A novel Gossypium barbadense ERF transcription factor, GbERFb, regulation host response and resistance to Verticillium dahliae in tobacco

Transcriptomic analysis towards identification of defence-responsive genes and pathways upon application of Sargassum seaweed extract on tomato plants infected with Macrophominaphaseolina

The charcoal-rot caused by Macrophomina phaseolina is one of the major disease in many economically important crop plants including tomato. The molecular responses of the host plant against the M. phaseolina are poorly stated. In the present study, for the first time the molecular insight of tomato-Macrophomina interaction and Sargassum tenerrimum extract (SE) toward managing disease through RNA-seq approach is established. A total of 449 million high-quality reads (HQRs) were obtained and aligned to the tomato genome with an average mapping of 89.12%. The differentially expressed genes (DEGs) regulated across the different treatment pairs were identified. Several DEGs, such as receptor-like kinases (SlRLKs), transcription factors including SlWRKY70, SlGRAS4, SlERF4, SlERF25, pathogenesis related-1 (SlPR1), SlPR2, endochitinase and peroxidase were significantly up-regulated in SE + Macrophomina treated sample as compared to only Macrophomina treated sample. The crosstalk between salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) was a key factor to regulate resistance in tomato during SE + Macrophomina treatment. The KEGG pathway including plant hormone signal transduction, plant-pathogen interaction and mitogen-activated protein kinase (MAPK) signaling pathway were significantly enriched. The RNA-seq data were validated through qPCR using 12 disease-responsive genes and correlated significantly with R2 = 0.73. The present study suggests that SE act as an elicitor molecule and activate the defence-related pathways similar to PAMP-triggered immunity in tomato. The jasmonic acid (JA) mediated signaling pathway was identified as a key factor to induce resistance in tomato against Macrophomina infection. The present study depicts the beneficial effects of SE by regulating molecular mechanism towards defence responses in tomato against Macrophomina infection. The application of SE brings out new prospects to induce disease tolerance in the agricultural crops.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03565-4.

Genome-wide identification and comparative expression profiling of the WRKY transcription factor family in two Citrus species with different Candidatus Liberibacter asiaticus susceptibility

BACKGROUND

Salicylic Acid (SA) is a pivotal phytohormone in plant innate immunity enhancement of triggered by various pathogens, such as Candidatus Liberibacter asiaticus (CLas), the causal agent of Huanglongbing (HLB). WRKY is a plant specific transcription factor (TF) family, which plays crucial roles in plant response to biotic stresses. So far, the evolutionary history, functions, and expression patterns under SA treatment and CLas infection of WRKY family are poorly understood in Citrus, despite the release of the genome of several Citrus species. A comprehensive genomic and expressional analysis is worth to conduct for this family.

RESULTS

Here, a genome-wide identification of WRKY TFs was performed in two Citrus species: Citrus sinensis (HLB-sensitive) and Poncirus trifoliata (HLB-tolerant). In total, 52 CsWRKYs and 51 PtrWRKYs were identified, whose physical and chemical properties, chromosome locations, phylogenetic relationships and structural characteristics were comparatively analyzed. Especially, expression patterns of these WRKY genes before and after SA treatment and CLas infection were compared. Based on this result, seven pairs of orthologous WRKY genes showing opposite expression patterns in two Citrus species were screened out. Moreover, two pairs of orthologous WRKY genes with significant differences in the number or type of stress-responsive cis-elements in the promoter regions were discovered. Subcellular localization and transcriptional activation activity assays revealed that these two pairs of orthologous genes are classic WRKY TFs localize in the nucleus and could function as transcriptional activators.

CONCLUSION

In this study, we systematically analyzed the genomic characterization of WRKY family in two Citrus species, together with the analyses of expression patterns under SA signaling and CLas infection. Our study laid a foundation for further study on the function of WRKY TFs in HLB response and SA signaling of Citrus.

Defense Mechanisms of Cotton Fusarium and Verticillium Wilt and Comparison of Pathogenic Response in Cotton and Humans

Cotton is an important economic crop. Fusarium and Verticillium are the primary pathogenic fungi that threaten both the quality and sustainable production of cotton. As an opportunistic pathogen, Fusarium causes various human diseases, including fungal keratitis, which is the most common. Therefore, there is an urgent need to study and clarify the resistance mechanisms of cotton and humans toward Fusarium in order to mitigate, or eliminate, its harm. Herein, we first discuss the resistance and susceptibility mechanisms of cotton to Fusarium and Verticillium wilt and classify associated genes based on their functions. We then outline the characteristics and pathogenicity of Fusarium and describe the multiple roles of human neutrophils in limiting hyphal growth. Finally, we comprehensively compare the similarities and differences between animal and plant resistance to Fusarium and put forward new insights into novel strategies for cotton disease resistance breeding and treatment of Fusarium infection in humans.

MicroRNA candidate miRcand137 in apple is induced by Botryosphaeria dothidea for impairing host defense

MicroRNA (miRNA)-mediated gene silencing is a master gene regulatory pathway in plant-pathogen interactions. The differential accumulation of miRNAs among plant varieties alters the expression of target genes, affecting plant defense responses and causing resistance differences among varieties. Botryosphaeria dothidea is an important phytopathogenic fungus of apple (Malus domestica). Malus hupehensis (Pamp.) Rehder, a wild apple species, is highly resistant, whereas the apple cultivar "Fuji" is highly susceptible. Here, we identified a 22-nt miRNA candidate named miRcand137 that compromises host resistance to B. dothidea infection and whose processing was affected by precursor sequence variation between M. hupehensis and "Fuji." miRcand137 guides the direct cleavage of and produced target-derived secondary siRNA against Ethylene response factor 14 (ERF14), a transcriptional activator of pathogenesis-related homologs that confers disease resistance to apple. We showed that miRcand137 acts as an inhibitor of apple immunity by compromising ERF14-mediated anti-fungal defense and revealed a negative association between miRcand137 expression and B. dothidea sensitivity in both resistant and susceptible apples. Furthermore, MIRCAND137 was transcriptionally activated by the invading fungi but not by the fungal elicitor, implying B. dothidea induced host miRcand137 as an infection strategy. We propose that the inefficient miRcand137 processing in M. hupehensis decreased pathogen-initiated miRcand137 accumulation, leading to higher resistance against B. dothidea.

GhKWL1 Upregulates GhERF105 but Its Function Is Impaired by Binding with VdISC1, a Pathogenic Effector of Verticillium dahliae

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease for many important crops, including cotton. Kiwellins (KWLs), a group of cysteine-rich proteins synthesized in many plants, have been shown to be involved in response to various phytopathogens. To evaluate genes for their function in resistance to Verticillium wilt, we investigated KWL homologs in cotton. Thirty-five KWL genes (GhKWLs) were identified from the genome of upland cotton (Gossypium hirsutum). Among them, GhKWL1 was shown to be localized in nucleus and cytosol, and its gene expression is induced by the infection of V. dahliae. We revealed that GhKWL1 was a positive regulator of GhERF105. Silencing of GhKWL1 resulted in a decrease, whereas overexpression led to an increase in resistance of transgenic plants to Verticillium wilt. Interestingly, through binding to GhKWL1, the pathogenic effector protein VdISC1 produced by V. dahliae could impair the defense response mediated by GhKWL1. Therefore, our study suggests there is a GhKWL1-mediated defense response in cotton, which can be hijacked by V. dahliae through the interaction of VdISC1 with GhKWL1.

Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BACKGROUND

Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as 'Frantoio' (resistant) and 'Picual' (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars.

RESULTS

The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed.

CONCLUSION

According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

The mechanism of sesame resistance against Macrophomina phaseolina was revealed via a comparison of transcriptomes of resistant and susceptible sesame genotypes

BACKGROUND

Sesame (Sesamum indicum) charcoal rot, a destructive fungal disease caused by Macrophomina phaseolina (Tassi) Goid (MP), is a great threat to the yield and quality of sesame. However, there is a lack of information about the gene-for-gene relationship between sesame and MP, and the molecular mechanism behind the interaction is not yet clear. The aim of this study was to interpret the molecular mechanism of sesame resistance against MP in disease-resistant (DR) and disease-susceptible (DS) genotypes based on transcriptomics. This is the first report of the interaction between sesame and MP using this method.

RESULTS

A set of core genes that response to MP were revealed by comparative transcriptomics and they were preferentially associated with GO terms such as ribosome-related processes, fruit ripening and regulation of jasmonic acid mediated signalling pathway. It is also exhibited that translational mechanism and transcriptional mechanism could co-activate in DR so that it can initiate the immunity to MP more rapidly. According to weighted gene co-expression network analysis (WGCNA) of differentially expressed gene sets between two genotypes, we found that leucine-rich repeat receptor-like kinase (LRR-RLK) proteins may assume an important job in sesame resistance against MP. Notably, compared with DS, most key genes were induced in DR such as pattern recognition receptors (PRRs) and resistance genes, indicating that DR initiated stronger pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Finally, the study showed that JA/ET and SA signalling pathways all play an important role in sesame resistance to MP.

CONCLUSIONS

The defence response to MP of sesame, a complex bioprocess involving many phytohormones and disease resistance-related genes, was illustrated at the transcriptional level in our investigation. The findings shed more light on further understanding of different responses to MP in resistant and susceptible sesame.

Regulatory Network of Cotton Genes in Response to Salt, Drought and Wilt Diseases (Verticillium and Fusarium): Progress and Perspective

In environmental conditions, crop plants are extremely affected by multiple abiotic stresses including salinity, drought, heat, and cold, as well as several biotic stresses such as pests and pathogens. However, salinity, drought, and wilt diseases (e.g., Fusarium and Verticillium) are considered the most destructive environmental stresses to cotton plants. These cause severe growth interruption and yield loss of cotton. Since cotton crops are central contributors to total worldwide fiber production, and also important for oilseed crops, it is essential to improve stress tolerant cultivars to secure future sustainable crop production under adverse environments. Plants have evolved complex mechanisms to respond and acclimate to adverse stress conditions at both physiological and molecular levels. Recent progresses in molecular genetics have delivered new insights into the regulatory network system of plant genes, which generally includes defense of cell membranes and proteins, signaling cascades and transcriptional control, and ion uptake and transport and their relevant biochemical pathways and signal factors. In this review, we mainly summarize recent progress concerning several resistance-related genes of cotton plants in response to abiotic (salt and drought) and biotic (Fusarium and Verticillium wilt) stresses and classify them according to their molecular functions to better understand the genetic network. Moreover, this review proposes that studies of stress related genes will advance the security of cotton yield and production under a changing climate and that these genes should be incorporated in the development of cotton tolerant to salt, drought, and fungal wilt diseases (Verticillium and Fusarium).

Trichoderma-Induced Ethylene Responsive Factor MsERF105 Mediates Defense Responses in Malus sieversii

Trichoderma can induce plant hormone signal pathways mediating plant defenses, resulting in broad-spectrum resistance to phytopathogens. Herein, Malus sieversii seedlings were treated with Trichoderma biofertilizer and/or Alternaria alternata f. sp. mali, and transcriptome analysis revealed significant differential expression. There was a high similarity between the transcriptome expression profiles of Trichoderma-induced and A. alternata-infected M. sieversii samples for genes related to jasmonic acid (JA), ethylene, and salicylic acid (SA) signaling pathways. Additionally, Trichoderma biofertilizer activated numerous disease-resistant genes (ERF, NAC, bHLH, and STK) and defense response genes (DRP, ABC, and HSP). Among transcription factors, members of the ERF family were the most differentially expressed (18 ERFs), indicating that they may be closely related to defense responses. Among ERFs, differential expression of MsERF105 was the most significant (upregulated 27.6-fold compared to controls). MsERF105 was heterologously expressed in PdPap poplar (Populus davidiana × Populus alba var. pyramidalis Louche), and following infection with A. alternata (Aal), transgenic PdPap-MsERF105s plants displayed lower malondialdehyde (downregulated 41.4%) and reactive oxygen species (ROSs) levels, and higher reductase activities, especially superoxide dismutase (SOD; upregulated 77.5% compared to PdPap-ROK2 plants). Furthermore, the lesion areas of PdPap-MsERF105s leaves were significantly smaller (0.2%) than those of PdPap-ROK2 leaves (∼26.0%), and the cell membrane integrity was superior for PdPap-MsERF105s leaves. Thus, MsERF105 enhanced the resistance of PaPap poplar to Aal, presumably because MsERF105 activates the expression of PR1 and PDF1.2. In conclusion, Trichoderma biofertilizer modulated the differential expression of numerous disease resistance genes and defense response genes in M. sieversii in response to pathogen attack, and MsERF105 played important roles in this process.

An Overview of the Molecular Genetics of Plant Resistance to the Verticillium Wilt Pathogen Verticillium dahliae

Verticillium dahliae is a soil-borne hemibiotrophic fungus that can lead to plant vascular disease and significant economic loss worldwide. Its hosts include over 400 dicotyledon plant species, such as annual herbs, perennials, and woody plants. The average yield loss of cotton crop caused by Verticillium wilt is approximately 10–35%. As the control of this disease is an urgent task for many countries, further understanding of the interaction between plants and V. dahliae is essential. Fungi can promote or inhibit plant growth, which is important; however, the most important relationship between plants and fungi is the host–pathogen relationship. Plants can become resistant to V. dahliae through diverse mechanisms such as cell wall modifications, extracellular enzymes, pattern recognition receptors, transcription factors, and salicylic acid (SA)/jasmonic acid (JA)/ethylene (ET)-related signal transduction pathways. Over the last decade, several studies on the physiological and molecular mechanisms of plant resistance to V. dahliae have been undertaken. In this review, many resistance-related genes are summarised to provide a theoretical basis for better understanding of the molecular genetic mechanisms of plant resistance to V. dahliae. Moreover, it is intended to serve as a resource for research focused on the development of genetic resistance mechanisms to combat Verticillium wilt.

GhWRKY70D13 Regulates Resistance to Verticillium dahliae in Cotton Through the Ethylene and Jasmonic Acid Signaling Pathways

Verticillium wilt caused by Verticillium dahliae is a destructive cotton disease causing severe yield and quality losses worldwide. WRKY transcription factors play important roles in plant defense against pathogen infection. However, little has been reported on the functions of WRKYs in cotton's resistance to V. dahliae. Here, we identified 5, 5, and 10 WRKY70 genes in Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum, respectively, and investigated the expression profiles of all GhWRKY70 genes in various cotton tissues and in response to hormone treatment or V. dahliae infection. Reverse transcription-quantitative PCR analysis showed that GhWRKY70D13 was expressed higher in roots and stems than in other tissues, and up-regulated after V. dahliae inoculation. Knock-down of GhWRKY70D13 improved resistance to V. dahliae in both resistant and susceptible cotton cultivars. Comparative analysis of transcriptomes generated from wild-type and stable RNAi (RNA interference) plant with down-regulated GhWRKY70D13 showed that genes involved in ethylene (ET) and jasmonic acid (JA) biosynthesis and signaling were significantly upregulated in the GhWRKY70D13 RNAi plants. Consistently, the contents of 1-aminocyclopropane-1-carboxylic (ACC), JA, and JA-isoleucine levels were significantly higher in the GhWRKY70D13 RNAi plants than in wild-type. Following V. dahliae infection, the levels of ACC and JA decreased in the GhWRKY70D13 RNAi plants but still significantly higher (for ACC) than that in wild-type or at the same level (for JA) as in non-infected wild-type plants. Collectively, our results suggested that GhWRKY70D13 negatively regulates cotton's resistance to V. dahliae mainly through its effect on ET and JA biosynthesis and signaling pathways.

Functional characterization of LkERF-B2 for improved salt tolerance ability in Arabidopsis thaliana

The ethylene response factors have been reported to play critical roles in developmental and environmental responses in plants. In the present study, an ERF transcription factor gene was aimed to be identified from Larix kaempferi. Molecular characteristics and function of this gene were further explored. The result showed that a 1344 bp ERF transcription factor gene containing initiation and termination codon was obtained by RT-PCR and named LkERF-B2. LkERF-B2 gene encoded 447 amino acids containing a typical AP2/ERF domain. Alignment of predicted amino acid sequence of LkERF-B2 in various plant species showed that this ERF transcription factor was highly homologous (79.0%) with that of Picea sitchensi. To elucidate the function of LkERF-B2, LkERF-B2 overexpression vector was successfully constructed and transformed to Arabidopsis thaliana via dip flower. Compared with control plant, LkERF-B2 overexpressed transgenic A. thaliana showed a significantly higher survival rate under cold, heat, NaCl and drought stresses. NaCl stress analysis revealed that control and transgenic Arabidopsis were both flowering earlier under 100 and 150 mM/L NaCl treatment. While under 200-300 mM/L NaCl treatment, the growth of control plant was significantly inhibited compared with transgenic A. thaliana. Salt injury rate and salt injury index of transgenic Arabidopsis were lower than those of the control. Further investigation showed that transgenic Arabidopsis exhibited much higher content of chloroplast pigments under different NaCl concentration. Meanwhile, the activity of SOD and POD was also enhanced in transgenic A. thaliana. These results suggested that LkERF-B2 was a key transcription factor and could lead to enhanced salt stress tolerance.

Transcriptome Sequencing Analysis Provides Insights Into the Response to Fusarium oxysporum in Lilium pumilum

Lily basal rot, caused by Fusarium oxysporum f. sp. lilii, is one of the most serious diseases of lily. Although the lily germplasm which is resistant to F. oxysporum has been used in disease-resistant breeding, few studies on its molecular mechanism of disease resistance have been reported. To comprehensively study the mechanism of resistance to F. oxysporum, transcriptome sequencings of root tissues from Lilium pumilum inoculated with F. oxysporum or sterile water for 6, 12, or 24 h were performed. A total of 50 GB of data were obtained from the transcriptome sequencings of the 6 L. pumilum samples, and 217 098 Unigenes were obtained after the de novo assembly, of which 38.36% Unigenes were annotated. The sequencing results showed that the numbers of differentially expressed genes at 6, 12, and 24 h after inoculation compared with the control were 111, 254, and 2500, respectively. The functional enrichment analysis of the differentially expressed genes showed that several pathways were involved in responses of L. pumilum, mainly including starch and sucrose metabolism, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, vitamin B6 (VB6) biosynthesis, acid biosynthesis, proteasome, and ribosome. Transcription factor analysis revealed that the WRKY and ERF families played important roles in responses of L. pumilum to F. oxysporum. The results of this study elucidate the molecular responses to F. oxysporum in lily and lay a theoretical foundation for improving lily breeding and strategies for lily basal rot resistance.

Transcriptome analysis reveals differentially expressed ERF transcription factors associated with salt response in cotton

Salinity is a major abiotic stress limiting plant growth and development that has caused severe damage to yield and quality of cotton fiber. Uncovering the mechanisms of response to salt stress is important in breeding salt-tolerant cotton varieties. Transcriptome analysis identified 2356 differentially expressed genes in cotton under salt stress, of which 9.4% were predicted transcription factors (TFs). Approximately 17.6% (39 out of 222) of the differentially expressed TFs belonged to the ethylene response factor (ERF) family. Expression pattern analysis showed significant changes in these ERFs during salt stress. Moreover, the number of down-regulated ERFs was more than that of the up-regulated ERFs. Two of the ERFs, GhERF4L and GhERF54L, showed increased (12-15 times) expression after 12 h of salt treatment. Silencing of GhERF4L and GhERF54L significantly reduced salt tolerance of cotton seedlings, indicating their role in regulating cotton response to salt stress. This study revealed the essential role of ERF transcription factors in the salt response mechanism of plants, and provided important genetic resources for breeding salt-tolerant cotton.

Physiological and molecular mechanism of defense in cotton against Verticillium dahliae

Cotton, a natural fiber producing crop of huge importance for textile industry, has been reckoned as the backbone in the economy of many developing countries. Verticillium wilt caused by Verticillium dahliae reflected as the most devastating disease of cotton crop in several parts of the world. Average losses due to attack of this disease are tremendous every year. There is urgent need to develop strategies for effective control of this disease. In the last decade, progress has been made to understand the interaction between cotton-V. dahliae and several growth and pathogenicity related genes were identified. Still, most of the molecular components and mechanisms of cotton defense against Verticillium wilt are poorly understood. However, from existing knowledge, it is perceived that cotton defense mechanism primarily depends on the pre-formed defense structures including thick cuticle, synthesis of phenolic compounds and delaying or hindering the expansion of the invader through advanced measures such as reinforcement of cell wall structure, accumulation of reactive oxygen species (ROS), release of phytoalexins, the hypersensitive response and the development of broad spectrum resistance named as, systemic acquired resistance (SAR). Investigation of these defense tactics provide valuable information about the improvement of cotton breeding strategies for the development of durable, cost effective, and broad spectrum resistant varieties. Consequently, this management approach will help to reduce the use of fungicides and also minimize other environmental hazards. In the present paper, we summarized the V. dahliae virulence mechanism and comprehensively discussed the cotton molecular mechanisms of defense such as physiological, biochemical responses with the addition of signaling pathways that are implicated towards attaining resistance against Verticillium wilt.