonal signaling, and potential applications of endophytic microbes to mediate stress tolerance in medicinal plants

The global healthcare market in the post-pandemic era emphasizes a constant pursuit of therapeutic, adaptogenic, and immune booster drugs. Medicinal plants are the only natural resource to meet this by supplying an array of bioactive secondary metabolites in an economic, greener and sustainable manner. Driven by the thrust in demand for natural immunity imparting nutraceutical and life-saving plant-derived drugs, the acreage for commercial cultivation of medicinal plants has dramatically increased in recent years. Limited resources of land and water, low productivity, poor soil fertility coupled with climate change, and biotic (bacteria, fungi, insects, viruses, nematodes) and abiotic (temperature, drought, salinity, waterlogging, and metal toxicity) stress necessitate medicinal plant productivity enhancement through sustainable strategies. Plants evolved intricate physiological (membrane integrity, organelle structural changes, osmotic adjustments, cell and tissue survival, reclamation, increased root-shoot ratio, antibiosis, hypersensitivity, etc.), biochemical (phytohormones synthesis, proline, protein levels, antioxidant enzymes accumulation, ion exclusion, generation of heat-shock proteins, synthesis of allelochemicals. etc.), and cellular (sensing of stress signals, signaling pathways, modulating expression of stress-responsive genes and proteins, etc.) mechanisms to combat stresses. Endophytes, colonizing in different plant tissues, synthesize novel bioactive compounds that medicinal plants can harness to mitigate environmental cues, thus making the agroecosystems self-sufficient toward green and sustainable approaches. Medicinal plants with a host set of metabolites and endophytes with another set of secondary metabolites interact in a highly complex manner involving adaptive mechanisms, including appropriate cellular responses triggered by stimuli received from the sensors situated on the cytoplasm and transmitting signals to the transcriptional machinery in the nucleus to withstand a stressful environment effectively. Signaling pathways serve as a crucial nexus for sensing stress and establishing plants' proper molecular and cellular responses. However, the underlying mechanisms and critical signaling pathways triggered by endophytic microbes are meager. This review comprehends the diversity of endophytes in medicinal plants and endophyte-mediated plant-microbe interactions for biotic and abiotic stress tolerance in medicinal plants by understanding complex adaptive physiological mechanisms and signaling cascades involving defined molecular and cellular responses. Leveraging this knowledge, researchers can design specific microbial formulations that optimize plant health, increase nutrient uptake, boost crop yields, and support a resilient, sustainable agricultural system.

Comparative transcriptome provides insights into gene regulation network associated with the resistance to Fusarium wilt in grafted wax gourd Benincasa hispida

Introduction

Wilt is a soil-borne disease caused by Fusarium that has become a serious threat to wax gourd production. Disease-resistant graft wax gourds are an effective treatment for Fusarium wilt. However, there are few reports on the defense mechanism of graft wax gourd against wilt diseases.

Methods

In the present study, disease and growth indices were compared between grafted and original wax gourds after infection with Fusarium. High level of disease resistance was observed in the grafted wax gourd, with a lower disease index and low impacts on growth after infection. RNA-seq was performed to identify the differentially expressed genes (DEGs) between the adjacent treatment time points in the grafted and original wax gourds, respectively. Then a comparative temporal analysis was performed and a total of 1,190 genes were identified to show different gene expression patterns between the two wax gourd groups during Fusarium infection.

Result and discussion

Here, high level of disease resistance was observed in the grafted wax gourd, with a lower disease index and low impacts on growth after infection. The DEG number was higher in grafted group than original group, and the enriched functional categories and pathways of DEGs were largely inconsistent between the two groups. These genes were enriched in multiple pathways, of which the mitogen-activated protein kinase (MAPK) signaling pathway enhanced the early defense response, and cutin, suberin, and wax biosynthesis signaling pathways enhanced surface resistance in grafted wax gourd in comparison to original group. Our study provides insights into the gene regulatory mechanisms underlying the resistance of grafted wax gourds to Fusarium wilt infection, which will facilitate the breeding and production of wilt-resistant rootstocks.

A pathogen's spatial range is not constrained by geographical features in the flax rust pathosystem

Climate change and shifting environmental conditions can allow pathogens to spread into previously unburdened areas. For plant pathogens, this dynamic has the potential to disrupt natural ecosystem equilibria and human agriculture, making predicting plant pathogen range shifts increasingly important. Although such predictions will hinge on an accurate understanding of the determinants of pathogen range-namely the environmental, geographical, and host range characteristics that modulate local pathogen habitation-few studies to date have probed these in natural plant populations. Here, we characterize range determinants for the model system of Lewis flax (Linum lewisii) and its pathogen, flax rust (Melampsora lini), in the Rocky Mountains. Transect surveys were performed to assess three relationships: (i) the effect of geographical features-elevation, slope aspect, slope grade, and land cover-on flax presence and density, (ii) the effect of geographical features on flax rust presence and prevalence, and (iii) the effects of flax's local population density and metapopulation structure on flax rust presence and prevalence. We found that flax population density, but not host metapopulation structure, influences the distribution of flax rust. Additionally, we showed that, while the distribution of flax was broadly constrained to a relatively narrow range of geographical and resulting environmental features, flax rust was evenly distributed across the full range of settings measured. These results indicate that a warming environment, which is expected to modulate such features, may restrict the optimal range of the plant more than that of its pathogen. Importantly, our results also suggest that even if flax shifts its spatial range to escape increasing climatic pressures, flax rust will not face any significant barriers to track this movement.

Effects of combined drought and pathogen stress on growth, resistance and gene expression in young Norway spruce trees

Drought-induced mortality is a major direct effect of climate change on tree health, but drought can also affect trees indirectly by altering their susceptibility to pathogens. Here, we report how a combination of mild or severe drought and pathogen infection affected the growth, pathogen resistance and gene expression in potted 5-year-old Norway spruce trees [Picea abies (L.) Karst.]. After 5 weeks of drought, trees were inoculated with the fungal pathogen Endoconidiophora polonica. Combined drought-pathogen stress over the next 8 weeks led to significant reductions in the growth of drought-treated trees relative to well-watered trees and more so in trees subjected to severe drought. Belowground, growth of the smallest fine roots was most affected. Aboveground, shoot diameter change was most sensitive to the combined stress, followed by shoot length growth and twig biomass. Both drought-related and some resistance-related genes were upregulated in bark samples collected after 5 weeks of drought (but before pathogen infection), and gene expression levels scaled with the intensity of drought stress. Trees subjected to severe drought were much more susceptible to pathogen infection than well-watered trees or trees subjected to mild drought. Overall, our results show that mild drought stress may increase the tree resistance to pathogen infection by upregulating resistance-related genes. Severe drought stress, on the other hand, decreased tree resistance. Because drought episodes are expected to become more frequent with climate change, combined effects of drought and pathogen stress should be studied in more detail to understand how these stressors interactively influence tree susceptibility to pests and pathogens.

The OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice

Recurrent heat stress and pathogen invasion seriously threaten crop production, and abiotic stress often antagonizes biotic stress response against pathogens. However, the molecular mechanisms of trade-offs between thermotolerance and defense remain obscure. Here, we identify a rice thermo-sensitive mutant that displays a defect in floret development under high temperature with a mutation in SUPPRESSOR OF GENE SILENCING 3a (OsSGS3a). OsSGS3a interacts with its homolog OsSGS3b and modulates the biogenesis of trans-acting small interfering RNA (tasiRNA) targeting AUXIN RESPONSE FACTORS (ARFs). We find that OsSGS3a/b positively, while OsARF3a/b and OsARF3la/lb negatively modulate thermotolerance. Moreover, OsSGS3a negatively, while OsARF3a/b and OsARF3la/lb positively regulate disease resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and the fungal pathogen Magnaporthe oryzae (M. oryzae). Taken together, our study uncovers a previously unknown trade-off mechanism that regulates distinct immunity and thermotolerance through the OsSGS3-tasiRNA-OsARF3 module, highlighting the regulation of abiotic-biotic stress response trade-off in plants.

Pathogenesis-related protein 10 in resistance to biotic stress: progress in elucidating functions, regulation and modes of action

Introduction

The Family of pathogenesis-related proteins 10 (PR-10) is widely distributed in the plant kingdom. PR-10 are multifunctional proteins, constitutively expressed in all plant tissues, playing a role in growth and development or being induced in stress situations. Several studies have investigated the preponderant role of PR-10 in plant defense against biotic stresses; however, little is known about the mechanisms of action of these proteins. This is the first systematic review conducted to gather information on the subject and to reveal the possible mechanisms of action that PR-10 perform.

Methods

Therefore, three databases were used for the article search: PubMed, Web of Science, and Scopus. To avoid bias, a protocol with inclusion and exclusion criteria was prepared. In total, 216 articles related to the proposed objective of this study were selected.

Results

The participation of PR-10 was revealed in the plant's defense against several stressor agents such as viruses, bacteria, fungi, oomycetes, nematodes and insects, and studies involving fungi and bacteria were predominant in the selected articles. Studies with combined techniques showed a compilation of relevant information about PR-10 in biotic stress that collaborate with the understanding of the mechanisms of action of these molecules. The up-regulation of PR-10 was predominant under different conditions of biotic stress, in addition to being more expressive in resistant varieties both at the transcriptional and translational level.

Discussion

Biological models that have been proposed reveal an intrinsic network of molecular interactions involving the modes of action of PR-10. These include hormonal pathways, transcription factors, physical interactions with effector proteins or pattern recognition receptors and other molecules involved with the plant's defense system.

Conclusion

The molecular networks involving PR-10 reveal how the plant's defense response is mediated, either to trigger susceptibility or, based on data systematized in this review, more frequently, to have plant resistance to the disease.

Cold-responsive transcription factors in Arabidopsis and rice: A regulatory network analysis using array data and gene co-expression network

Plant growth and development can be influenced by cold stress. Responses of plants to cold are regulated in part by transcription factors (TFs) and microRNAs, which their determination would be necessary in comprehension of the corresponding molecular cues. Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. Among 181 Arabidopsis and 168 rice differentially expressed TF genes, 37 (26 novel) were up- and 16 (8 novel) were downregulated. Common TF encoding genes were from ERF, MYB, bHLH, NFY, bZIP, GATA, HSF and WRKY families. NFY A4/C2/A10 were the significant hub TFs in both plants. Phytohormone responsive cis-elements such as ABRE, TGA, TCA and LTR were the common cis-elements in TF promoters. Arabidopsis had more responsive TFs compared to rice possibly due to its greater adaptation to ranges geographical latitudes. Rice had more relevant miRNAs probably because of its bigger genome size. The interacting partners and co-expressed genes were different for the common TFs so that of the downstream regulatory networks and the corresponding metabolic pathways. Identified cold-responsive TFs in (A + R) seemed to be more engaged in energy metabolism esp. photosynthesis, and signal transduction, respectively. At post-transcriptional level, miR5075 showed to target many identified TFs in rice. In comparison, the predictions showed that identified TFs are being targeted by diverse groups of miRNAs in Arabidopsis. Novel TFs, miRNAs and co-expressed genes were introduced as cold-responsive markers that can be harnessed in future studies and development of crop tolerant varieties.

Effects of chitin and chitosan on root growth, biochemical defense response and exudate proteome of Cannabis sativa

Fungal pathogens pose a major threat to Cannabis sativa production, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects on C. sativa will advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in the in vitro Root-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3-5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. In contrast, chitin treatments had no significant impact on any defense parameters, including enzymatic activities, hormone quantities, gene expression levels and root secreted proteins. These results indicate that colloidal chitosan, significantly enhancing defense responses in C. sativa root system, could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases.

Phosphorylation and ubiquitination of OsWRKY31 are integral to OsMKK10-2-mediated defense responses in rice

Mitogen-activated protein kinase (MPK) cascades play vital roles in plant innate immunity, growth, and development. Here, we report that the rice (Oryza sativa) transcription factor gene OsWRKY31 is a key component in a MPK signaling pathway involved in plant disease resistance in rice. We found that the activation of OsMKK10-2 enhances resistance against the rice blast pathogen Magnaporthe oryzae and suppresses growth through an increase in jasmonic acid and salicylic acid accumulation and a decrease of indole-3-acetic acid levels. Knockout of OsWRKY31 compromises the defense responses mediated by OsMKK10-2. OsMKK10-2 and OsWRKY31 physically interact, and OsWRKY31 is phosphorylated by OsMPK3, OsMPK4, and OsMPK6. Phosphomimetic OsWRKY31 has elevated DNA-binding activity and confers enhanced resistance to M. oryzae. In addition, OsWRKY31 stability is regulated by phosphorylation and ubiquitination via RING-finger E3 ubiquitin ligases interacting with WRKY 1 (OsREIW1). Taken together, our findings indicate that modification of OsWRKY31 by phosphorylation and ubiquitination functions in the OsMKK10-2-mediated defense signaling pathway.

Revisiting the role of MAPK signalling pathway in plants and its manipulation for crop improvement

The mitogen-activated protein kinase (MAPK) pathway is an important signalling event associated with every aspect of plant growth, development, yield, abiotic and biotic stress adaptation. Being a central metabolic pathway, it is a vital target for manipulation for crop improvement. In this review, we have summarised recent advancements in understanding involvement of MAPK signalling in modulating abiotic and biotic stress tolerance, architecture and yield of plants. MAPK signalling cross talks with reactive oxygen species (ROS) and abscisic acid (ABA) signalling events in bringing about abiotic stress adaptation in plants. The intricate involvement of MAPK pathway with plant's pathogen defence ability has also been identified. Further, recent research findings point towards participation of MAPK signalling in shaping plant architecture and yield. These make MAPK pathway an important target for crop improvement and we discuss here various strategies to tweak MAPK signalling components for designing future crops with improved physiology and phenotypes.

Arbuscular mycorrhizal fungi-mediated activation of plant defense responses in direct seeded rice (Oryza sativa L.) against root-knot nematode Meloidogyne graminicola

Rhizosphere is the battlefield of beneficial and harmful (so called phytopathogens) microorganisms. Moreover, these microbial communities are struggling for their existence in the soil and playing key roles in plant growth, mineralization, nutrient cycling and ecosystem functioning. In the last few decades, some consistent pattern have been detected so far that link soil community composition and functions with plant growth and development; however, it has not been studied in detail. AM fungi are model organisms, besides potential role in nutrient cycling; they modulate biochemical pathways directly or indirectly which lead to better plant growth under biotic and abiotic stress conditions. In the present investigations, we have elucidated the AM fungi-mediated activation of plant defense responses against Meloidogyne graminicola causing root-knot disease in direct seeded rice (Oryza sativa L.). The study describes the multifarious effects of Funneliformis mosseae, Rhizophagus fasciculatus, and Rhizophagus intraradices inoculated individually or in combination under glasshouse conditions in rice plants. It was found that F. mosseae, R. fasciculatus and R. intraradices when applied individually or in combination modulated the biochemical and molecular mechanisms in the susceptible and resistant inbred lines of rice. AM inoculation significantly increased various plant growth attributes in plants with simultaneous decrease in the root-knot intensity. Among these, the combined application of F. mosseae, R. fasciculatus, and R. intraradices was found to enhance the accumulation and activities of biomolecules and enzymes related to defense priming as well as antioxidation in the susceptible and resistant inbred lines of rice pre-challenged with M. graminicola. The application of F. mosseae, R. fasciculatus and R. intraradices, induced the key genes involved in plant defense and signaling and it has been demonstrated for the first time. Results of the present investigation advocated that the application of F. mosseae, R. fasciculatus and R. intraradices, particularly a combination of all three, not only helped in the control of root-knot nematodes but also increased plant growth as well as enhances the gene expression in rice. Thus, it proved to be an excellent biocontrol as well as plant growth-promoting agent in rice even when the crop is under biotic stress of the root-knot nematode, M. graminicola.

The OsBDR1-MPK3 module negatively regulates blast resistance by suppressing the jasmonate signaling and terpenoid biosynthesis pathway

Receptor-like kinases (RLKs) may initiate signaling pathways by perceiving and transmitting environmental signals to cellular machinery and play diverse roles in plant development and stress responses. The rice genome encodes more than one thousand RLKs, but only a small number have been characterized as receptors for phytohormones, polypeptides, elicitors, and effectors. Here, we screened the function of 11 RLKs in rice resistance to the blast fungus Magnaporthe oryzae (M. oryzae) and identified a negative regulator named BDR1 (Blast Disease Resistance 1). The expression of BDR1 was rapidly increased under M. oryzae infection, while silencing or knockout of BDR1 significantly enhanced M. oryzae resistance in two rice varieties. Protein interaction and kinase activity assays indicated that BDR1 directly interacted with and phosphorylated mitogen-activated kinase 3 (MPK3). Knockout of BDR1 compromised M. oryzae-induced MPK3 phosphorylation levels. Moreover, transcriptome analysis revealed that M. oryzae-elicited jasmonate (JA) signaling and terpenoid biosynthesis pathway were negatively regulated by BDR1 and MPK3. Mutation of JA biosynthetic (allene oxide cyclase (AOC)/signaling (MYC2) genes decreased rice resistance to M. oryzae. Besides diterpenoid, the monoterpene linalool and the sesquiterpene caryophyllene were identified as unique defensive compounds against M. oryzae, and their biosynthesis genes (TPS3 and TPS29) were transcriptionally regulated by JA signaling and suppressed by BDR1 and MPK3. These findings demonstrate the existence of a BDR1-MPK3 cascade that negatively mediates rice blast resistance by affecting JA-related defense responses.

Harnessing the role of mitogen-activated protein kinases against abiotic stresses in plants

Crop plants are vulnerable to various biotic and abiotic stresses, whereas plants tend to retain their physiological mechanisms by evolving cellular regulation. To mitigate the adverse effects of abiotic stresses, many defense mechanisms are induced in plants. One of these mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signaling pathway used in the transduction of extracellular stimuli into intercellular responses. This stress signaling pathway is activated by a series of responses involving MAPKKKs→MAPKKs→MAPKs, consisting of interacting proteins, and their functions depend on the collaboration and activation of one another by phosphorylation. These proteins are key regulators of MAPK in various crop plants under abiotic stress conditions and also related to hormonal responses. It is revealed that in response to stress signaling, MAPKs are characterized as multigenic families and elaborate the specific stimuli transformation as well as the antioxidant regulation system. This pathway is directed by the framework of proteins and stopping domains confer the related associates with unique structure and functions. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in plants, such as Arbodiposis, tomato, potato, alfalfa, poplar, rice, wheat, maize, and apple. In this review, we summarized the recent work on MAPK response to abiotic stress and the classification of MAPK cascade in crop plants. Moreover, we highlighted the modern research methodologies such as transcriptomics, proteomics, CRISPR/Cas technology, and epigenetic studies, which proposed, identified, and characterized the novel genes associated with MAPKs and their role in plants under abiotic stress conditions. In-silico-based identification of novel MAPK genes also facilitates future research on MAPK cascade identification and function in crop plants under various stress conditions.

Exogenous abscisic acid prolongs the dormancy of recalcitrant seed of Panax notoginseng

The seeds of Panax notoginseng (Burk.) F. H. Chen are typically characterized by their recalcitrance and after-ripening process and exhibit a high water content at harvest as well as a high susceptibility to dehydration. Storage difficulty and the low germination of recalcitrant seeds of P. notoginseng are known to cause an obstacle to agricultural production. In this study, the ratio of embryo to endosperm (Em/En) in abscisic acid (ABA) treatments (1 mg·l^-1 and 10 mg·l^-1, LA and HA) was 53.64% and 52.34%, respectively, which were lower than those in control check (CK) (61.98%) at 30 days of the after-ripening process (DAR). A total of 83.67% of seeds germinated in the CK, 49% of seeds germinated in the LA treatment, and 37.33% of seeds germinated in the HA treatment at 60 DAR. The ABA, gibberellin (GA), and auxin (IAA) levels were increased in the HA treatment at 0 DAR, while the jasmonic acid (JA) levels were decreased. ABA, IAA, and JA were increased, but GA was decreased with HA treatment at 30 DAR. A total of 4,742, 16,531, and 890 differentially expressed genes (DEGs) were identified between the HA-treated and CK groups, respectively, along with obvious enrichment in the ABA-regulated plant hormone pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The expression of pyracbactin resistance-like (PYL) and SNF1-related protein kinase subfamily 2 (SnRK2s) increased in the ABA-treated groups, whereas the expression of type 2C protein phosphatase (PP2C) decreased, both of which are related to the ABA signaling pathway. As a result of the changes in expression of these genes, increased ABA signaling and suppressed GA signaling could inhibit the growth of the embryo and the expansion of developmental space. Furthermore, our results demonstrated that MAPK signaling cascades might be involved in the amplification of hormone signaling. Meanwhile, our study uncovered that the exogenous hormone ABA could inhibit embryonic development, promote dormancy, and delay germination in recalcitrant seeds. These findings reveal the critical role of ABA in regulating the dormancy of recalcitrant seeds, and thereby provide a new insight into recalcitrant seeds in agricultural production and storage.

Enzymatic Investigation of Spongospora subterranea Zoospore Attachment to Roots of Potato Cultivars Resistant or Susceptible to Powdery Scab Disease

For potato crops, host resistance is currently the most effective and sustainable tool to manage diseases caused by the plasmodiophorid Spongospora subterranea. Arguably, zoospore root attachment is the most critical phase of infection; however, the underlying mechanisms remain unknown. This study investigated the potential role of root-surface cell-wall polysaccharides and proteins in cultivars resistant/susceptible to zoospore attachment. We first compared the effects of enzymatic removal of root cell-wall proteins, N-linked glycans and polysaccharides on S. subterranea attachment. Subsequent analysis of peptides released by trypsin shaving (TS) of root segments identified 262 proteins that were differentially abundant between cultivars. These were enriched in root-surface-derived peptides but also included intracellular proteins, e.g., proteins associated with glutathione metabolism and lignin biosynthesis, which were more abundant in the resistant cultivar. Comparison with whole-root proteomic analysis of the same cultivars identified 226 proteins specific to the TS dataset, of which 188 were significantly different. Among these, the pathogen-defence-related cell-wall protein stem 28 kDa glycoprotein and two major latex proteins were significantly less abundant in the resistant cultivar. A further major latex protein was reduced in the resistant cultivar in both the TS and whole-root datasets. In contrast, three glutathione S-transferase proteins were more abundant in the resistant cultivar (TS-specific), while the protein glucan endo-1,3-beta-glucosidase was increased in both datasets. These results imply a particular role for major latex proteins and glucan endo-1,3-beta-glucosidase in regulating zoospore binding to potato roots and susceptibility to S. subterranea.

Combined physiological responses and differential expression of drought-responsive genes preliminarily explain the drought resistance mechanism of Lotus corniculatus

Lotus corniculatus L. is a perennial high-quality legume forage species but is vulnerable to drought, and water deficit reduces productivity. To understand the drought response mechanism of L. corniculatus , we investigated physiological responses under drought stress and constructed suppression subtractive hybridisation (SSH) cDNA libraries to isolate drought-inducible genes and quantitatively study the expression levels of candidate drought- responsive genes. Genes encoding calmodulin-like protein, mitogen-activated protein kinase, indole-3-acetic acid-induced protein, ser/thr-protein phosphatase homolog-related proteins, and β -galactosidase-related protein with hydrolysis activity were isolated and considered the main factors that explained the resistance of L. corniculatus to drought. Approximately 632 expressed sequence tags (ESTs) were identified and confirmed in the constructed SSH library. The Gene Ontology (GO) analysis revealed that these genes were involved mainly in transcription processes, protein synthesis, material metabolism, catalytic reactions, sugar metabolism, and photosynthesis. The interaction between the functions of these drought-related genes and the physiological responses preliminarily explains the drought resistance mechanisms of L. corniculatus .

Heat-Killed Tobacco Mosaic Virus Mitigates Plant Abiotic Stress Symptoms

Since the discovery of the tobacco mosaic virus in the 1890s, awareness has grown in regard to how viruses affect the environment. Viral infections are now known to cause various effects besides pathogenicity, with some viruses in fact having a beneficial impact on plants. Although research has focused on disease-causing viruses that can infect plants, many wild plants are also infected with non-pathogenic viral agents. Traditionally, abiotic, and biotic stresses have been studied as isolated stimuli that trigger signaling pathways within the plant. However, both biotic and abiotic stress can trigger complex molecular interactions within plants, which in turn drive interconnected response pathways. Here, we demonstrate that heat-killed tobacco mosaic virus (TMV) can increase abiotic stress tolerance in plants, an effect that could potentially be implemented in challenging growth environments. To our knowledge, this is the first report of plant abiotic stress tolerance following treatment with heat-killed viral particles.

Transcriptomic Analysis Provides Insight into the ROS Scavenging System and Regulatory Mechanisms in Atriplex canescens Response to Salinity

Atriplex canescens is a representative halophyte with excellent tolerance to salt. Previous studies have revealed certain physiological mechanisms and detected functional genes associated with salt tolerance. However, knowledge on the ROS scavenging system and regulatory mechanisms in this species when adapting to salinity is limited. Therefore, this study further analyzed the transcriptional changes in genes related to the ROS scavenging system and important regulatory mechanisms in A. canescens under saline conditions using our previous RNA sequencing data. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in signal transduction- and reactive oxygen species-related biological processes, including "response to oxidative stress", "oxidoreductase activity", "protein kinase activity", "transcription factor activity", and "plant hormone signal transduction". Further analyses suggested that the transcription abundance of many genes involved in SOD, the AsA-GSH cycle, the GPX pathway, PrxR/Trx, and the flavonoid biosynthesis pathway were obviously enhanced. These pathways are favorable for scavenging excessive ROS induced by salt and maintaining the integrity of the cell membrane. Meanwhile, many vital transcription factor genes (WRKY, MYB, ZF, HSF, DREB, and NAC) exhibited increased transcripts, which is conducive to dealing with saline conditions by regulating downstream salt-responsive genes. Furthermore, a larger number of genes encoding protein kinases (RLK, CDPK, MAPK, and CTR1) were significantly induced by saline conditions, which is beneficial to the reception/transduction of salt-related signals. This study describes the abundant genetic resources for enhancing the salt tolerance in salt-sensitive plants, especially in forages and crops.

Fine-tuning OsCPK18/OsCPK4 activity via genome editing of phosphorylation motif improves rice yield and immunity

Plants have evolved complex signalling networks to regulate growth and defence responses under an ever-changing environment. However, the molecular mechanisms underlying the growth-defence tradeoff are largely unclear. We previously reported that rice CALCIUM-DEPENDENT PROTEIN KINASE 18 (OsCPK18) and MITOGEN-ACTIVATED PROTEIN KINASE 5 (OsMPK5) mutually phosphorylate each other and that OsCPK18 phosphorylates and positively regulates OsMPK5 to suppress rice immunity. In this study, we found that OsCPK18 and its paralog OsCPK4 positively regulate plant height and yield-related traits. Further analysis reveals that OsCPK18 and OsMPK5 synergistically regulate defence-related genes but differentially regulate development-related genes. In vitro and in vivo kinase assays demonstrated that OsMPK5 phosphorylates C-terminal threonine (T505) and serine (S512) residues of OsCPK18 and OsCPK4, respectively. The kinase activity of OsCPK18T505D , in which T505 was replaced by aspartic acid to mimic T505 phosphorylation, displayed less calcium sensitivity than that of wild-type OsCPK18. Interestingly, editing the MAPK phosphorylation motif in OsCPK18 and its paralog OsCPK4, which deprives OsMPK5-mediated phosphorylation but retains calcium-dependent activation of kinase activity, simultaneously increases rice yields and immunity. This editing event also changed the last seven amino acid residues of OsCPK18 and attenuated its binding with OsMPK5. This study presents a new regulatory circuit that fine tunes the growth-defence tradeoff by modulating OsCPK18/4 activity and suggests that CRISPR/Cas9-mediated engineering phosphorylation pathways could simultaneously improve crop yield and immunity.

Knockout of a papain-like cysteine protease gene OCP enhances blast resistance in rice

Papain-like cysteine proteases (PLCPs) play an important role in the immune response of plants. In Arabidopsis, several homologous genes are known to be involved in defending against pathogens. However, the effects of PLCPs on diseases that afflict rice are largely unknown. In this study, we show that a PLCP, an oryzain alpha chain precursor (OCP), the ortholog of the Arabidopsis protease RD21 (responsive to dehydration 21), participates in regulating resistance to blast disease with a shorter lesion length characterizing the knockout lines (ocp-ko), generated via CRISPR/Cas9 technology. OCP was expressed in all rice tissues and mainly located in the cytoplasm. We prove that OCP, featuring cysteine protease activity, interacts with OsRACK1A (receptor for activated C kinase 1) and OsSNAP32 (synaptosome-associated protein of 32 kD) physically in vitro and in vivo, and they co-locate in the rice cytoplasm but cannot form a ternary complex. Many genes related to plant immunity were enriched in the ocp-ko1 line whose expression levels changed significantly. The expression of jasmonic acid (JA) and ethylene (ET) biosynthesis and regulatory genes were up-regulated, while that of auxin efflux transporters was down-regulated in ocp-ko1. Therefore, OCP negatively regulates blast resistance in rice by interacting with OsRACK1A or OsSNAP32 and influencing the expression profiles of many resistance-related genes. Moreover, OCP might be the cornerstone of blast resistance by suppressing the activation of JA and ET signaling pathways as well as promoting auxin signaling pathways. Our research provides a comprehensive resource of PLCPs for rice plants in defense against pathogens that is also of potential breeding value.

Knockout of MITOGEN-ACTIVATED PROTEIN KINASE 3 causes barley root resistance against Fusarium graminearum

The roles of mitogen-activated protein kinases (MAPKs) in plant-fungal pathogenic interactions are poorly understood in crops. Here, microscopic, phenotypic, proteomic, and biochemical analyses revealed that roots of independent transcription activator-like effector nuclease (TALEN)-based knockout lines of barley (Hordeum vulgare L.) MAPK 3 (HvMPK3 KO) were resistant against Fusarium graminearum infection. When co-cultured with roots of the HvMPK3 KO lines, F. graminearum hyphae were excluded to the extracellular space, the growth pattern of extracellular hyphae was considerably deregulated, mycelia development was less efficient, and number of appressoria-like structures and their penetration potential were substantially reduced. Intracellular penetration of hyphae was preceded by the massive production of reactive oxygen species (ROS) in attacked cells of the wild-type (WT), but ROS production was mitigated in the HvMPK3 KO lines. Suppression of ROS production in these lines coincided with elevated abundance of catalase (CAT) and ascorbate peroxidase (APX). Moreover, differential proteomic analysis revealed downregulation of several defense-related proteins in WT, and the upregulation of pathogenesis-related protein 1 (PR-1) and cysteine proteases in HvMPK3 KO lines. Proteins involved in suberin formation, such as peroxidases, lipid transfer proteins (LTPs), and the GDSL esterase/lipase (containing "GDSL" aminosequence motif) were differentially regulated in HvMPK3 KO lines after F. graminearum inoculation. Consistent with proteomic analysis, microscopic observations showed enhanced suberin accumulation in roots of HvMPK3 KO lines, most likely contributing to the arrested infection by F. graminearum. These results suggest that TALEN-based knockout of HvMPK3 leads to barley root resistance against Fusarium root rot.

Auxin and abscisic acid antagonistically regulate ascorbic acid production via the SlMAPK8-SlARF4-SlMYB11 module in tomato

Ascorbic acid (AsA) is a multifunctional phytonutrient that is essential for the human diet as well as plant development. While much is known about AsA biosynthesis in plants, how this process is regulated in tomato (Solanum lycopersicum) fruits remains unclear. Here, we found that auxin treatment inhibited AsA accumulation in the leaves and pericarps of tomato. The auxin response factor gene SlARF4 is induced by auxin to mediate auxin-induced inhibition of AsA accumulation. Specifically, SlARF4 transcriptionally inhibits the transcription factor gene SlMYB11, thereby modulating AsA accumulation by regulating the transcription of the AsA biosynthesis genes l-galactose-1-phosphate phosphatase, l-galactono-1,4-lactone dehydrogenase, and dehydroascorbate. By contrast, abscisic acid (ABA) treatment increased AsA accumulation in tomato under drought stress. ABA induced the expression of the mitogen-activated protein kinase gene SlMAPK8. We demonstrate that SlMAPK8 phosphorylates SlARF4 and inhibits its transcriptional activity, whereas SlMAPK8 phosphorylates SlMYB11 and activates its transcriptional activity. SlMAPK8 functions in ABA-induced AsA accumulation and drought stress tolerance. Moreover, ABA antagonizes the effects of auxin on AsA biosynthesis. Therefore, auxin- and ABA-induced regulation of AsA accumulation is mediated by the SlMAPK8-SlARF4-SlMYB11 module in tomato during fruit development and drought stress responses, shedding light on the roles of phytohormones in regulating AsA accumulation to mediate stress tolerance.

Comparison of anther transcriptomes in response to cold stress at the reproductive stage between susceptible and resistant Japonica rice varieties

BACKGROUND

Rice is one of the most important cereal crops in the world but is susceptible to cold stress (CS). In this study, we carried out parallel transcriptomic analysis at the reproductive stage on the anthers of two Japonica rice varieties with contrasting CS resistance: cold susceptible Longjing11 (LJ11) and cold resistant Longjing25 (LJ25).

RESULTS

According to the obtained results, a total of 16,762 differentially expressed genes (DEGs) were identified under CS, including 7,050 and 14,531 DEGs in LJ25 and LJ11, respectively. Examining gene ontology (GO) enrichment identified 35 up- and 39 down-regulated biological process BP GO terms were significantly enriched in the two varieties, with 'response to heat' and 'response to cold' being the most enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 33 significantly enriched pathways. Only the carbon metabolism and amino acid biosynthesis pathways with down-regulated DEGs were enriched considerably in LJ11, while the plant hormone signal transduction pathway (containing 153 DEGs) was dramatically improved. Eight kinds of plant hormones were detected in the pathway, while auxin, abscisic acid (ABA), salicylic acid (SA), and ethylene (ETH) signaling pathways were found to be the top four pathways with the most DEGs. Furthermore, the protein-protein interaction (PPI) network analysis identified ten hub genes (co-expressed gene number ≥ 30), including six ABA-related genes. Various DEGs (such as OsDREB1A, OsICE1, OsMYB2, OsABF1, OsbZIP23, OsCATC, and so on) revealed distinct expression patterns among rice types when the DEGs between LJ11 and LJ25 were compared, indicating that they are likely responsible for CS resistance of rice in cold region.

CONCLUSION

Collectively, our findings provide comprehensive insights into complex molecular mechanisms of CS response and can aid in CS resistant molecular breeding of rice in cold regions.

A detailed landscape of CRISPR-Cas-mediated plant disease and pest management

Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.

A secreted fungal effector suppresses rice immunity through host histone hypoacetylation

Histone acetylation is a critical epigenetic modification that regulates plant immunity. Fungal pathogens secrete effectors that modulate host immunity and facilitate infection, but whether fungal pathogens have evolved effectors that directly target plant histone acetylation remains unknown. Here, we identified a secreted protein, UvSec117, from the rice false smut fungus, Ustilaginoidea virens, as a key effector that can target the rice histone deacetylase OsHDA701 and negatively regulates rice broad-spectrum resistance against rice pathogens. UvSec117 disrupts host immunity by recruiting OsHDA701 to the nucleus and enhancing OsHDA701-modulated deacetylation, thereby reducing histone H3K9 acetylation levels in rice plants and interfering with defense gene activation. Host-induced gene silencing of UvSec117 promotes rice resistance to U. virens, thus providing an alternative way for developing rice false smut-resistant plants. This is the first direct evidence demonstrating that a fungal effector targets a histone deacetylase to suppress plant immunity. Our data provided insight into a counter-defense mechanism in a plant pathogen that inactivates host defense responses at the epigenetic level.

Rice MPK17 Plays a Negative Role in the Xa21-Mediated Resistance Against Xanthomonas oryzae pv. oryzae

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most serious diseases affecting rice production worldwide. Xa21 was the first disease resistance gene cloned in rice, which encodes a receptor kinase and confers broad resistance against Xoo stains. Dozens of components in the Xa21-mediated pathway have been identified in the past decades, however, the involvement of mitogen-activated protein kinase (MAPK) genes in the pathway has not been well described. To identify MAPK involved in Xa21-mediated resistance, the level of MAPK proteins was profiled using Western blot analysis. The abundance of OsMPK17 (MPK17) was found decreased during the rice-Xoo interaction in the background of Xa21. To investigate the function of MPK17, MPK17-RNAi and over-expression (OX) transgenic lines were generated. The RNAi lines showed an enhanced resistance, while OX lines had impaired resistance against Xoo, indicating that MPK17 plays negative role in Xa21-mediated resistance. Furthermore, the abundance of transcription factor WRKY62 and pathogenesis-related proteins PR1A were changed in the MPK17 transgenic lines when inoculated with Xoo. We also observed that the MPK17-RNAi and -OX rice plants showed altered agronomic traits, indicating that MPK17 also plays roles in the growth and development. On the basis of the current study and published results, we propose a "Xa21-MPK17-WRKY62-PR1A" signaling that functions in the Xa21-mediated disease resistance pathway. The identification of MPK17 advances our understanding of the mechanism underlying Xa21-mediated immunity, specifically in the mid- and late-stages.

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

Salt stress is one of the factors that limits rice production, and an important task for researchers is to cultivate rice with strong salt tolerance. In this study, 211 rice accessions were used to determine salt tolerance germinability (STG) indices and conduct a genome-wide association study (GWAS) using 36,727 SNPs. The relative germination energy (RGE), relative germination index (RGI), relative vigor index (RVI), relative mean germination time (RMGT), relative shoot length (RSL), and relative root length (RRL) were used to determine the STG indices in rice. A total of 43 QTLs, including 15 for the RGE, 6 for the RGI, 7 for the RVI, 3 for the RMGT, 1 for the RSL, and 11 for the RRL, were identified on nine chromosome regions under 60 and 100 mM NaCl conditions. For these STG-related QTLs, 18 QTLs were co-localized with previous studies, and some characterized salt-tolerance genes, such as OsCOIN, OsHsp17.0, and OsDREB2A, are located in these QTL candidates. Among the 25 novel QTLs, qRGE60-1-2 co-localized with qRGI60-1-1 on chromosome 1, and qRGE60-3-1 and qRVI60-3-1 co-localized on chromosome 3. According to the RNA-seq database, 16 genes, including nine for qRGE60-1-2 (qRGI60-1-1) and seven for qRGE60-3-1 (qRVI60-3-1), were found to show significant differences in their expression levels between the control and salt treatments. Furthermore, the expression patterns of these differentially expressed genes were analyzed, and nine genes (five for qRGE60-1-2 and four for qRGE60-3-1) were highly expressed in embryos at the germination stage. Haplotype analysis of these nine genes showed that the rice varieties with elite haplotypes in the LOC_Os03g13560, LOC_Os03g13840, and LOC_Os03g14180 genes had high STG. GWAS validated the known genes underlying salt tolerance and identified novel loci that could enrich the current gene pool related to salt tolerance. The resources with high STG and significant loci identified in this study are potentially useful in breeding for salt tolerance.

OsMPK4 promotes phosphorylation and degradation of IPA1 in response to salt stress to confer salt tolerance in rice

Salt stress adversely affects plant growth, development, and crop yield. Rice (Oryza sativa L.) is one of the most salt-sensitive cereal crops, especially at the early seedling stage. Mitogen-activated protein kinase (MAPK/MPK) cascades have been shown to play critical roles in salt response in Arabidopsis. However, the roles of the MPK cascade signaling in rice salt response and substrates of OsMPK remain largely unknown. Here, we report that the salt-induced OsMPK4-Ideal Plant Architecture 1 (IPA1) signaling pathway regulates the salt tolerance in rice. Under salt stress, OsMPK4 could interact with IPA1 and phosphorylate IPA1 at Thr180, leading to degradation of IPA1. Genetic evidence shows that IPA1 is a negative regulator of salt tolerance in rice, whereas OsMPK4 promotes salt response in an IPA1-dependent manner. Taken together, our results uncover an OsMPK4-IPA1 signal cascade that modulates the salt stress response in rice and sheds new light on the breeding of salt-tolerant rice varieties.

Expression profiling of the mitogen-activated protein kinase gene family reveals their diverse response pattern in two different salt-tolerant Glycyrrhiza species

BACKGROUND

Mitogen-activated protein kinases (MPKs) play important role in response to environmental stress as crucial signal receptors or sensors. Our previous study indicated that salt stress acts as a positive factor to stimulate the production of pharmacodynamic metabolites in the medicinal plant Glycyrrhiza uralensis. Currently, little is known about the MPK gene family and their functions in the medicinal plant G. uralensis.

OBJECTIVE

Identification, comprehensive bioinformatic analysis, expression profiling, and response pattern under salt stress of the G. uralensis GuMPK gene family.

METHODS

Genome-wide investigation and expression profiling of the MPK gene family in G. uralensis, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, promoter cis-acting element, and expression pattern under salt stress in two different salt-tolerant Glycyrrhiza species were performed.

RESULTS

A total of 20 G. uralensis GuMPK genes were identified and categorized into five groups, and had conserved gene structure and motif distribution. Expression profiling of GuMPK genes suggested their potentially diverse functions in plant growth and in response to phytohormones and environmental stress, particularly GuMPK1, 2, 5, and 10 as key components for G. uralensis in response to abiotic stress. Further expression analysis under NaCl treatment in two different salt-tolerant Glycyrrhiza species displayed the MPKs' different response patterns, emphasizing the role of MPK2, 5, 7, and 16 as potentially crucial genes for Glycyrrhiza to respond to salt stress.

CONCLUSION

Our results provide a genome-wide identification and expression profiling of MPK gene family in G. uralensis, and establish the foundation for screening key responsive genes and understanding the potential function and regulatory mechanism of GuMPKs in salt responsiveness.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Genome-Wide Identification and Expression of MAPK Gene Family in Cultivated Strawberry and Their Involvement in Fruit Developing and Ripening

Studies on many plants have shown that mitogen-activated protein kinases (MAPKs) are key proteins involved in regulating plant responses to biotic and abiotic stresses. However, their involvement in cultivated strawberry development and ripening remains unclear. In this study, 43 FaMAPK gene family members were identified in the genome of cultivated strawberry (Fragaria × ananassa), phylogenetic analysis indicated that FaMAPKs could be classified into four groups. Systematic analysis of the conserved motif, exon-intron structure showed that there were significant varieties between different groups in structure, but in the same group they were similar. Multiple cis-regulatory elements associated with phytohormone response, and abiotic and biotic stresses were predicted in the promoter regions of FaMAPK genes. Transcriptional analysis showed that all FaMAPK genes were expressed at all developmental stages. Meanwhile, the effect of exogenous ABA and sucrose on the expression profile of FaMAPKs was investigated. Exogenous ABA, sucrose, and ABA plus sucrose treatments upregulated the expression of FaMAPK genes and increased the content of endogenous ABA, sucrose, and anthocyanin in strawberry fruits, suggesting that ABA and sucrose might be involved in the FaMAPK-mediated regulation of strawberry fruit ripening. Based on the obtained results, MAPK genes closely related to the ripening of strawberries were screened to provide a theoretical basis and support for future research on strawberries.

OsMAPK6 phosphorylates a zinc finger protein OsLIC to promote downstream OsWRKY30 for rice resistance to bacterial blight and leaf streak

Rice OsLIC encoding a CCCH zinc finger transcription factor plays an important role in immunity. However, the immune signaling pathways that OsLIC-involved and the underlying mechanisms that OsLIC-conferred resistance against pathogens are largely unclear. Here, we show that OsLIC, as a substrate for OsMAPK6, negatively regulates resistance to Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) by directly suppressing OsWRKY30 transcription. Biochemical assays showed that OsLIC bound to OsWRKY30 promoter and suppressed its transcription. Genetic assays confirmed that the osilc knockout mutants and OsWRKY30-overexpressing plants exhibited enhanced resistance to Xoo and Xoc, knocking out OsWRKY30 in the oslic mutants attenuated the resistance against bacterial pathogens. OsMAPK6 physically interacted with and phosphorylated OsLIC leading to decreased OsLIC DNA-binding activity, therefore, overexpression of OsLIC partially suppressed OsMAPK6-mediated rice resistance. In addition, both OsMAPK6-phosphorylated activation of OsLIC and phosphorylation-mimic OsLIC^5D had reduced DNA-binding activity towards OsWRKY30 promoter, thereby promoting OsWRKY30 transcription. Collectively, these results reveal that OsMAPK6-mediated phosphorylation of OsLIC positively regulates rice resistance to Xoo and Xoc by modulating OsWRKY30 transcription, suggesting that OsMAPK6-OsLIC-OsWRKY30 module is an immune signaling pathway in response to the bacterial pathogens.

Identification of essential genes involved in metabolism-based resistance mechanism to fenoxaprop-P-ethyl in Polypogon fugax

BACKGROUND

Metabolic resistance is a worldwide concern for weed control but has not yet been well-characterized at the genetic level. Previously, we have identified an Asia minor bluegrass (Polypogon fugax Nees ex Steud.) population AHHY exhibiting cytochrome P450 (P450)-involved metabolic resistance to fenoxaprop-P-ethyl. In this study, we aimed to confirm the metabolic fenoxaprop-P-ethyl resistance in AHHY and uncover the potential herbicide metabolism-related genes in this economically damaging weed species.

RESULTS

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays indicated the metabolic rates of fenoxaprop-P-ethyl were significantly faster in resistant (R, AHHY) than in susceptible (S, SDTS) plants. The amount of phytotoxic fenoxaprop-P peaked at 12 h after herbicide treatment (HAT) and started to decrease at 24 HAT in both biotypes. R and S plants at 24 HAT were sampled to conduct isoform-sequencing (Iso-Seq) and RNA-sequencing (RNA-Seq). A reference transcriptome containing 24 972 full-length isoforms was obtained, of which 24 329 unigenes were successfully annotated. Transcriptomic profiling identified 28 detoxifying enzyme genes constitutively and/or herbicide-induced up-regulated in R than in S plants. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed 17 genes were consistently up-regulated in R and its F1 generation plants. They were selected as potential fenoxaprop-P-ethyl metabolism-related genes, including ten P450s, one glutathione-S-transferase, one UDP-glucosyltransferase, and five adenosine triphosphate (ATP)-binding cassette transporters.

CONCLUSION

This study revealed that the enhanced rates of fenoxaprop-P-ethyl metabolism in P. fugax were very likely driven by the herbicide metabolism-related genes. The transcriptome data generated by Iso-Seq combined with RNA-Seq will provide abundant gene resources for understanding the molecular mechanisms of resistance in P. fugax.

High-value pleiotropic genes for developing multiple stress-tolerant biofortified crops for 21st-century challenges

The agriculture-based livelihood systems that are already vulnerable due to multiple challenges face immediate risk of increased crop failures due to weather vagaries. As breeders and biotechnologists, our strategy is to advance and innovate breeding for weather-proofing crops. Plant stress tolerance is a genetically complex trait. Additionally, crops rarely face a single type of stress in isolation, and it is difficult for plants to deal with multiple stresses simultaneously. One of the most helpful approaches to creating stress-resilient crops is genome editing and trans- or cis-genesis. Out of hundreds of stress-responsive genes, many have been used to impart tolerance against a particular stress factor, while a few used in combination for gene pyramiding against multiple stresses. However, a better approach would be to use multi-role pleiotropic genes that enable plants to adapt to numerous environmental stresses simultaneously. Herein we attempt to integrate and present the scattered information published in the past three decades about these pleiotropic genes for crop improvement and remodeling future cropping systems. Research articles validating functional roles of genes in transgenic plants were used to create groups of multi-role pleiotropic genes that could be candidate genes for developing weather-proof crop varieties. These biotech crop varieties will help create 'high-value farms' to meet the goal of a sustainable increase in global food productivity and stabilize food prices by ensuring a fluctuation-free assured food supply. It could also help create a gene repository through artificial gene synthesis for 'resilient high-value food production' for the 21st century.