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

Fusarium wilt constrains mungbean yield due to reduction in source availability

Mungbean is an important source of plant protein for consumers and a high-value export crop for growers across Asia, Australia and Africa. However, many commercial cultivars are highly vulnerable to biotic stresses, which rapidly reduce yield within the season. Fusarium oxysporum is a soil-borne pathogen that is a growing concern for mungbean growers globally. This pathogen causes Fusarium wilt by infecting the root system of the plant resulting in devastating yield reductions. To understand the impact of Fusarium on mungbean development and productivity and to identify tolerant genotypes, a panel of 23 diverse accessions was studied. Field trials conducted in 2016 and 2021 in Warwick, Queensland, Australia under rainfed conditions investigated the variation in phenology, canopy and yield component traits under disease and disease-free conditions. Analyses revealed a high degree of genetic variation for all traits. By comparing the performance of these traits across these two environments, we identified key traits that underpin yield under disease and disease-free conditions. Aboveground biomass components at 50 % flowering were identified as significant drivers of yield development under disease-free conditions and when impacted by Fusarium resulted in up to 96 % yield reduction. Additionally, eight genotypes were identified to be tolerant to Fusarium. These genotypes were found to display differing phenological and morphological behaviours, thereby demonstrating the potential to breed tolerant lines with a range of diverse trait variations. The identification of tolerant genotypes that sustain yield under disease pressure may be exploited in crop improvement programs.

Identification of novel sources of partial and incomplete hypersensitive resistance to rust and associated genomic regions in common bean

Common bean (Phaseolus vulgaris) is one of the legume crops most consumed worldwide and bean rust is one of the most severe foliar biotrophic fungal diseases impacting its production. In this work, we searched for new sources of rust resistance (Uromyces appendiculatus) in a representative collection of the Portuguese germplasm, known to have accessions with an admixed genetic background between Mesoamerican and Andean gene pools. We identified six accessions with incomplete hypersensitive resistance and 20 partially resistant accessions of Andean, Mesoamerican, and admixed origin. We detected 11 disease severity-associated single-nucleotide polymorphisms (SNPs) using a genome-wide association approach. Six of the associations were related to partial (incomplete non-hypersensitive) resistance and five to incomplete hypersensitive resistance, and the proportion of variance explained by each association varied from 4.7 to 25.2%. Bean rust severity values ranged from 0.2 to 49.1% and all the infection types were identified, reflecting the diversity of resistance mechanisms deployed by the Portuguese germplasm.The associations with U. appendiculatus partial resistance were located in chromosome Pv08, and with incomplete hypersensitive resistance in chromosomes Pv06, Pv07, and Pv08, suggesting an oligogenic inheritance of both types of resistance. A resolution to the gene level was achieved for eight of the associations. The candidate genes proposed included several resistance-associated enzymes, namely β-amylase 7, acyl-CoA thioesterase, protein kinase, and aspartyl protease. Both SNPs and candidate genes here identified constitute promising genomics targets to develop functional molecular tools to support bean rust resistance precision breeding.

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.

Pathotypes of Fusarium oxysporum f. sp. fragariae express discrete repertoires of accessory genes and induce distinct host transcriptional responses during root infection

Convergent evolution of phytopathogenicity is poorly described, especially among multiple strains of a single microbial species. We investigated this phenomenon with genetically diverse isolates of Fusarium oxysporum f. sp. fragariae (Fof) that cause one of two syndromes: chlorosis and wilting (the 'yellows-fragariae' pathotype), or only wilting (the 'wilt-fragariae' pathotype). We challenged strawberry (Fragaria × ananassa) plants to root infection by five fungal isolates: three yellows-fragariae, one wilt-fragariae and one that is not pathogenic to strawberry. All Fof isolates had chromosome-level assemblies; three were newly generated. The two pathotypes triggered distinct host responses, especially among phytohormone-associated genes; yellows-fragariae isolates strongly induced jasmonic acid-associated genes, whereas the wilt-fragariae isolate primarily induced ethylene biosynthesis and signalling. The differentially expressed genes on fungal accessory chromosomes were almost entirely distinct between pathotypes. We identified an ~150 kbp 'pathogenicity island' that was horizontally transferred between wilt-fragariae strains. This predicted pathogenicity island was enriched with differentially expressed genes whose predicted functions were related to plant infection, and only one of these genes was also upregulated in planta by yellows-fragariae isolates. These results support the conclusion that wilt- and yellows-fragariae cause physiologically distinct syndromes by the expression of discrete repertoires of genes on accessory chromosomes.

The Developmental Delay of Seedlings With Cotyledons Only Confers Stress Tolerance to Suaeda aralocaspica (Chenopodiaceae) by Unique Performance on Morphology, Physiology, and Gene Expression

Cotyledons play an important role in seedling establishment, although they may just exist for a short time and become senescent upon the emergence of euphylla. So far, the detailed function of cotyledons has not been well understood. Suaeda aralocaspica is an annual halophyte distributed in cold deserts; its cotyledons could exist for a longer time, even last until maturity, and they must exert a unique function in seedling development. Therefore, in this study, we conducted a series of experiments to investigate the morphological and physiological performances of cotyledons under salt stress at different developmental stages. The results showed that the cotyledons kept growing slowly to maintain the normal physiological activities of seedlings by balancing phytohormone levels, accumulating osmoprotectants and antioxidants, and scavenging reactive oxygen species (ROS). Salt stress activated the expression of osmoprotectant-related genes and enhanced the accumulation of related primary metabolites. Furthermore, differentially expressed transcriptional profiles of the cotyledons were also analyzed by cDNA-AFLP to gain an understanding of cotyledons in response to development and salt stress, and the results revealed a progressive increase in the expression level of development-related genes, which accounted for a majority of the total tested TDFs. Meanwhile, key photosynthetic and important salt stress-related genes also actively responded. All these performances suggest that "big cotyledons" are experiencing a delayed but active developmental process, by which S. aralocaspica may survive the harsh condition of the seedling stage.

Changes in xylem morphology and activity of defense-related enzymes are associated with bean resistance during Fusarium oxysporum colonization

Genetic resistance is the main strategy to control Fusarium wilt in common bean. Despite this, few studies have focused on defense mechanisms involved in bean resistance to Fusarium oxysporum f. sp. phaseoli (Fop). Thus, the present study aimed to investigate the changes in xylem morphology and involvement of phenylpropanoid compounds and their biosynthetic enzymes in bean resistance against Fop. Uirapuru and UFSC-01 genotypes characterized, respectively, as susceptible and resistant were used. In roots and hypocotyls, guaiacol peroxidase (GPX), phenylalanine ammonia-lyase (PAL), and polyphenol oxidase (PPO) activities were determined at 0, 1, 2, 3, 4, 5, and 6 days after inoculation (dai), and flavonoids, total phenolics, and lignin content were quantified at 0, 3, and 6 dai. Cross sections of taproots and hypocotyls were examined under epifluorescence (at 1, 3, and 6 dai) and transmission electron (at 6 dai) microscopic to analyze the morphology of xylem cell walls. Overall, there was an increase in the activity of all studied enzymes in resistant bean plants, mainly during advanced colonization stages. Modifications in xylem morphology were more intense in roots of resistant genotype resulting in an increase of occluded cells, organelles, and cell wall strengthening. This study provides evidence that bean resistance is associated with increased phenylpropanoid enzymatic activity and cell wall reinforcement of some xylem cells.

Implication of plant growth-promoting rhizobacteria of Bacillus spp. as biocontrol agents against wilt disease caused by Fusarium oxysporum Schlecht. in Vicia faba L

Out of seven Fusarium spp. isolated from infected faba bean roots, two Fusarium oxysporum were selected and showed faba bean-wilt disease severity with percentages of 68% and 47% under greenhouse conditions. The F. oxysporum showed the highest wilt disease was selected to complete the current study. Three rhizobacterial strains were isolated and identified as Bacillus velezensis Vb1, B. paramycoides Vb3, and B. paramycoides Vb6. These strains showed the highest in-vitro antagonistic activity by the dual-culture method against selected F. oxysporum with inhibition percentages of 59±0.2, 46±0.3, and 52±0.3% for Vb1, Vb3, and Vb6, respectively. These rhizobacterial strains exhibit varied activity for nitrogen-fixing and phosphate-solubilizing. Moreover, these strains showed positive results for ammonia, HCN, and siderophores production. The phytohormones production (indole-3-acetic acid, ABA, benzyl, kinten, ziaten, and GA₃) and secretion of various lytic enzymes were recorded by these strains with varying degrees. Under greenhouse conditions, the rhizobacterial strains Vb1, Vb3, Vb6, and their consortium can protect faba bean from wilt caused by F. oxysporum with percentages of 70, 60, 65, and 82%, respectively. Under field conditions, the inoculation with the rhizobacterial consortium (Vb1+Vb3+Vb6) significantly increases the growth performance of the F. oxysporum-infected faba bean plant and recorded the highest wilt protection (83.3%).

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.

A methyl esterase 1 (PvMES1) promotes the salicylic acid pathway and enhances Fusarium wilt resistance in common beans

Methyl esterase (MES), PvMES1, contributes to the defense response toward Fusarium wilt in common beans by regulating the salicylic acid (SA) mediated signaling pathway from phenylpropanoid synthesis and sugar metabolism as well as others. Common bean (Phaseolus vulgaris L.) is an important food legume. Fusarium wilt caused by Fusarium oxysporum f. sp. phaseoli is one of the most serious soil-borne diseases of common bean found throughout the world and affects the yield and quality of the crop. Few sources of Fusarium wilt resistance exist in legumes and most are of quantitative inheritance. In this study, we have identified a methyl esterase (MES), PvMES1, that contributes to plant defense response by regulating the salicylic acid (SA) mediated signaling pathway in response to Fusarium wilt in common beans. The result showed the role of PvMES1 in regulating SA levels in common bean and thus the SA signaling pathway and defense response mechanism in the plant. Overexpression of the PvMES1 gene enhanced Fusarium wilt resistance; while silencing of the gene caused susceptibility to the diseases. RNA-seq analysis with these transiently modified plants showed that genes related to SA level changes included the following gene ontologies: (a) phenylpropanoid synthesis; (b) sugar metabolism; and (c) interaction between host and pathogen as well as others. These key signal elements activated the defense response pathway in common bean to Fusarium wilt. Collectively, our findings indicate that PvMES1 plays a pivotal role in regulating SA biosynthesis and signaling, and increasing Fusarium wilt resistance in common bean, thus providing novel insight into the practical applications of both SA and MES genes and pathways they contribute to for developing elite crop varieties with enhanced broad-spectrum resistance to this critical disease.

Salicylic acid and nitric oxide cross-talks to improve innate immunity and plant vigor in tomato against Fusarium oxysporum stress

Foliar application of SA cross-talks and induce endogenous nitric oxide and reactive oxygen species to improve innate immunity and vigor of tomato plant against Fusarium oxysporum stress. The present investigation was aimed to demonstrate the efficacy of salicylic acid (SA), as a powerful elicitor or plant growth regulator (PGR) and its cross-talk with nitric oxide (NO) in tomato against the biotic stress caused by wilt pathogen, Fusarium oxysporum f. sp. lycopersici. Different defense-related enzymes and gene expression, phenol, flavonoid, and phenolic acid content along with NO generation and other physiological characters have been estimated after foliar application of SA. Total chlorophyll content was steadily maintained and the amount of death of cells was negligible after 72 h of SA treatment. Significant reduction of disease incidence was also recorded in SA treated sets. Simultaneously, NO generation was drastically improved at this stage, which has been justified by both spectrophotometrically and microscopically. A direct correlation between reactive oxygen species (ROS) generation and NO has been established. Production of defense enzymes, gene expressions, different phenolic acids was positively influenced by SA treatment. However, tomato plants treated with SA along with NO synthase (NOS) inhibitor or NO scavenger significantly reduce all those parameters tested. On the other hand, NO donor-treated plants showed the same inductive effect like SA. Furthermore, SA treated seeds of tomato also showed improved physiological parameters like higher seedling vigor index, shoot and root length, mean trichome density, etc. It is speculated that the cross-talk between SA and endogenous NO have tremendous ability to improve defense responses and growth of the tomato plant. It can be utilized in future sustainable agriculture for bimodal action.

Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean

Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop's resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.

Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana

BACKGROUND

Banana plant height is an important trait for horticultural practices and semi-dwarf cultivars show better resistance to damages by wind and rain. However, the molecular mechanisms controlling the pseudostem height remain poorly understood. Herein, we studied the molecular changes in the pseudostem of a semi-dwarf banana mutant Aifen No. 1 (Musa spp. Pisang Awak sub-group ABB) as compared to its wild-type dwarf cultivar using a combined transcriptome and metabolome approach.

RESULTS

A total of 127 differentially expressed genes and 48 differentially accumulated metabolites were detected between the mutant and its wild type. Metabolites belonging to amino acid and its derivatives, flavonoids, lignans, coumarins, organic acids, and phenolic acids were up-regulated in the mutant. The transcriptome analysis showed the differential regulation of genes related to the gibberellin pathway, auxin transport, cell elongation, and cell wall modification. Based on the regulation of gibberellin and associated pathway-related genes, we discussed the involvement of gibberellins in pseudostem elongation in the mutant banana. Genes and metabolites associated with cell wall were explored and their involvement in cell extension is discussed.

CONCLUSIONS

The results suggest that gibberellins and associated pathways are possibly developing the observed semi-dwarf pseudostem phenotype together with cell elongation and cell wall modification. The findings increase the understanding of the mechanisms underlying banana stem height and provide new clues for further dissection of specific gene functions.

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

Fusarium wilt is a destructive soil-borne disease that threatens the production of mung bean. Mung bean lines Zheng8-4 and Zheng8-20 show high resistance and high susceptibility to Fusarium wilt, respectively. Transcriptome analysis was carried out to identify candidate genes involved in Fusarium wilt resistance using Zheng8-4 and Zheng8-20 at 0, 0.5, 1, 2, and 4 days post inoculation (dpi). Differential expression analysis showed that 3,254 genes responded to pathogen infection and were differentially expressed in the resistant and susceptible lines. Weighted gene co-expression network analysis (WGCNA) was also performed to identify five modules highly correlated with Fusarium wilt resistance, in which 453 differentially expressed genes (DEGs) were considered likely to be involved in Fusarium wilt resistance. Among these DEGs, we found 24 genes encoding resistance (R) proteins, 22 encoding protein kinases, 20 belonging to transcription factor families, 34 encoding proteins with oxidoreductase activity, 17 involved in stimulation/stress responses, and 54 annotated to pathogen resistance-related pathways. Finally, 27 annotated genes were further selected as candidate genes of Fusarium wilt resistance in mung bean. This study identifies novel potential resistance-related genes against Fusarium wilt and provides a theoretical basis for further investigation of Fusarium wilt resistance in mung bean breeding.

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.

Redox status regulation and action of extra- and intravascular defense mechanisms are associated with bean resistance against Fusarium oxysporum f. sp. phaseoli

Genetic resistance is the main strategy to control one of the most destructive diseases of common bean (Phaseolus vulgaris L), i.e., the Fusarium wilt caused by Fusarium oxysporum f. sp. phaseoli (Fop). However, little is known on host defense reactions in Fop-bean interaction. Thus, this work examined the defense mechanisms in root and hypocotyl tissues of common bean against Fop. Resistant and susceptible bean plants were inoculated by dipping their roots in a conidial suspension. Cross sections of roots and hypocotyls were observed in light microscopy at 1, 3, 6, and 9 days after inoculation (dai) to monitor Fop colonization, and at 3 and 9 dai to detect callose, carbohydrates, lipids, phenolics, and protein, and under electronic microscopy at 9 dai to observe ultrastructural changes in xylem cells. The content of hydrogen peroxide (H₂O₂), lipid peroxidation, and activity of the antioxidant enzymes ascorbate peroxidase (EC 1.11.1.11) and catalase (EC 1.11.1.6) were monitored spectrophotometrically in roots and hypocotyls at 0, 1, 3, 6, and 9 dai. Fop colonized inter- and intracellularly the epidermis and cortex reaching the xylem vessels faster in susceptible genotype. Fop inoculation induced phenolics and carbohydrates accumulation, callose deposition, and formation of occlusion material inside xylem vessels mainly in resistant genotype. Lipid peroxidation occurred mainly in susceptible plants. In contrast, the antioxidant enzymes seem to have contributed to reducing damage caused by H₂O₂ accumulation in resistant plants. This study gives evidences that inter- and intracellular physicochemical mechanisms can act together to delay Fop colonization in resistant plants.

Natural Variation in Portuguese Common Bean Germplasm Reveals New Sources of Resistance Against Fusarium oxysporum f. sp. phaseoli and Resistance-Associated Candidate Genes

Common bean (Phaseolus vulgaris) is one of the most consumed legume crops in the world, and Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. phaseoli, is one of the major diseases affecting its production. Portugal holds a very promising common bean germplasm with an admixed genetic background that may reveal novel genetic resistance combinations between the original Andean and Mesoamerican gene pools. To identify new sources of Fusarium wilt resistance and detect resistance-associated single-nucleotide polymorphisms (SNPs), we explored, for the first time, a diverse collection of the underused Portuguese common bean germplasm by using genome-wide association analyses. The collection was evaluated for Fusarium wilt resistance under growth chamber conditions, with the highly virulent F. oxysporum f. sp. phaseoli strain FOP-SP1 race 6. Fourteen of the 162 Portuguese accessions evaluated were highly resistant and 71 intermediate. The same collection was genotyped with DNA sequencing arrays, and SNP-resistance associations were tested via a mixed linear model accounting for the genetic relatedness between accessions. The results from the association mapping revealed nine SNPs associated with resistance on chromosomes Pv04, Pv05, Pv07, and Pv08, indicating that Fusarium wilt resistance is under oligogenic control. Putative candidate genes related to phytoalexin biosynthesis, hypersensitive response, and plant primary metabolism were identified. The results reported here highlight the importance of exploring underused germplasm for new sources of resistance and provide new genomic targets for the development of functional markers to support selection in future disease resistance breeding programs.

Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) is a major legume and is frequently attacked by fungal pathogens, including Fusarium solani f. sp. phaseoli (FSP), which cause Fusarium root rot. FSP substantially reduces common bean yields across the world, including China, but little is known about how common bean plants defend themselves against this fungal pathogen. In the current study, we combined next-generation RNA sequencing and metabolomics techniques to investigate the changes in gene expression and metabolomic processes in common bean infected with FSP. There were 29,722 differentially regulated genes and 300 differentially regulated metabolites between control and infected plants. The combined omics approach revealed that FSP is perceived by PAMP-triggered immunity and effector-triggered immunity. Infected seedlings showed that common bean responded by cell wall modification, ROS generation, and a synergistic hormone-driven defense response. Further analysis showed that FSP induced energy metabolism, nitrogen mobilization, accumulation of sugars, and arginine and proline metabolism. Importantly, metabolic pathways were most significantly enriched, which resulted in increased levels of metabolites that were involved in the plant defense response. A correspondence between the transcript pattern and metabolite profile was observed in the discussed pathways. The combined omics approach enhances our understanding of the less explored pathosystem and will provide clues for the development of common bean cultivars' resistant to FSP.

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.

Differential responses of molecular mechanisms and physiochemical characters in wild and cultivated soybeans against invasion by the pathogenic Fusarium oxysporum Schltdl

Cultivated soybean (Glycine max) was derived from the wild soybean (Glycine soja), which has genetic resources that can be critically important for improving plant stress resistance. However, little information is available pertaining to the molecular and physiochemical comparison between the cultivated and wild soybeans in response to the pathogenic Fusarium oxysporum Schltdl. In this study, we first used comparative phenotypic and paraffin section analyses to indicate that wild soybean is indeed more resistant to F. oxysporum than cultivated soybean. Genome-wide RNA-sequencing approach was then used to elucidate the genetic mechanisms underlying the differential physiological and biochemical responses of the cultivated soybean, and its relative, to F. oxysporum. A greater number of genes related to cell wall synthesis and hormone metabolism were significantly altered in wild soybean than in cultivated soybean under F. oxysporum infection. Accordingly, a higher accumulation of lignins was observed in wild soybean than cultivated soybean under F. oxysporum infection. Collectively, these results indicated that secondary metabolites and plant hormones may play a vital role in differentiating the response between cultivated and wild soybeans against the pathogen. These important findings may provide future direction to breeding programs to improve resistance to F. oxysporum in the elite soybean cultivars by taking advantage of the genetic resources within wild soybean germplasm.

Hairy root transgene expression analysis of a secretory peroxidase (PvPOX1) from common bean infected by Fusarium wilt

Plant peroxidases (POXs) are one of the most important redox enzymes in the defense responses. However, the large number of different plant POX genes makes it necessary to carefully confirm the function of each paralogous POX gene in specific tissues and disease interactions. Fusarium wilt is a devastating disease of common bean caused by Fusarium oxysporum f. sp. phaseoli. In this study, we evaluated a peroxidase gene, PvPOX1, from a resistant common bean genotype, CAAS260205 and provided direct evidence for PvPOX1's role in resistance by transforming the resistant allele into a susceptible common bean genotype, BRB130, via hairy root transformation using Agrobacterium rhizogenes. Analysis of PvPOX1 gene over-expressing hairy roots showed it increased resistance to Fusarium wilt both in the roots and the rest of transgenic plants. Meanwhile, the PvPOX1 expressive level, the peroxidase activity and hydrogen peroxide (H₂O₂) accumulation were also enhanced in the interaction. The result showed that the PvPOX1 gene played an essential role in Fusarium wilt resistance through the occurrence of reactive oxygen species (ROS) induced hypersensitive response. Therefore, PvPOX1 expression was proven to be a valuable gene for further analysis which can strengthen host defense response against Fusarium wilt through a ROS activated resistance mechanism.

Fine Mapping of Ur-3, a Historically Important Rust Resistance Locus in Common Bean

Bean rust, caused by Uromyces appendiculatus, is a devastating disease of common bean (Phaseolus vulgaris) in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome other rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker-assisted selection produce false results. Here, we describe the fine mapping of the Ur-3 locus for the development of highly accurate markers linked to Ur-3 An F2 population from the cross Pinto 114 (susceptible) × Aurora (resistant with Ur-3) was evaluated for its reaction to four different races of U. appendiculatus A bulked segregant analysis using the SNP chip BARCBEAN6K_3 placed the approximate location of Ur-3 in the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean varieties positioned Ur-3 in a 46.5 kb genomic region from 46.96 to 47.01 Mb on Pv11. We discovered in this region the SS68 KASP marker that was tightly linked to Ur-3 Validation of SS68 on a panel of 130 diverse common bean cultivars containing all known rust resistance genes revealed that SS68 was highly accurate and produced no false results. The SS68 marker will be of great value in pyramiding Ur-3 with other rust resistance genes. It will also significantly reduce time and labor associated with the current phenotypic detection of Ur-3 This is the first utilization of fine mapping to discover markers linked to rust resistance in common bean.

Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

BACKGROUND

Pathogenic members of the Fusarium oxysporum species complex are responsible for vascular wilt disease on many important crops including legumes, where they can be one of the most destructive disease causing necrotrophic fungi. We previously developed a model legume-infecting pathosystem based on the reference legume Medicago truncatula and a pathogenic F. oxysporum forma specialis (f. sp.) medicaginis (Fom). To dissect the molecular pathogenicity arsenal used by this root-infecting pathogen, we sequenced its transcriptome during infection of a susceptible and resistant host accession.

RESULTS

High coverage RNA-Seq of Fom infected root samples harvested from susceptible (DZA315) or resistant (A17) M. truncatula seedlings at early or later stages of infection (2 or 7 days post infection (dpi)) and from vegetative (in vitro) samples facilitated the identification of unique and overlapping sets of in planta differentially expressed genes. This included enrichment, particularly in DZA315 in planta up-regulated datasets, for proteins associated with sugar, protein and plant cell wall metabolism, membrane transport, nutrient uptake and oxidative processes. Genes encoding effector-like proteins were identified, including homologues of the F. oxysporum f. sp. lycopersici Secreted In Xylem (SIX) proteins, and several novel candidate effectors based on predicted secretion, small protein size and high in-planta induced expression. The majority of the effector candidates contain no known protein domains but do share high similarity to predicted proteins predominantly from other F. oxysporum ff. spp. as well as other Fusaria (F. solani, F. fujikori, F. verticilloides, F. graminearum and F. pseudograminearum), and from another wilt pathogen of the same class, a Verticillium species. Overall, this suggests these novel effector candidates may play important roles in Fusaria and wilt pathogen virulence.

CONCLUSION

Combining high coverage in planta RNA-Seq with knowledge of fungal pathogenicity protein features facilitated the identification of differentially expressed pathogenicity associated genes and novel effector candidates expressed during infection of a resistant or susceptible M. truncatula host. The knowledge from this first in depth in planta transcriptome sequencing of any F. oxysporum ff. spp. pathogenic on legumes will facilitate the dissection of Fusarium wilt pathogenicity mechanisms on many important legume crops.

Comparative Transcriptome Analysis of Resistant and Susceptible Common Bean Genotypes in Response to Soybean Cyst Nematode Infection

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) reproduces on the roots of common bean (Phaseolus vulgaris L.) and can cause reductions in plant growth and seed yield. The molecular changes in common bean roots caused by SCN infection are unknown. Identification of genetic factors associated with SCN resistance could help in development of improved bean varieties with high SCN resistance. Gene expression profiling was conducted on common bean roots infected by SCN HG type 0 using next generation RNA sequencing technology. Two pinto bean genotypes, PI533561 and GTS-900, resistant and susceptible to SCN infection, respectively, were used as RNA sources eight days post inoculation. Total reads generated ranged between ~ 3.2 and 5.7 million per library and were mapped to the common bean reference genome. Approximately 70-90% of filtered RNA-seq reads uniquely mapped to the reference genome. In the inoculated roots of resistant genotype PI533561, a total of 353 genes were differentially expressed with 154 up-regulated genes and 199 down-regulated genes when compared to the transcriptome of non- inoculated roots. On the other hand, 990 genes were differentially expressed in SCN-inoculated roots of susceptible genotype GTS-900 with 406 up-regulated and 584 down-regulated genes when compared to non-inoculated roots. Genes encoding nucleotide-binding site leucine-rich repeat resistance (NLR) proteins, WRKY transcription factors, pathogenesis-related (PR) proteins and heat shock proteins involved in diverse biological processes were differentially expressed in both resistant and susceptible genotypes. Overall, suppression of the photosystem was observed in both the responses. Furthermore, RNA-seq results were validated through quantitative real time PCR. This is the first report describing genes/transcripts involved in SCN-common bean interaction and the results will have important implications for further characterization of SCN resistance genes in common bean.

Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview

The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term “Next-Generation Sequencing (NGS)” with another less confusing synonym such as “RNA-seq”, “high throughput sequencing”, or “massively parallel sequencing” to avoid confusion with any future sequencing technologies.

Jasmonate Signalling and Defence Responses in the Model Legume Medicago truncatula-A Focus on Responses to Fusarium Wilt Disease

Jasmonate (JA)-mediated defences play important roles in host responses to pathogen attack, in particular to necrotrophic fungal pathogens that kill host cells in order to extract nutrients and live off the dead plant tissue. The root-infecting fungal pathogen Fusarium oxysporum initiates a necrotrophic growth phase towards the later stages of its lifecycle and is responsible for devastating Fusarium wilt disease on numerous legume crops worldwide. Here we describe the use of the model legume Medicago truncatula to study legume-F. oxysporum interactions and compare and contrast this against knowledge from other model pathosystems, in particular Arabidopsis thaliana-F. oxysporum interactions. We describe publically-available genomic, transcriptomic and genetic (mutant) resources developed in M. truncatula that enable dissection of host jasmonate responses and apply aspects of these herein during the M. truncatula--F. oxysporum interaction. Our initial results suggest not all components of JA-responses observed in M. truncatula are shared with Arabidopsis in response to F. oxysporum infection.