Unraveling the involvement of WRKY TFs in regulating plant disease defense signaling

The biochemical and molecular mechanisms of plants: a review on insect herbivory

Biochemical and molecular mechanisms have been essential mechanisms to reduce various insect attacks on plants. The biochemical methods are wide involving direct and indirect defenses. The defensive chemical substances are secreted effectively to the wound caused by the herbivores (insects and phytopathogens) on plants. Plants responded by producing VOCs which draw the natural enemies of the insects and phytopathogens. The progress observed in the cognition of the stimulus in plants and their potential to control the responses is characterized by the modification observed in molecular mechanisms which shifts our attention to the development of the endogenous resistance methods of preserving crops. The main objective of implementing a biotechnological mechanism in crop production is to employ durable and multimechanistic alternatives to insect pests via the stimulus the plant produces upon encountering the insect attack.

Identification of critical transition signal (CTS) to characterize regulated stochasticity during ABA-induced growth-to-defense transition

BACKGROUND

Abscisic acid (ABA) plays a central role in regulating plant responses to abiotic stress. It orchestrates a complex regulatory network that facilitates the transition from growth to defense. Understanding the molecular mechanisms underlying this ABA-induced transition from growth to defense is essential for elucidating plant adaptive strategies under environmental stress conditions.

RESULTS

In this study, we used a refined dynamic network biomarker (DNB) approach to quantitatively identify the critical transition signal (CTS) and characterize the regulated stochasticity during the ABA-induced transition from growth to defense in Arabidopsis thaliana. By integrating high-resolution time-series RNA-seq data with dynamic network analysis, we identified a set of DNB genes that serve as key molecular regulators of this transition. The critical transition phase was identified precisely at the ninth time point (6 h after treatment), which marks the crucial switch from a growth-dominated to a defense -oriented state. Gene Ontology (GO) enrichment analysis revealed a significant overrepresentation of defense-related biological processes, while STRING network analysis revealed strong functional interactions between DNB genes and differentially expressed genes (DEGs) and highlighted key regulatory hubs. In particular, key hub genes such as PIF4, TPS8, NIA1, and HSP90-5 were identified as potential master regulators of ABA-mediated defense activation, highlighting their importance for plant stress adaptation.

CONCLUSIONS

By integrating a network-driven transcriptomic analysis, this study provides new insights into the molecular basis of ABA-induced transitions from growth to defense. The identification of CTS provides a new perspective on regulated stochasticity in plant stress responses and provides a conceptual framework for improving crop stress resistance. In addition, the establishment of a comprehensive database of ABA-responsive defense genes represents a valuable resource for future research on plant adaptation and resilience.

Pyrus pyrifolia WRKY31 activates the ribosomal protein gene RPL12 to confer black spot resistance

Ribosomal proteins (RPs) are essential for genetic transcription and translation, playing a key role in plant growth, development, and stress responses, including disease resistance. However, the function and transcriptional regulation of RPL12 remain poorly understood. Investigating the gene function and the transcription factors that govern its expression is crucial to understanding its mechanism. In this study, a novel transcription factor gene, PpWRKY31, was isolated from Pyrus pyrifolia. The PpWRKY31 protein is expressed in the nucleus and belongs to Group IIb WRKY transcription factors. qRT-PCR analysis revealed that its expression was upregulated under the treatment of Alternaria alternata, as well as to exogenous hormonal treatments. Using yeast one-hybrid (Y1H) assay, dual-luciferase eporter assay, and electrophoretic mobility shift assay (EMSA), we demonstrated that PpWRKY31 can bind to the W-box element in the promoter region of PpRPL12. Overexpression of either PpWRKY31 or PpRPL12 enhanced the resistance of both pear and Arabidopsis thaliana plants to black spot disease, evidenced by reduced lesion size and increased activity of defense enzyme. Conversely, silencing of PpWRKY31 or PpRPL12 markedly diminished the resistance of pear to black spot disease. PpWRKY31 overexpression was observed to notably enhance the expression of PpRPL12 and genes associated with salicylic acid, inducing changes in the activity of enzymes related to the phenylpropanoid pathway, such as phenylalanine ammonia-lyase (PAL). In conclusion, this study elucidates a novel PpWRKY31-PpRPL12 signaling pathway that enhances resistance to pear black spot disease, providing insights into the regulatory networks underpinning plant defense responses. CORE: Pear black spot disease, caused by Alternaria alternata, seriously affects fruit quality and yield. We identified that PpWRKY31 transgenic calli responded to Alternaria alternata in pear. PpWRKY31 binds to the W-box cis-element of the PpRPL12 promoter, upregulating the expression of PpRPL12. The PpWRKY31-PpRPL12 regulatory module indirectly influences the downstream salicylic acid and phenylpropanoid pathways, ultimately enhancing the pear's black spot resistance. GENE AND ACCESSION NUMBERS: The sequence information used in this study is available in the Pear Genome Database (http://peargenome.njau.edu.cn/), the National Center for Biotechnology Information (NCBI) database, and The Arabidopsis Information Resource, see Table S2.

Overexpression of ZmEREB211 confers enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 in Arabidopsis

Genes in the ERF family encode trasnscripiton regulators involved in plant developmental and physiological processes. However, the function of the ERF family gene in regulation of plant susceptibility to pathogens has rarely been reported. In this study, An ERF family gene ZmEREB211 (AP2-EREBP-transcription factor 211), whose expression was significantly upregulated in response to biotic stress (Bipolaris maydis), was isolated from maize (Zea mays L.). Based on sequence homology and phylogenetic analysis, ZmEREB211 has 792bp in length and was characterized as an ERF family trasnscripiton regulator with single conserved APETALA2 (AP2) domain. Transient expression of ZmEREB211 in Nicotiana benthamiana revealed that its subcellular localization was distributed in the nucleus. Moreover, overexpression of ZmEREB211 in Arabidopsis thaliana resulted in increased susceptibility to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Examination of disease-related physiological indicators showed that overexpression of ZmEREB211 in A. thaliana led to the accumulation of membrane lipid peroxide malondialdehyde, reduced levels of hydrogen peroxide, phenylalanine ammonia lyase (PAL) activity, and peroxidase (POD) Activity, thereby enhancing the plant susceptibility. Additionally, transcriptome and qRT-PCR data indicated that the expression of genes related to the salicylic acid (SA) pathway was suppressed upon Pst DC3000 inoculation in ZmEREB211-overexpressing A. thaliana compared with wild type, while the expression of genes related to the ethylene (ET) pathway was induced at the same time. These findings collectively suggest that the transfer of ZmEREB211 gene into A. thaliana may confer increased susceptibility to the plant by inhibiting the SA pathway and inducing ET pathway, and provide novel susceptible gene resources for crop disease resistance breeding.

Ecotype-specific phenolic acid accumulation and root softness in Salvia miltiorrhiza are driven by environmental and genetic factors

Salvia miltiorrhiza Bunge, a renowned medicinal herb in traditional Chinese medicine, displays distinctive root texture and high phenolic acid content, traits influenced by genetic and environmental factors. However, the underlying regulatory networks remain unclear. Here, we performed multi-omics analyses on ecotypes from four major Chinese regions, focusing on environmental impacts on root structure, phenolic acid accumulation and lignin composition. Lower temperatures and increased UV-B radiation were associated with elevated rosmarinic acid (RA) and salvianolic acid B (SAB) levels, particularly in the Sichuan ecotype. Structural models indicated that the radial arrangement of xylem conduits contributes to greater root hardness. Genomic assembly and comparative analysis of the Sichuan ecotype revealed a unique phenolic acid metabolism gene cluster, including SmWRKY40, a WRKY transcription factor essential for RA and SAB biosynthesis. Overexpression of SmWRKY40 enhanced phenolic acid levels and lignin content, whereas its knockout reduced root hardness. Integrating high-throughput (DNA affinity purification sequencing) and point-to-point (Yeast One-Hybrid, Dual-Luciferase and Electrophoretic Mobility Shift Assay) protein-DNA interaction detection platform further identified SmWRKY40 binding sites across ecotypes, revealing specific regulatory networks. Our findings provide insights into the molecular basis of root texture and bioactive compound accumulation, advancing breeding strategies for quality improvement in S. miltiorrhiza.

Comparative transcriptome and genome analysis between susceptible Zhefang rice variety Diantun 502 and its resistance variety Diantun 506 upon Magnaporthe oryzae infection

BACKGROUND

Rice blast caused by Magnaporthe oryzae is the most severe and devastating disease in rice results in serious losses worldwide. Based on this, the interaction between rice and M. oryzae has been studied extensively for decades, but the pathogen always has a negative effect on the new and emerging rice varieties.

RESULTS

The present study employed comparative transcriptome strand-specific RNA sequencing and genome approaches of Diantun rice susceptible (D502) and resistance (D506) lines (leaves) in the presence of blast fungus, M. oryzae. Overall differential expression genes (DEGs) displayed 5838 and 3719 DEGs in D502 and D506, respectively 24hpi, however, the expression of DEGs in the former line was 5113, and in later line it was 4794 after 48hpi. Interestingly, only 2493 and 2418 DEGs were similar at both time hour points in both lines, respectively. Among DEGs, mostly exhibited down-regulated expression only in D502 major pathways, including plant hormones signal transduction and starch and sucrose metabolism at both time hours, suggesting susceptibility D502 on upon pathogen infection. Additionally, protein-protein interaction network analysis based on DEGs was performed between both varieties to find possible connections and increase interaction network complexity at 24h to 48h in D506, that might result in resistance to M. oryzae. We found many up and down-regulated DEGs only in D506 after pathogen infection, which might have a significant role in PTI and ETI immunity response. Next, through genomic analysis, different non-synonymous single nucleotide polymorphisms (nsSNPs) were identified between both D502 and D506 rice varieties. Here, four up-regulated genes, including WAK1, WAK4, WAK5, and OsDja9 harboring nsSNPs were found only in resistant D506 variety. Following alignment of open reading frame (ORF) region sequences revealed that the exonic SNPs lead the amino acid variation.

CONCLUSION

Our study proved that SNPs in these four genes were related to providing resistance in D506 line upon pathogen infection. In summary, we conclude that above-targeted rice defense and resistance genes identified through gene transcripts and modern genomic approaches could help us provide robust rice breeding and agricultural practices in future.

WRKY transcription factors: Hubs for regulating plant growth and stress responses

As sessile organisms, plants must directly face various stressors. Therefore, plants have evolved a powerful stress resistance system and can adjust their growth and development strategies appropriately in different stressful environments to adapt to complex and ever-changing conditions. Nevertheless, prioritizing defensive responses can hinder growth; this is a crucial factor for plant survival but is detrimental to crop production. As such, comprehending the impact of adverse environments on plant growth is not only a fundamental scientific inquiry but also imperative for the agricultural industry and for food security. The traditional view that plant growth is hindered during defense due to resource allocation trade-offs is challenged by evidence that plants exhibit both robust growth and defensive capabilities through human intervention. These findings suggest that the growth‒defense trade-off is not only dictated by resource limitations but also influenced by intricate transcriptional regulatory mechanisms. Hence, it is imperative to conduct thorough investigations on the central genes that govern plant resistance and growth in unfavorable environments. Recent studies have consistently highlighted the importance of WRKY transcription factors in orchestrating stress responses and plant-specific growth and development, underscoring the pivotal role of WRKYs in modulating plant growth under stressful conditions. Here, we review recent advances in understanding the dual roles of WRKYs in the regulation of plant stress resistance and growth across diverse stress environments. This information will be crucial for elucidating the intricate interplay between plant stress response and growth and may aid in identifying gene loci that could be utilized in future breeding programs to develop crops with enhanced stress resistance and productivity.

Pathogenesis related-1 proteins in plant defense: regulation and functional diversity

Climate change-related environmental stresses can negatively impact crop productivity and pose a threat to sustainable agriculture. Plants have a remarkable innate ability to detect a broad array of environmental cues, including stresses that trigger stress-induced regulatory networks and signaling pathways. Transcriptional activation of plant pathogenesis related-1 (PR-1) proteins was first identified as an integral component of systemic acquired resistance in response to stress. Consistent with their central role in immune defense, overexpression of PR-1s in diverse plant species is frequently used as a marker for salicylic acid (SA)-mediated defense responses. Recent advances demonstrated how virulence effectors, SA signaling cascades, and epigenetic modifications modulate PR-1 expression in response to environmental stresses. We and others showed that transcriptional regulatory networks involving PR-1s could be used to improve plant resilience to stress. Together, the results of these studies have re-energized the field and provided long-awaited insights into a possible function of PR-1s under extreme environmental stress.

Genome-wide identification and characterization of transcription factors involved in defense responses against Sclerotinia sclerotiorum in Brassica juncea

Sclerotinia sclerotiorum could cause significant yield losses of up to 70% in rapeseed cultivation. Nevertheless, the availability of immune or highly resistant germplasm and mechanisms to combat S. sclerotiorum, particularly in B. juncea, remains insufficient. Transcription factors (TFs) are recognized for their critical role in plant defense against S. sclerotiorum. In the present study, a total of 4807 TFs from 48 families were expressed and identified at 12, 24, and 36 h after inoculation (HAI) in two B. juncea lines: G21-912, exhibiting higher S. sclerotiorum resistance (HR), and G21-853, displaying lower S. sclerotiorum resistance (LR). The number of differentially expressed TFs (DETs) between the HR and the LR lines peaked at 24 HAI, with 202 upregulated and 105 downregulated TFs. Through expression and subcellular localization analyses, three candidate DETs, namely BjuA037408 (ETHYLENE RESPONSIVE FACTOR 59, ERF59), BjuB028842 (RELATED TO ABI3/VP1 1, RAV1), and BjuA016484 (WRKY25), were identified as the primary TFs in defense against S. sclerotiorum inoculation. The expression of these three genes was validated in the double haploid lines of BC3 (the third backcrossing generation) derived from the HR×LR cross. This study serves as a valuable case study for the characterization of TFs associated with defense mechanisms against S. sclerotiorum in B. juncea. The confirmed resistant B. juncea line of HR, along with the three key DETs, is expected to significantly contribute to future breeding efforts aimed at developing Sclerotinia-resistant varieties.

A transcription factor SlWRKY71 activated the H2S generating enzyme SlDCD1 enhancing the response to Pseudomonas syringae pv DC3000 in tomato leaves

H2S is a well-known gaseous signaling molecule that plays important roles in plant response to biotic stresses. Pseudomonas syringae pv tomato (Pst) could cause enormous loss, while whether H2S could modulate plant defense against Pst is still unclear. By CRISPR/Cas9, the Sldcd1 gene editing mutant showed reduced endogenous H2S content and attenuated resistance, whereas treatment with exogenous H2S could enhance the resistance. A transcription factor, SlWRKY71, was screened and identified to promote the transcription of SlDCD1 via yeast one-hybrid, dual-luciferase reporter system, electrophoretic mobility shift assays, and transient overexpression. Here, it was found that exogenous H2S relieved the symptoms of bacterial speck disease in tomato leaves, conferring tolerance to Pst. DC3000, and the expression of the H2S-producing enzyme SlDCD1 was significantly induced. The Slwrky71 mutant also showed reduced defense in tomato leaves against Pst. DC3000, whereas SlWRKY71-OE tomato leaves showed increased tolerance. Transient overexpression of SlDCD1 in the context of Slwrky71 with exogenous H2S treatment has stronger resistance, and the overexpression of SlWRKY71 in the context of Sldcd1 showed relatively weak disease resistance, and with the addition of H2S enhanced the effect. Therefore, we concluded that SlWRKY71 could activate SlDCD1 expression and promote endogenous H2S production, thereby improving tomato leaves resistance to Pst. DC3000.

Insights into mungbean defense response to Cercospora leaf spot based on transcriptome analysis

Several mungbean (Vigna radiata (L.) Wilczek) cultivars are susceptible to Cercospora leaf spot (CLS) caused by Cercospora canescens Ellis & Martin, and it is necessary to explore resistance sources and understand resistance mechanisms. However, the CLS resistance mechanisms have not yet been explored. The response to CLS revealed significantly different disease severity scores in both mungbean genotypes. Hypersensitive response (HR) started to appear at 2 days after inoculation (DAI) in SUPER5 but was never observed in CN84-1. SUPER5 exhibited fewer and smaller lesions than CN84-1 during CLS infection, resulting in SUPER5 being resistant while CN84-1 was susceptible to CLS. In this study, RNA sequencing (RNA-seq) analysis was used to unravel the mechanisms of resistance to CLS in a resistant line (SUPER5) and a susceptible variety (CN84-1) upon CLS infection. A total of 9510 DEGs including 4615 up-regulated and 4895 down-regulated genes were revealed. Of these 3242 and 1027 genes were uniquely up-regulated only in the SUPER5 and CN84-1, respectively, while 2902 and 734 genes were down-regulated only in SUPER5 and CN84-1, respectively. The 843 DEGs were enriched in biological processes mainly associated with plant defense responses, defense response to fungus, protein phosphorylation and response to chitin in Gene Ontology (GO) terms analysis. KEGG pathway analysis showed that these genes were represented in plant-pathogen interaction, the MAPK signaling pathway, plant hormone signal transduction, and cell wall component biosynthesis in response to the CLS infection specifically in SUPER5. In addition, the qRT-PCR was used to analyze the expression pattern of 22 candidate DEGs belonging to pathogenesis related (PR) proteins, resistance (R) proteins, transcription factors, hypersensitive response (HR), and the essential genes involved in cell wall activity during CLS-infected V. radiata. It was found that the expression of these genes was consistent with the RNA-seq analysis, showing a highly significant correlation with a coefficient of 0.7163 (p < 0.01). The co-expression network illustrated the interactions among these genes, which were involved in multiple functions related to the defense response. Interestingly, the ones encoding PR-2, thaumatin, peroxidase, defensin, RPM1, pectinesterase, chalcone synthase, auxin efflux carrier, and transcription factors (Pti1, Pti5, Pti6 and WRKY40) were highly significantly up-regulated in SUPER5 but not in CN84-1 upon CLS infection, suggesting that they might be involved in the CLS resistance mechanisms. Moreover, SUPER5 was found to have higher β-1,3-glucanase and chitinase activity levels than CN84-1. Our findings contribute to an understanding of the CLS resistance mechanisms and may advocate the development of more effective disease management approaches.

Synergistic interaction between wheat streak mosaic virus and Triticum mosaic virus modulates wheat transcriptome to favor disease severity

Wheat streak mosaic virus (WSMV; Tritimovirus tritici) and Triticum mosaic virus (TriMV; Poacevirus tritici), the type members of the genera Tritimovirus and Poacevirus, respectively, in the family Potyviridae, are economically important wheat viruses in the Great Plains region of the USA. Co-infection of wheat by WSMV and TriMV results in disease synergism. Wheat transcriptome from singly (WSMV or TriMV) and doubly (WSMV+TriMV) infected upper uninoculated leaves were analyzed by RNA-Seq at 9, 12, and 21 days postinoculation. A total of 31,754 differentially expressed wheat genes were identified among all comparisons. Weighted gene co-expression network analysis resulted in 11 co-expression modules that broadly indicated gene expression profiles attributable to control, single, and double infections. Gene ontology, protein domain and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that genes specifically related to photosynthesis, growth, stress, senescence, and defense were differentially enriched. Analyses of transcription factor families indicated that genes encoding MADS-Box and ARFs were strongly enriched in control plants, moderately repressed in TriMV-infected plants, and more strongly repressed in WSMV- and doubly-infected plants, whereas genes encoding WRKYs and NACs were more enriched in WSMV or doubly infected plants. Synergistic interactions between WSMV and TriMV drastically enhanced disease phenotype compared to individual virus infections. The progression of disease phenotype was correlated to transcriptomic changes, indicating the strong disruption to plant metabolism and likely channeling of energy and metabolites for viral replication. There also appeared to be a connection between viral replication and plastid health, with stronger downregulation of genes needed for chloroplast functions and integrity and increased synergism between TriMV and WSMV. This study provides an overview of transcriptomic changes distinctly influenced by TriMV and WSMV either singly or in combination and provides a good correlation between specific transcription factors and genes associated with metabolism to observed phenotypic changes in plant growth and disease synergism.

Genome-wide identification and expression analysis of the WRKY gene family in Mikania micrantha

BACKGROUND

WRKY transcription factors (TFs) regulate plant responses to environmental stimuli and development, including flowering. Despite extensive research on different species, their role in the invasive plant Mikania micrantha remains to be explored. The aim of this study was to identify and analyze WRKY genes in M. micrantha to understand their function in flowering and adaptation mechanisms.

RESULTS

By analysing the whole genome of M. micrantha, a total of 77 M. micrantha WRKY (MmWRKY) genes were identified. Based on phylogenetic relationships, sequence alignment, and structural domain diversity, the MmWRKY gene family was preliminarily classified into three major groups and five subgroups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Expression profiles showed tissue-specific expression patterns, with many WRKY genes highly expressed in flowers, indicating potential roles in floral development. Real-time quantitative PCR confirmed that the selected 11 genes were highly expressed in floral tissues, supporting their functional significance in flowering.

CONCLUSION

In this study, 77 WRKY genes were identified in M micrantha, and their phylogenetic relationships, structural domains, and expression patterns across various tissues and organs were comprehensively analyzed. This work provides a foundation for future functional characterization of WRKY genes in M. micrantha, which may contribute to the development of more effective strategies to control its rapid spread.

Genome-wide identification of TaeGRASs responsive to biotic stresses and functional analysis of TaeSCL6 in wheat resistance to powdery mildew

BACKGROUND

Powdery mildew is a devastating fungal disease that poses a significant threat to wheat yield and quality worldwide. Identifying resistance genes is highly advantageous for the molecular breeding of resistant cultivars. GRAS proteins are important transcription factors that regulate plant development and stress responses. Nonetheless, their roles in wheat-pathogen interactions remain poorly understood.

RESULTS

In this study, we used bioinformatics tools to identify and analyze wheat GRAS family genes responsive to biotic stresses and elucidated the function of TaeSCL6 within this family. A total of 179 GRAS genes in wheat were unevenly distributed on 7 chromosomes, and classified into 12 subfamilies based on phylogenetic relationship analysis. Gene duplication analysis revealed 13 pairs of tandem repeats and 142 pairs of segmental duplications, which may account for the rapid expansion of the wheat GRAS family. Expression pattern analysis revealed that 75% of the expressed TaeGRAS genes are responsive to biotic stresses. Few studies have focused on the roles of HAM subfamily genes. Consequently, we concentrated our analysis on the members of the HAM subfamily. Fourteen motifs were identified in the HAM family proteins from both Triticeae species and Arabidopsis, indicating that these motifs were highly conserved during evolution. Promoter analysis indicated that the promoters of HAM genes contain several cis-regulatory elements associated with hormone response, stress response, light response, and growth and development. Both qRT-PCR and RNA-seq data analyses demonstrated that TaeSCL6 responds to Blumeria graminis infection. Therefore, we investigated the role of TaeSCL6 in regulating wheat resistance via RNA interference and barley stripe mosaic virus induced gene silencing. Wheat plants with silenced TaeSCL6 exhibited increased susceptibility to powdery mildew.

CONCLUSIONS

In summary, this study not only validates the positive role of TaeSCL6 in wheat resistance to powdery mildew, but also provides candidate gene resources for future breeding of disease-resistance wheat cultivars.

Unravelling the role of WRKY transcription factors in leaf senescence: Genetic and molecular insights

BACKGROUND

Leaf senescence (LS), the final phase in leaf development, is an important and precisely regulated process crucial for plant well-being and the redistribution of nutrients. It is intricately controlled by various regulatory factors, including WRKY transcription factors (TFs). WRKYs are one of the most significant plant TF families, and several of them are differentially regulated and important during LS. Recent research has enhanced our understanding of the structural and functional characteristics of WRKY TFs, providing insights into their regulatory roles.

AIM OF REVIEW

This review aims to elucidate the genetic and molecular mechanisms underlying the intricate regulatory networks associated with LS by investigating the role of WRKY TFs. We seek to highlight the importance of WRKY-mediated signaling pathways in understanding LS, plant evolution, and response to varying environmental conditions.

KEY SCIENTIFIC CONCEPTS OF REVIEW

WRKY TFs exhibit specific DNA-binding activity at the N-terminus and dynamic interactions of the intrinsically disordered domain at the C-terminus with various proteins. These WRKY TFs not only control the activity of other WRKYs, but also interact with either WRKYs or other TFs, thereby fine- tuning the expression of target genes. By unraveling the complex interactions and regulatory mechanisms of WRKY TFs, this review broadens our knowledge of the genetic and molecular basis of LS. Understanding WRKY-mediated signalling pathways provides crucial insights into specific aspects of plant development, such as stress-induced senescence, and offers potential strategies for improving crop resilience to environmental stresses like drought and pathogen attacks. By targeting these pathways, it may be possible to enhance specific productivity traits, such as increased yield stability under adverse conditions, thereby contributing to more reliable agricultural outputs.

RNA-Seq Analysis and Candidate Gene Mining of Gossypium hirsutum Stressed by Verticillium dahliae Cultured at Different Temperatures

The occurrence and spread of Verticillium dahliae (V. dahliae) in cotton depends on the combined effects of pathogens, host plants, and the environment, among which temperature is one of the most important environmental factors. Studying how temperature impacts the occurrence of V. dahliae in cotton and the mechanisms governing host defense responses is crucial for disease prevention and control. Understanding the dual effects of temperature on both pathogens and hosts can provide valuable insights for developing effective strategies to manage this destructive fungal infection in cotton. This study was based on the deciduous V. dahliae Vd-3. Through cultivation at different temperatures, Vd-3 formed the most microsclerotia and had the largest colony diameter at 25 °C. Endospore toxins were extracted, and 48 h was determined to be the best pathogenic time point for endotoxins to infect cotton leaves through a chlorophyll fluorescence imaging system and phenotypic evaluation. Transcriptome sequencing was performed on cotton leaves infected with Vd-3 endotoxins for 48 h at different culture temperatures. A total of 34,955 differentially expressed genes (DEGs) were identified between each temperature and CK (no pathogen inoculation), including 17,422 common DEGs. The results of the enrichment analysis revealed that all the DEGs were involved mainly in photosynthesis and sugar metabolism. Among the 34,955 DEGs, genes in the biosynthesis and signal transduction pathways of jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) were identified, and their expression patterns were determined. A total of 5652 unique DEGs were clustered into six clusters using the k-means clustering algorithm, and the functions and main transcription factors (TFs) of each cluster were subsequently annotated. In addition, we constructed a gene regulatory network via weighted correlation network analysis (WGCNA) and identified twelve key genes related to cotton defense against V. dahliae at different temperatures, including four genes encoding transcription factors. These findings provide a theoretical foundation for investigating temperature regulation in V. dahliae infecting cotton and introduce novel genetic resources for enhancing resistance to this disease in cotton plants.

OsWRKY70 Plays Opposite Roles in Blast Resistance and Cold Stress Tolerance in Rice

The transcription factor WRKYs play pivotal roles in the adapting to adverse environments in plants. Prior research has demonstrated the involvement of OsWRKY70 in resistance against herbivores and its response to abiotic stress. Here, we reported the functional analysis of OsWRKY70 in immunity against fungal diseases and cold tolerance. The results revealed that OsWRKY70 was induced by various Magnaporthe oryzae strains. Knock out mutants of OsWRKY70, which were generated by the CRISPR/Cas9 system, exhibited enhanced resistance to M. oryzae. This was consistent with fortifying the reactive oxygen species (ROS) burst after inoculation in the mutants, elevated transcript levels of defense-responsive genes (OsPR1b, OsPBZ1, OsPOX8.1 and OsPOX22.3) and the observation of the sluggish growth of invasive hyphae under fluorescence microscope. RNA sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) validations demonstrated that differentially expressed genes were related to plant-pathogen interactions, hormone transduction and MAPK cascades. Notably, OsbHLH6, a key component of the JA signaling pathway, was down-regulated in the mutants compared to wild type plants. Further investigation confirmed that OsWRKY70 bound to the promoter of OsbHLH6 by semi-in vivo chromatin immunoprecipitation (ChIP). Additionally, the loss-function of OsWRKY70 impaired cold tolerance in rice. The enhanced susceptibility in the mutants characterized by excessive ROS production, elevated ion leakage rate and increased malondialdehyde content, as well as decreased activity of catalase (CAT) and peroxidase (POD) under low temperature stress was, which might be attributed to down-regulation of cold-responsive genes (OsLti6b and OsICE1). In conclusion, our findings indicate that OsWRKY70 negatively contributes to blast resistance but positively regulates cold tolerance in rice, providing a strategy for crop breeding with tolerance to stress.

Transcriptome, hormonal, and secondary metabolite changes in leaves of DEFENSE NO DEATH 1 (DND1) silenced potato plants

DEFENSE NO DEATH 1 (DND1) is a cyclic nucleotide-gated ion channel protein. Earlier, it was shown that the silencing of DND1 in the potato (Solanum tuberosum L.) leads to resistance to late blight, powdery mildew, and gray mold diseases. At the same time, however, it can reduce plant growth and cause leaf necrosis. To obtain knowledge of the molecular events behind the pleiotropic effect of DND1 downregulation in the potato, metabolite and transcriptome analyses were performed on three DND1 silenced lines of the cultivar 'Désirée.' A massive increase in the salicylic acid content of leaves was detected. Concentrations of jasmonic acid and chlorogenic acid and their derivatives were also elevated. Expression of 1866 genes was altered in the same way in all three DND1 silenced lines, including those related to the synthesis of secondary metabolites. The activation of several alleles of leaf rust, late blight, and other disease resistance genes, as well as the induction of pathogenesis-related genes, was detected. WRKY and NAC transcription factor families were upregulated, whereas bHLHs were downregulated, indicating their central role in transcriptome changes. These results suggest that the maintenance of the constitutive defense state leads to the reduced growth of DND1 silenced potato plants.

Multi-omics analyses reveal the responses of wheat (Triticum aestivum L.) and rhizosphere bacterial community to nano(micro)plastics stress

The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 μm), and polystyrene-MPs (PS-MPs, 10 μm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs.

Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants

The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.