A molecular insight into the early events of chickpea (Cicer arietinum) and Fusarium oxysporum f. sp. ciceri (race 1) interaction through cDNA-AFLP analysis

A pattern for the early, middle, and late phase of tea chrysanthemum response to Fusarium oxysporum

Chrysanthemum morifolium is cultivated worldwide and has high ornamental, tea, and medicinal value. With the increasing area of chrysanthemum cultivation and years of continuous cropping, Fusarium wilt disease frequently occurs in various production areas, seriously affecting the quality and yield and causing huge economic losses. However, the molecular response mechanism of Fusarium wilt infection remains unclear, which limits the molecular breeding process for disease resistance in chrysanthemums. In the present study, we analyzed the molecular response mechanisms of 'Huangju,' one of the tea chrysanthemum cultivars severely infested with Fusarium wilt in the field at the early, middle, and late phases of F. oxysporum infestation. 'Huangju' responded to the infestation mainly through galactose metabolism, plant-pathogen interaction, auxin, abscisic acid, and ethylene signalling in the early phase; galactose metabolism, plant-pathogen interaction, auxin, salicylic acid signal, and certain transcription factors (e.g., CmWRKY48) in the middle phase; and galactose metabolism in the late phase. Notably, the galactose metabolism was important in the early, middle, and late phases of 'Huangju' response to F. oxysporum. Meanwhile, the phytohormone auxin was involved in the early and middle responses. Furthermore, silencing of CmWRKY48 in 'Huangju' resulted in resistance to F. oxysporum. Our results revealed a new molecular pattern for chrysanthemum in response to Fusarium wilt in the early, middle, and late phases, providing a foundation for the molecular breeding of chrysanthemum for disease resistance.

Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Introduction

The yield of chickpea is severely hampered by infection wilt caused by several races of Fusarium oxysporum f. sp. ciceris (Foc).

Methods

To understand the underlying molecular mechanisms of resistance against Foc4 Fusarium wilt, RNA sequencing-based shoot transcriptome data of two contrasting chickpea genotypes, namely KWR 108 (resistant) and GL 13001 (susceptible), were generated and analyzed.

Results and Discussion

The shoot transcriptome data showed 1,103 and 1,221 significant DEGs in chickpea genotypes KWR 108 and GL 13001, respectively. Among these, 495 and 608 genes were significantly down and up-regulated in genotypes KWR 108, and 427 and 794 genes were significantly down and up-regulated in genotype GL 13001. The gene ontology (GO) analysis of significant DEGs was performed and the GO of the top 50 DEGs in two contrasting chickpea genotypes showed the highest cellular components as membrane and nucleus, and molecular functions including nucleotide binding, metal ion binding, transferase, kinase, and oxidoreductase activity involved in biological processes such as phosphorylation, oxidation-reduction, cell redox homeostasis process, and DNA repair. Compared to the susceptible genotype which showed significant up-regulation of genes involved in processes like DNA repair, the significantly up-regulated DEGs of the resistant genotypes were involved in processes like energy metabolism and environmental adaptation, particularly host-pathogen interaction. This indicates an efficient utilization of environmental adaptation pathways, energy homeostasis, and stable DNA molecules as the strategy to cope with Fusarium wilt infection in chickpea. The findings of the study will be useful in targeting the genes in designing gene-based markers for association mapping with the traits of interest in chickpea under Fusarium wilt which could be efficiently utilized in marker-assisted breeding of chickpea, particularly against Foc4 Fusarium wilt.

Comprehensive transcriptome analyses of Fusarium-infected root xylem tissues to decipher genes involved in chickpea wilt resistance

Fusarium wilt is the most destructive soil-borne disease that poses a major threat to chickpea production. To comprehensively understand the interaction between chickpea and Fusarium oxysporum, the xylem-specific transcriptome analysis of wilt-resistant (WR315) and wilt-susceptible (JG62) genotypes at an early timepoint (4DPI) was investigated. Differential expression analysis showed that 1368 and 348 DEGs responded to pathogen infection in resistant and susceptible genotypes, respectively. Both genotypes showed transcriptional reprogramming in response to Foc2, but the responses in WR315 were more severe than in JG62. Results of the KEGG pathway analysis revealed that most of the DEGS in both genotypes with enrichment in metabolic pathways, secondary metabolite biosynthesis, plant hormone signal transduction, and carbon metabolism. Genes associated with defense-related metabolites synthesis such as thaumatin-like protein 1b, cysteine-rich receptor-like protein kinases, MLP-like proteins, polygalacturonase inhibitor 2-like, ethylene-responsive transcription factors, glycine-rich cell wall structural protein-like, beta-galactosidase-like, subtilisin-like protease, thioredoxin-like protein, chitin elicitor receptor kinase-like, proline transporter-like, non-specific lipid transfer protein and sugar transporter were mostly up-regulated in resistant as compared to susceptible genotypes. The results of this study provide disease resistance genes, which would be helpful in understanding the Foc resistance mechanism in chickpea.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03803-9.

Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea

Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.

Molecular insights into the jasmonate signaling and associated defense responses against wilt caused by Fusarium oxysporum

Biotic and abiotic stress factors drastically limit plant growth and development as well as alter the physiological, biochemical and cellular processes. This negatively impacts plant productivity, ultimately leading to agricultural and economical loss. Plant defense mechanisms elicited in response to these stressors are crucially regulated by the intricate crosstalk between defense hormones such as jasmonic acid (JA), salicylic acid and ethylene. These hormones orchestrate adaptive responses by modulating the gene regulatory networks leading to sequential changes in the root architecture, cell wall composition, secondary metabolite production and expression of defense-related genes. Fusarium wilt is a widespread vascular disease in plants caused by the soil-borne ascomycete Fusarium oxysporum and is known to attack several economically important plant cultivars. JA along with its conjugated forms methyl jasmonate and jasmonic acid isoleucine critically tunes plant defense mechanisms by regulating the expression of JA-associated genes imparting resistance phenotype. However, it should be noted that some members of F. oxysporum utilize the JA signaling pathway for disease development leading to susceptibility in plants. Therefore, JA signaling pathway becomes one of the important targets amenable for modulation to develop resistance response against Fusarium wilt in plants. In this review, we have emphasized on the physiological and molecular aspects of JA and its significant role in mounting an early defense response against Fusarium wilt disease. Further, utilization of the inherent JA signaling pathway and/or exogenous application of JA in generating Fusarium wilt resistant plants is discussed.

Comparative transcriptomic profiling of susceptible and resistant cultivars of pigeonpea demonstrates early molecular responses during Fusarium udum infection

Vascular wilt caused by Fusarium udum Butler is the most important disease of pigeonpea throughout the world. F. udum isolate MTCC 2204 (M1) inoculated pigeonpea plants of susceptible (ICP 2376) and resistant (ICP 8863) cultivars were taken at invasion stage of pathogenesis process for transcriptomic profiling to understand defense signaling reactions that interplay at early stage of this plant-pathogen encounter. Differential transcriptomic profiles were generated through cDNA-AFLP from M1 inoculated resistant and susceptible pigeonpea root tissues. Twenty five percent of transcript derived fragments (TDFs) were found to be pathogen induced. Among them 73 TDFs were re-amplified and sequenced. Homology search of the TDFs in available databases and thorough study of scientific literature identified several pathways, which could play crucial role in defense responses of the F. udum inoculated resistant plants. Some of the defense responsive pathways identified to be active during this interaction are, jasmonic acid and salicylic acid mediated defense responses, cell wall remodeling, vascular development and pattering, abscisic acid mediated responses, effector triggered immunity, and reactive oxygen species mediated signaling. This study identified important wilt responsive regulatory pathways in pigeonpea which will be helpful for further exploration of these resistant components for pigeonpea improvement.

Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes

Fusarium wilt (FW) disease is the key constraint to grain legume production worldwide. The projected climate change is likely to exacerbate the current scenario. Of the various plant protection measures, genetic improvement of the disease resistance of crop cultivars remains the most economic, straightforward and environmental-friendly option to mitigate the risk. We begin with a brief recap of the classical genetic efforts that provided first insights into the genetic determinants controlling plant response to different races of FW pathogen in grain legumes. Subsequent technological breakthroughs like sequencing technologies have enhanced our understanding of the genetic basis of both plant resistance and pathogenicity. We present noteworthy examples of targeted improvement of plant resistance using genomics-assisted approaches. In parallel, modern functional genomic tools like RNA-seq are playing a greater role in illuminating the various aspects of plant-pathogen interaction. Further, proteomics and metabolomics have also been leveraged in recent years to reveal molecular players and various signaling pathways and complex networks participating in host-pathogen interaction. Finally, we present a perspective on the challenges and limitations of high-throughput phenotyping and emerging breeding approaches to expeditiously develop FW-resistant cultivars under the changing climate.

Inhibition of multiple defense responsive pathways by CaWRKY70 transcription factor promotes susceptibility in chickpea under Fusarium oxysporum stress condition

BACKGROUND

Suppression and activation of plant defense genes is comprehensively regulated by WRKY family transcription factors. Chickpea, the non-model crop legume suffers from wilt caused by Fusarium oxysporum f. sp. ciceri Race1 (Foc1), defense response mechanisms of which are poorly understood. Here, we attempted to show interaction between WRKY70 and several downstream signaling components involved in susceptibility/resistance response in chickpea upon challenge with Foc1.

RESULTS

In the present study, we found Cicer arietinum L. WRKY70 (CaWRKY70) negatively governs multiple defense responsive pathways, including Systemic Acquired Resistance (SAR) activation in chickpea upon Foc1 infection. CaWRKY70 is found to be significantly accumulated at shoot tissues of susceptible (JG62) chickpea under Foc1 stress and salicylic acid (SA) application. CaWRKY70 overexpression promotes susceptibility in resistant chickpea (WR315) plants to Foc1 infection. Transgenic plants upon Foc1 inoculation demonstrated suppression of not only endogenous SA concentrations but expression of genes involved in SA signaling. CaWRKY70 overexpressing chickpea roots exhibited higher ion-leakage and Foc1 biomass accumulation compared to control transgenic (VC) plants. CaWRKY70 overexpression suppresses H₂O₂ production and resultant reactive oxygen species (ROS) induced cell death in Foc1 infected chickpea roots, stem and leaves. Being the nuclear targeted protein, CaWRKY70 suppresses CaMPK9-CaWRKY40 signaling in chickpea through its direct and indirect negative regulatory activities. Protein-protein interaction study revealed CaWRKY70 and CaRPP2-like CC-NB-ARC-LRR protein suppresses hyper-immune signaling in chickpea. Together, our study provides novel insights into mechanisms of suppression of the multiple defense signaling components in chickpea by CaWRKY70 under Foc1 stress.

CONCLUSION

CaWRKY70 mediated defense suppression unveils networking between several immune signaling events negatively affecting downstream resistance mechanisms in chickpea under Foc1 stress.

Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection

Molecular changes elicited by common bean (Phaseolus vulgaris L.) in response to Fusarium oxysproum f. sp. Phaseoli (FOP) remain elusive. We studied the changes in root metabolism during common bean–FOP interactions using a combined de novo transcriptome and metabolome approach. Our results demonstrated alterations of transcript levels and metabolite concentrations in common bean roots 24 h post infection as compared to control. The transcriptome and metabolome responses in common bean roots revealed significant changes in structural defense i.e., cell-wall loosening and weakening characterized by hyper accumulation of cell-wall loosening and degradation related transcripts. The levels of pathogenesis related genes were significantly higher upon FOP inoculation. Interestingly, we found the involvement of glycosylphosphatidylinositol- anchored proteins (GPI-APs) in signal transduction in response to FOP infection. Our results confirmed that hormones have strong role in signaling pathways i.e., salicylic acid, jasmonate, and ethylene pathways. FOP induced energy metabolism and nitrogen mobilization in infected common bean roots as compared to control. Importantly, the flavonoid biosynthesis pathway was the most significantly enriched pathway in response to FOP infection as revealed by the combined transcriptome and metabolome analysis. Overall, the observed modulations in the transcriptome and metabolome flux as outcome of several orchestrated molecular events are determinant of host’s role in common bean–FOP interactions.

Genomics of Plant Disease Resistance in Legumes

The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.

CaMPK9 increases the stability of CaWRKY40 transcription factor which triggers defense response in chickpea upon Fusarium oxysporum f. sp. ciceri Race1 infection

Physical interaction and phosphorylation by CaMPK9 protects the degradation of CaWRKY40 that induces resistance response in chickpea to Fusarium wilt disease by modulating the transcription of defense responsive genes. WRKY transcription factors (TFs) are the global regulators of plant defense signaling that modulate immune responses in host plants by regulating transcription of downstream target genes upon challenged by pathogens. However, very little is known about immune responsive role of Cicer arietinum L. (Ca) WRKY TFs particularly. Using two contrasting chickpea genotypes with respect to resistance against Fusarium oxysporum f. sp. ciceri Race1 (Foc1), we demonstrate transcript accumulation of different CaWRKYs under multiple stresses and establish that CaWRKY40 triggers defense. CaWRKY40 overexpressing chickpea mounts resistance to Foc1 by positively modulating the defense related gene expression. EMSA, ChIP assay and real-time PCR analyses suggest CaWRKY40 binds at the promoters and positively regulates transcription of CaDefensin and CaWRKY33. Further studies revealed that mitogen Activated Protein Kinase9 (CaMPK9) phosphorylates CaWRKY40 by directly interacting with its two canonical serine residues. Interestingly, CaMPK9 is unable to interact with CaWRKY40 when the relevant two serine residues were replaced by alanine. Overexpression of serine mutated WRKY40 isoform in chickpea fails to provide resistance against Foc1. Mutated WRKY40^{Ser.224/225 to AA} overexpressing chickpea resumes its ability to confer resistance against Foc1 after application of 26S proteasomal inhibitor MG132, suggests that phosphorylation is essential to protect CaWRKY40 from proteasomal degradation. CaMPK9 silencing also led to susceptibility in chickpea to Foc1. Altogether, our results elucidate positive regulatory roles of CaMPK9 and CaWRKY40 in modulating defense response in chickpea upon Foc1 infection.

Epigenetic and transcriptional control of chickpea WRKY40 promoter activity under Fusarium stress and its heterologous expression in Arabidopsis leads to enhanced resistance against bacterial pathogen

Promoters of many defense related genes are enriched with W-box elements serving as binding sites for plant specific WRKY transcription factors. In this study, expression of WRKY40 transcription factor was analyzed in two contrasting susceptible (JG62) and resistant (WR315) genotypes of chickpea infected with Foc1. The resistant plants showed up-regulation of WRKY40 under Fusarium stress, whereas in susceptible plants WRKY40 expression was absent. Additionally, global changes in the histone modification patterns were studied in above two chickpea genotypes by immunoblotting and real-time PCR analyses under control and Fusarium infected conditions. Notably, region specific Histone 3 lysine 9 acetylation, a positive marker of transcription gets enriched at WRKY40 promoter during resistant interaction with Foc1. H3K9 Ac is less enriched at WRKY40 promoter in Foc1 infected susceptible plants. WRKY40 promoter activity was induced by jasmonic acid and pathogen treatment, while salicylic acid failed to stimulate such activity. Moreover, WRKY40 was found to bind to its own promoter and auto-regulates its activity. The present study also showed that heterologous over-expression of chickpea WRKY40 triggers defense response in Arabidopsis against Pseudomonas syringae. Overall, we present epigenetic and transcriptional control of WRKY40 in chickpea under Fusarium stress and its immunomodulatory role is tested in Arabidopsis.

Physical interaction between nuclear accumulated CC-NB-ARC-LRR protein and WRKY64 promotes EDS1 dependent Fusarium wilt resistance in chickpea

Fusarium wilt is one of the most serious diseases affecting chickpea (Cicer arietinum L.). Here, we identified a putative Resistance Gene Analog (CaRGA) from chickpea, encoding a coiled-coil (CC) nucleotide-binding oligomerization domain (NB-ARC) containing leucine-rich repeat (LRR) protein (CC-NLR protein) that confers resistance against Fusarium oxysporum f. sp. ciceri race1 (Foc1). Over-expression and silencing of CaRGA in chickpea resulted in enhanced resistance and hyper-susceptibility, respectively against Foc1. Furthermore, defense response to Foc1 depends on CC-NLR interaction with WRKY64 transcription factor. CaRGA mediated wilt resistance largely compromised when WRKY64 was silenced. We also determined in planta intramolecular interactions and self-association of chickpea CC-NLR protein. The study shows CC domain suppressing auto-activation of the full-length CC-NLR protein in the absence of pathogen through self-inhibitory intramolecular interaction with NB-ARC domain, which is attenuated by self-interactions to LRR domain. Chickpea CC-NLR protein forms homocomplexes and then interacts with WRKY64. CC-NLR protein further phosphorylates WRKY64 thereby, ubiquitination and proteasome mediated degradation are protected. Phosphorylated WRKY64 with increased stability binds to EDS1 promoter and stimulates its transcription that induces in planta ectopic cell-death. The detailed analysis of CC-NLR and WRKY interactions provide a better understanding of the immune regulation by NLR proteins under biotic stresses.

Analysis of differential transcript expression in chickpea during compatible and incompatible interactions with Fusarium oxysporum f. sp. ciceris Race 4

The present study reports the transcriptome analysis of resistance (WR315) and susceptible (JG62) genotypes of chickpea in response to Fusarium oxysporum f. sp. ciceris (Foc) race 4 using the method of suppression subtractive hybridization. Altogether, 162 chickpea-expressed sequence tags (ESTs) were identified from two libraries and analyzed to catalog eight functional categories. These ESTs could be assembled into 18 contigs and 144 singletons with 10 contigs and 68 singletons from compatible and 8 contigs and 70 singletons from incompatible interaction. The largest category consisted of ESTs which encode for proteins related to hypothetical proteins (22.8%), followed by energy and metabolism (20.3%)-related genes, defense and cell rescue-related genes (17.9%) and signal transduction-related genes (16%). Among them, 17.1 and 18.7% were defense-related genes in compatible and incompatible interaction, respectively. These ESTs mainly includes various putative genes related to oxidative burst, pathogenesis and secondary metabolism. Induction of putative superoxide dismutase, metallothionein, 4-coumarate-CoA ligase, heat shock proteins and cysteine proteases indicated oxidative burst after infection. The ESTs belonged to various functional categories which were directly and indirectly associated with defense signaling pathways. Quantitative and semi-quantitative polymerase chain reaction exhibited differential expression of candidate genes and detected higher levels in incompatible interaction compared to compatible interaction. The present study revealed partial molecular mechanism associated with the resistance in chickpea against Foc, which is the key to design a strategy for incorporation of resistance via either biotechnological means or introgression of resistance genes.

Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies

Fusarium wilt is one of the major biotic stresses reducing chickpea productivity. The use of wilt-resistant cultivars is the most appropriate means to combat the disease and secure productivity. As a step towards understanding the molecular basis of wilt resistance in chickpea, we investigated the transcriptomes of wilt-susceptible and wilt-resistant cultivars under both Fusarium oxysporum f.sp. ciceri (Foc) challenged and unchallenged conditions. Transcriptome profiling using LongSAGE provided a valuable insight into the molecular interactions between chickpea and Foc, which revealed several known as well as novel genes with differential or unique expression patterns in chickpea contributing to lignification, hormonal homeostasis, plant defense signaling, ROS homeostasis, R-gene mediated defense, etc. Similarly, several Foc genes characteristically required for survival and growth of the pathogen were expressed only in the susceptible cultivar with null expression of most of these genes in the resistant cultivar. This study provides a rich resource for functional characterization of the genes involved in resistance mechanism and their use in breeding for sustainable wilt-resistance. Additionally, it provides pathogen targets facilitating the development of novel control strategies.

Transcriptomic dissection reveals wide spread differential expression in chickpea during early time points of Fusarium oxysporum f. sp. ciceri Race 1 attack

Plants' reaction to underground microorganisms is complex as sessile nature of plants compels them to prioritize their responses to diverse microorganisms both pathogenic and symbiotic. Roots of important crops are directly exposed to diverse microorganisms, but investigations involving root pathogens are significantly less. Thus, more studies involving root pathogens and their target crops are necessitated to enrich the understanding of underground interactions. Present study reported the molecular complexities in chickpea during Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) infection. Transcriptomic dissections using RNA-seq showed significantly differential expression of molecular transcripts between infected and control plants of both susceptible and resistant genotypes. Radar plot analyses showed maximum expressional undulations after infection in both susceptible and resistant plants. Gene ontology and functional clustering showed large number of transcripts controlling basic metabolism of plants. Network analyses demonstrated defense components like peptidyl cis/trans isomerase, MAP kinase, beta 1,3 glucanase, serine threonine kinase, patatin like protein, lactolylglutathione lyase, coproporphyrinogen III oxidase, sulfotransferases; reactive oxygen species regulating components like respiratory burst oxidase, superoxide dismutases, cytochrome b5 reductase, glutathione reductase, thioredoxin reductase, ATPase; metabolism regulating components, myo inositol phosphate, carboxylate synthase; transport related gamma tonoplast intrinsic protein, and structural component, ubiquitins to serve as important nodals of defense signaling network. These nodal molecules probably served as hub controllers of defense signaling. Functional characterization of these hub molecules would not only help in developing better understanding of chickpea-Foc1 interaction but also place them as promising candidates for resistance management programs against vascular wilt of legumes.

Genome wide transcriptome profiling of Fusarium oxysporum f sp. ciceris conidial germination reveals new insights into infection-related genes

Vascular wilt caused by Fusarium oxysporum f. sp. ciceris (Foc) is a serious disease of chickpea (Cicer arietinum L.) accounting for approximately 10–15% annual crop loss. The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients. Infection is initiated by conidia that invade the host tissue often by penetration of intact epidermal cells. Here, we report the characterization of the transcriptome of Foc sequenced using Illumina Hiseq technology during its conidial germination at different time points. Genome-wide expression profiling revealed that genes linked to fungal development are transcribed in successive ways. Analysis showed that Foc have large sets of germination-related genes and families of genes encoding secreted effectors, cell wall/pectin-degrading enzymes, metabolism related enzymes, transporters and peptidases. We found that metabolism related enzymes are up-regulated at early time point whereas most transporters and secondary metabolites important for tissue colonization and pathogenicity are up-regulated later as evident from the qRT-PCR. The study demonstrated that early conidial germination in Foc is accompanied by rapid shifts in gene expression that prepare the fungus for germ tube outgrowth, host cell invasion and pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.

Differentially Expressed Genes in Resistant and Susceptible Common Bean (Phaseolus vulgaris L.) Genotypes in Response to Fusarium oxysporum f. sp. phaseoli

Fusarium wilt of common bean (Phaseolus vulgaris L.), caused by Fusarium oxysporum Schlechtend.:Fr. f.sp. phaseoli (Fop), is one of the most important diseases of common beans worldwide. Few natural sources of resistance to Fop exist and provide only moderate or partial levels of protection. Despite the economic importance of the disease across multiple crops, only a few of Fop induced genes have been analyzed in legumes. Therefore, our goal was to identify transcriptionally regulated genes during an incompatible interaction between common bean and the Fop pathogen using the cDNA amplified fragment length polymorphism (cDNA-AFLP) technique. We generated a total of 8,730 transcript-derived fragments (TDFs) with 768 primer pairs based on the comparison of a moderately resistant and a susceptible genotype. In total, 423 TDFs (4.9%) displayed altered expression patterns after inoculation with Fop inoculum. We obtained full amplicon sequences for 122 selected TDFs, of which 98 were identified as annotated known genes in different functional categories based on their putative functions, 10 were predicted but non-annotated genes and 14 were not homologous to any known genes. The 98 TDFs encoding genes of known putative function were classified as related to metabolism (22), signal transduction (21), protein synthesis and processing (20), development and cytoskeletal organization (12), transport of proteins (7), gene expression and RNA metabolism (4), redox reactions (4), defense and stress responses (3), energy metabolism (3), and hormone responses (2). Based on the analyses of homology, 19 TDFs from different functional categories were chosen for expression analysis using quantitative RT-PCR. The genes found to be important here were implicated at various steps of pathogen infection and will allow a better understanding of the mechanisms of defense and resistance to Fop and similar pathogens. The differential response genes discovered here could also be used as molecular markers in association mapping or QTL analysis.

Analysis of root proteome unravels differential molecular responses during compatible and incompatible interaction between chickpea (Cicer arietinum L.) and Fusarium oxysporum f. sp. ciceri Race1 (Foc1)

BACKGROUND

Vascular wilt caused by Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) is a serious disease of chickpea (Cicer arietinum L.) accounting for approximately 10-15% annual crop loss. The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients, finally resulting in wilting of the entire plant. Although comparative transcriptomic profiling have highlighted some important signaling molecules, but proteomic studies involving chickpea-Foc1 are limited. The present study focuses on comparative root proteomics of susceptible (JG62) and resistant (WR315) chickpea genotypes infected with Foc1, to understand the mechanistic basis of susceptibility and/or resistance.

RESULTS

The differential and unique proteins of both genotypes were identified at 48 h, 72 h, and 96 h post Foc1 inoculation. 2D PAGE analyses followed by MALDI-TOF MS and MS/MS identified 100 differentially (>1.5 fold<, p<0.05) or uniquely expressed proteins. These proteins were further categorized into 10 functional classes and grouped into GO (gene ontology) categories. Network analyses of identified proteins revealed intra and inter relationship of these proteins with their neighbors as well as their association with different defense signaling pathways. qRT-PCR analyses were performed to correlate the mRNA and protein levels of some proteins of representative classes.

CONCLUSIONS

The differential and unique proteins identified indicate their involvement in early defense signaling of the host. Comparative analyses of expression profiles of obtained proteins suggest that albeit some common components participate in early defense signaling in both susceptible and resistant genotypes, but their roles and regulation differ in case of compatible and/or incompatible interactions. Thus, functional characterization of identified PR proteins (PR1, BGL2, TLP), Trypsin protease inhibitor, ABA responsive protein, cysteine protease, protein disulphide isomerase, ripening related protein and albumins are expected to serve as important molecular components for biotechnological application and development of sustainable resistance against Foc1.

Understanding the molecular defence responses of host during chickpea-Fusarium interplay: where do we stand?

Fusarium oxysporum is known to cause vascular wilt and root rot of many important plants. Although extensive studies have been reported for the model plant Arabidopsis thaliana (L.) Heynh., the question of whether those experimental interpretations are extendable to other crop species requires experimentation. Chickpea is the most important crop legume of Indian subcontinent and ranks third in the world list of important legumes. However, productivity of this crop is severely curtailed by vascular wilt caused by Fusarium oxysporum f. sp. ciceri. Based on earlier reports, the present review discusses about the external manifestations of the disease, in planta fungal progression and establishment, and the molecular responses of chickpea that occur during Fusarium oxysporum f. sp. ciceri Race 1(Foc1) interaction. Foc1, known to enter the roots through the breaches of tap root, colonise the xylem vessels and block upward translocation of essential solutes causing wilt in compatible hosts. In contrast, pathogen invasion is readily perceived by the resistant host, which activates defence signalling cascades that are directed towards protecting its primary metabolism from the harmful consequences of pathogenic mayhem. Hence, understanding the dynamic complexities of chickpea-Foc1 interplay is prerequisite to providing sustainable solutions in wilt management programs.

Fusarium oxysporum f.sp. ciceri race 1 induced redox state alterations are coupled to downstream defense signaling in root tissues of chickpea (Cicer arietinum L.)

Reactive oxygen species are known to play pivotal roles in pathogen perception, recognition and downstream defense signaling. But, how these redox alarms coordinate in planta into a defensive network is still intangible. Present study illustrates the role of Fusarium oxysporum f.sp ciceri Race1 (Foc1) induced redox responsive transcripts in regulating downstream defense signaling in chickpea. Confocal microscopic studies highlighted pathogen invasion and colonization accompanied by tissue damage and deposition of callose degraded products at the xylem vessels of infected roots of chickpea plants. Such depositions led to the clogging of xylem vessels in compatible hosts while the resistant plants were devoid of such obstructions. Lipid peroxidation assays also indicated fungal induced membrane injury. Cell shrinkage and gradual nuclear adpression appeared as interesting features marking fungal ingress. Quantitative real time polymerase chain reaction exhibited differential expression patterns of redox regulators, cellular transporters and transcription factors during Foc1 progression. Network analysis showed redox regulators, cellular transporters and transcription factors to coordinate into a well orchestrated defensive network with sugars acting as internal signal modulators. Respiratory burst oxidase homologue, cationic peroxidase, vacuolar sorting receptor, polyol transporter, sucrose synthase, and zinc finger domain containing transcription factor appeared as key molecular candidates controlling important hubs of the defense network. Functional characterization of these hub controllers may prove to be promising in understanding chickpea-Foc1 interaction and developing the case study as a model for looking into the complexities of wilt diseases of other important crop legumes.

Quantitative and microscopic assessment of compatible and incompatible interactions between chickpea cultivars and Fusarium oxysporum f. sp. ciceris races

BACKGROUND

Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris, a main threat to global chickpea production, is managed mainly by resistant cultivars whose efficiency is curtailed by Fusarium oxysporum f. sp. ciceris races.

METHODOLOGY

We characterized compatible and incompatible interactions by assessing the spatial-temporal pattern of infection and colonization of chickpea cvs. P-2245, JG-62 and WR-315 by Fusarium oxysporum f. sp. ciceris races 0 and 5 labeled with ZsGreen fluorescent protein using confocal laser scanning microscopy.

FINDINGS

The two races colonized the host root surface in both interactions with preferential colonization of the root apex and subapical root zone. In compatible interactions, the pathogen grew intercellularly in the root cortex, reached the xylem, and progressed upwards in the stem xylem, being the rate and intensity of stem colonization directly related with the degree of compatibility among Fusarium oxysporum f. sp. ciceris races and chickpea cultivars. In incompatible interactions, race 0 invaded and colonized 'JG-62' xylem vessels of root and stem but in 'WR-315', it remained in the intercellular spaces of the root cortex failing to reach the xylem, whereas race 5 progressed up to the hypocotyl. However, all incompatible interactions were asymptomatic.

CONCLUSIONS

The differential patterns of colonization of chickpea cultivars by Fusarium oxysporum f. sp. ciceris races may be related to the operation of multiple resistance mechanisms.

Distinct colonization patterns and cDNA-AFLP transcriptome profiles in compatible and incompatible interactions between melon and different races of Fusarium oxysporum f. sp. melonis

BACKGROUND

Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by infection on appropriate cultivars. No molecular tools are available that can discriminate among the races, and the molecular basis of compatibility and disease progression are poorly understood. Resistance to races 1 and 2 is controlled by a single dominant gene, whereas only partial polygenic resistance to race 1,2 has been described. We carried out a large-scale cDNA-AFLP analysis to identify host genes potentially related to resistance and susceptibility as well as fungal genes associated with the infection process. At the same time, a systematic reisolation procedure on infected stems allowed us to monitor fungal colonization in compatible and incompatible host-pathogen combinations.

RESULTS

Melon plants (cv. Charentais Fom-2), which are susceptible to race 1,2 and resistant to race 1, were artificially infected with a race 1 strain of FOM or one of two race 1,2 w strains. Host colonization of stems was assessed at 1, 2, 4, 8, 14, 16, 18 and 21 days post inoculation (dpi), and the fungus was reisolated from infected plants. Markedly different colonization patterns were observed in compatible and incompatible host-pathogen combinations. Five time points from the symptomless early stage (2 dpi) to obvious wilting symptoms (21 dpi) were considered for cDNA-AFLP analysis. After successful sequencing of 627 transcript-derived fragments (TDFs) differentially expressed in infected plants, homology searching retrieved 305 melon transcripts, 195 FOM transcripts expressed in planta and 127 orphan TDFs. RNA samples from FOM colonies of the three strains grown in vitro were also included in the analysis to facilitate the detection of in planta-specific transcripts and to identify TDFs differentially expressed among races/strains.

CONCLUSION

Our data suggest that resistance against FOM in melon involves only limited transcriptional changes, and that wilting symptoms could derive, at least partially, from an active plant response.We discuss the pathogen-derived transcripts expressed in planta during the infection process and potentially related to virulence functions, as well as transcripts that are differentially expressed between the two FOM races grown in vitro. These transcripts provide candidate sequences that can be further tested for their ability to distinguish between races.Sequence data from this article have been deposited in GenBank, Accession Numbers: HO867279-HO867981.

In search of decoy/guardee to R genes: deciphering the role of sugars in defense against Fusarium wilt in chickpea

Plant responses are coordinately controlled by both external and internal signals. Apt perception of pathogen attack and its appropriate conversion to internal signals ultimately determine the outcome of innate immunity. The present review predicts the involvement of unconventional 'Guard/Decoy Model' in chickpea-Fusarium encounter. Rapid alkalinization factor is predicted to act as initial 'Gatekeeper decoy' counteracting fungal entry. Phospholipases and cystatins probably function as 'Guardees' being shielded by R gene(s). Serine Threonine Kinases decodes external pathogenic signals to in planta defense alarms. 14.3.3 provides clues to the wilt mechanism. The versatile sugars serve as signal generators and transmitters maintaining intra and inter cellular connectivity during stress.

Primary metabolism of chickpea is the initial target of wound inducing early sensed Fusarium oxysporum f. sp. ciceri race I

BACKGROUND

Biotrophic interaction between host and pathogen induces generation of reactive oxygen species that leads to programmed cell death of the host tissue specifically encompassing the site of infection conferring resistance to the host. However, in the present study, biotrophic relationship between Fusarium oxysporum and chickpea provided some novel insights into the classical concepts of defense signaling and disease perception where ROS (reactive oxygen species) generation followed by hypersensitive responses determined the magnitude of susceptibility or resistant potentiality of the host.

METHODOLOGY/PRINCIPAL FINDINGS

Microscopic observations detected wound mediated in planta pathogenic establishment and its gradual progression within the host vascular tissue. cDNA-AFLP showed differential expression of many defense responsive elements. Real time expression profiling also validated the early recognition of the wound inducing pathogen by the host. The interplay between fungus and host activated changes in primary metabolism, which generated defense signals in the form of sugar molecules for combating pathogenic encounter.

CONCLUSIONS/SIGNIFICANCE

The present study showed the limitations of hypersensitive response mediated resistance, especially when foreign encounters involved the food production as well as the translocation machinery of the host. It was also predicted from the obtained results that hypersensitivity and active species generation failed to impart host defense in compatible interaction between chickpea and Fusarium. On the contrary, the defense related gene(s) played a critical role in conferring natural resistance to the resistant host. Thus, this study suggests that natural selection is the decisive factor for selecting and segregating out the suitable type of defense mechanism to be undertaken by the host without disturbing its normal metabolism, which could deviate from the known classical defense mechanisms.