Genomic localization of tomato genes that control a hypersensitive reaction to Xanthomonas campestris pv. vesicatoria (Doidge) dye

The LeEIX Locus Determines Pathogen Resistance in Tomato

The mechanisms underlying the ability of plants to differentiate between pathogens and commensals in their environment are currently unresolved. It has been suggested that spatiotemporal regulation of pattern-recognition receptor (PRR) content could be one of the components providing plants with the ability to distinguish between pathogens and nonpathogenic microbes. The LeEIX PRRs recognize xylanases derived from beneficial or commensal plant colonizers of Trichoderma species, including the xylanase known as EIX. Here, we investigated possible general roles of PRRs from the LeEIX locus in immunity and pathogen resistance in tomato. Mutating the inhibitory PRR LeEIX1, or overexpressing the activating PRR LeEIX2, resulted in resistance to a wide range of pathogens and increased basal and elicited immunity. LeEIX1 knockout caused increases in the expression level of several tested PRRs, including FLS2, as well as bacterial pathogen resistance coupled with an increase in flg22-mediated immunity. The wild tomato relative Solanum pennellii contains inactive LeEIX PRR variants. S. pennellii does not respond to elicitation with the LeEIX PRR ligand EIX. Given that EIX is derived from a mostly nonpathogenic microbe, the connection of its PRRs to disease resistance has not previously been investigated directly. Here, we observed that compared with S. lycopersicum cultivar M82, S. pennellii was more sensitive to several fungal and bacterial pathogens. Our results suggest that the LeEIX locus might determine resistance to fungal necrotrophs, whereas the resistance to biotrophs is effected in combination with a gene/quantitative trait locus not within the LeEIX locus.

Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441

Late blight (LB), caused by the oomycete Phytophthora infestans, is one of the most destructive diseases of the cultivated tomato (Solanum lycopersicum L.) and potato (Solanum tuberosum L.) worldwide. Genetic changes in the pathogen have resulted in the emergence of new genotypes, overcoming formerly effective fungicides or host resistance genes. We previously reported the identification of a LB-resistant accession (PI 270441) of the wild tomato species S. pimpinellifolium L. and the high heritability of its resistance. In the present study, an F₂ population (n = 1,209), derived from a cross between PI 270441 and a LB-susceptible tomato breeding line (Fla. 8059), was screened for response to LB infection. Extreme resistant (n = 44) and susceptible (n = 39) F₂ individuals were selected and used in a trait-based marker analysis (TBA; a.k.a selective genotyping) to identify and map quantitative trait loci (QTLs) conferring LB resistance. Reduced representation libraries (RRLs) of Fla. 8059 and PI 270441 were constructed, sequenced, and mapped to the tomato genome. A total of 13,054 single-nucleotide polymorphisms (SNPs) were identified, of which, 200 were used to construct a genetic linkage map and locate QTLs. Four LB resistance QTLs were identified on chromosomes 1, 10, and 11 of PI 270441. The markers associated with these QTLs can be used to transfer LB resistance from PI 270441 into new tomato cultivars and to develop near-isogenic lines for fine mapping of the QTL.

Mapping and characterization of the Rx3 gene for resistance to Xanthomonas euvesicatoria pv. euvesicatoria race T1 in tomato

Rx3 encodes a typical CC-NBS-LRR resistance protein and confers the resistance to Xanthomonas euvesicatoria pv. euvesicatoria race T1 causing bacterial spot in tomato. Bacterial spot caused by at least four species of Xanthomonas is an epidemic disease severely affecting tomato production worldwide. The use of resistant cultivars is an economical and effective approach to control the disease. An unimproved tomato breeding line Hawaii 7988 has been considered as the most reliable source for resistance to X. euvesicatoria pv. euvesicatoria race T1, and the Rx3 locus located at a 4.53-Mb region on chromosome 5 (SL4.0) is the major locus for resistance to race T1 in this line. In the current study, the Rx3 locus was firstly located to a 1.05-Mb region based on comparisons of marker polymorphisms between the susceptible line Ohio 88119 and resistant lines Hawaii 7998, Ohio 9834 and FG02-7530. Using recombinant inbred lines (F_5:6, F_6:7, and F_7:8) derived from a cross between Ohio 88119 and Ohio 9834, the Rx3 locus was finally mapped to a 64.3-kb interval between markers MG-Rx3-4 and MG-Rx3-A6. The Solyc05g053980 gene, designated as Rx3, encoding a coiled-coil nucleotide-binding leucine-rich repeat protein was considered as the candidate for the Rx3 locus. Expression of the gene could be induced by the infection of race T1 strain. Knockout of the Solyc05g053980 gene through CRISPR/Cas9 editing system in the resistant line FG02-7530 decreased resistance to race T1 strain. These results provide a close step for understanding the resistance mechanism to race T1 in Hawaii 7998 and guide tomato breeders accordingly to improve bacterial spot disease resistance in tomato.

A centenary for bacterial spot of tomato and pepper

DISEASE SYMPTOMS

Symptoms include water-soaked areas surrounded by chlorosis turning into necrotic spots on all aerial parts of plants. On tomato fruits, small, water-soaked, or slightly raised pale-green spots with greenish-white halos are formed, ultimately becoming dark brown and slightly sunken with a scabby or wart-like surface.

HOST RANGE

Main and economically important hosts include different types of tomatoes and peppers. Alternative solanaceous and nonsolanaceous hosts include Datura spp., Hyoscyamus spp., Lycium spp., Nicotiana rustica, Physalis spp., Solanum spp., Amaranthus lividus, Emilia fosbergii, Euphorbia heterophylla, Nicandra physaloides, Physalis pubescens, Sida glomerata, and Solanum americanum.

TAXONOMIC STATUS OF THE PATHOGEN

Domain, Bacteria; phylum, Proteobacteria; class, Gammaproteobacteria; order, Xanthomonadales; family, Xanthomonadaceae; genus, Xanthomonas; species, X. euvesicatoria, X. hortorum, X. vesicatoria.

SYNONYMS (NONPREFERRED SCIENTIFIC NAMES)

Bacterium exitiosum, Bacterium vesicatorium, Phytomonas exitiosa, Phytomonas vesicatoria, Pseudomonas exitiosa, Pseudomonas gardneri, Pseudomonas vesicatoria, Xanthomonas axonopodis pv. vesicatoria, Xanthomonas campestris pv. vesicatoria, Xanthomonas cynarae pv. gardneri, Xanthomonas gardneri, Xanthomonas perforans.

MICROBIOLOGICAL PROPERTIES

Colonies are gram-negative, oxidase-negative, and catalase-positive and have oxidative metabolism. Pale-yellow domed circular colonies of 1-2 mm in diameter grow on general culture media.

DISTRIBUTION

The bacteria are widespread in Africa, Brazil, Canada and the USA, Australia, eastern Europe, and south-east Asia. Occurrence in western Europe is restricted.

PHYTOSANITARY CATEGORIZATION

A2 no. 157, EU Annex designation II/A2.

EPPO CODES

XANTEU, XANTGA, XANTPF, XANTVE.

Epidemiology, diversity, and management of bacterial spot of tomato caused by Xanthomonas perforans

Tomato is an important crop grown worldwide. Various plant diseases cause massive losses in tomato plants due to diverse biotic agents. Bacterial spot of tomato (BST) is a worldwide disease that results in high losses in processed and fresh tomato. Xanthomonas perforans, an aerobic, single-flagellated, rod-shaped, Gram-negative plant pathogenic bacterium, is one of the leading causes of BST. Over the past three decades, X. perforans has increasingly been reported from tomato-growing regions and became a major bacterial disease. X. perforans thrives under high humidity and high temperature, which is commonplace in tropical and subtropical climates. Distinguishing symptoms of BST are necrotic lesions that can coalesce and cause a shot-hole appearance. X. perforans can occasionally cause fruit symptoms depending on disease pressure during fruit development. Short-distance movement in the field is mainly dependent on wind-driven rain, whereas long distance movement occurs through contaminated seed or plant material. X. perforans harbors a suite of effectors that increase pathogen virulence, fitness, and dissemination. BST management mainly relies on copper-based compounds; however, resistance is widespread. Alternative compounds, such as nanomaterials, are currently being evaluated and show high potential for BST management. Resistance breeding remains difficult to attain due to limited resistant germplasm. While the increased genetic diversity and gain and loss of effectors in X. perforans limits the success of single-gene resistance, the adoption of effector-specific transgenes and quantitative resistance may lead to durable host resistance. However, further research that aims to more effectively implement novel management tools is required to curb disease spread. KEY POINTS: • Xanthomonas perforans causes bacterial spot on tomato epidemics through infected seedlings and movement of plant material. • Genetic diversity plays a major role in shaping populations which is evident in loss and gain of effectors. • Management relies on copper sprays, but nanoparticles are a promising alternative to reduce copper toxicity.

Development and Application of Gene-Specific Markers for Tomato Yellow Leaf Curl Virus Resistance in Both Field and Artificial Infections

Tomato yellow leaf curl virus (TYLCV) is a disease that is damaging to tomato production worldwide. Resistance to TYLCV has been intensively investigated, and single resistance genes such as Ty-1 have been widely deployed in breeding programs. However, resistance-breaking incidences are frequently reported, and achieving durable resistance against TYLCV in the field is important. In this study, gene-specific markers for Ty-2 and ty-5, and closely-linked markers for Ty-4 were developed and applied to distinguish TYLCV resistance in various tomato genotypes. Quantitative infectivity assays using both natural infection in the field and artificial inoculation utilizing infectious TYLCV clones in a growth chamber were optimized and performed to investigate the individual and cumulative levels of resistance. We confirmed that Ty-2 could also be an effective source of resistance for TYLCV control, together with Ty-1. Improvement of resistance as a result of gene-pyramiding was speculated, and breeding lines including both Ty-1 and Ty-2 showed the strongest resistance in both field and artificial infections.

Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4

Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato and is caused by multiple species of Xanthomonas. We performed the RNA sequencing (RNA-Seq) analysis of three tomato lines with different levels of resistance to Xanthomonas perforans race T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations. Analysis between inoculated and control samples revealed that resistant genotype Solanum pimpinellifolium accession PI 270443 had more DEGs (834), followed by susceptible genotype tomato (S. lycopersicum L) breeding line NC 714 (373), and intermediate genotype tomato breeding line NC 1CELBR (154). Gene ontology (GO) terms revealed that more GO terms (51) were enriched for upregulated DEGs in the resistant genotype PI 270443, and more downregulated DEGs (67) were enriched in the susceptible genotype NC 714. DEGs in the biotic stress pathway showed more upregulated biotic stress pathway DEGs (67) for PI 270443 compared to more downregulated DEGs (125) for the susceptible NC 714 genotype. Resistant genotype PI 270443 has three upregulated DEGs for pathogenesis-related (PR) proteins, and susceptible genotype NC 714 has one downregulated R gene. Sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chr11, which has multiple reported resistance quantitative trait loci (QTLs) to BS race T4, is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR resistance proteins with sequence variation between the resistant and susceptible tomato lines were near the known Rx4 resistance gene on chr11, and additional biotic stress associated DEGs near to the known Rx4 resistance gene were also identified from the susceptible NC 714 line.

Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato (Solanum lycopersicum L.)

Bacterial spot is a serious disease of tomato caused by at least four species of Xanthomonas. These include X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (races T3 and T4), and X. gardneri, with the distinct geographical distribution of each group. Currently, X. gardneri and X. perforans are two major bacterial pathogens of tomato in North America, with X. perforans (race T4) dominating in east-coast while X. gardneri dominating in the Midwest. The disease causes up to 66% yield loss. Management of this disease is challenging due to the lack of useful chemical control measures and commercial resistant cultivars. Although major genes for resistance (R) and quantitative resistance have been identified, breeding tomato for resistance to bacterial spot has been impeded by multiple factors including the emergence of new races of the pathogen that overcome the resistance, multigenic control of the resistance, linkage drag, non-additive components of the resistance and a low correlation between seedling assays and field resistance. Transgenic tomato with Bs2 and EFR genes was effective against multiple races of Xanthomonas. However, it has not been commercialized because of public concerns and complex regulatory processes. The genomics-assisted breeding, effectors-based genomics breeding, and genome editing technology could be novel approaches to achieve durable resistance to bacterial spot in tomato. The main goal of this paper is to understand the current status of bacterial spot of tomato including its distribution and pathogen diversity, challenges in disease management, disease resistance sources, resistance genetics and breeding, and future prospectives with novel breeding approaches.

Evaluating Quantitative Trait Locus Resistance in Tomato to Multiple Xanthomonas spp

Bacterial spot of tomato is a foliar disease caused by four Xanthomonas species. Identifying genetic resistance in wild tomatoes and subsequent breeding of varieties has been a strategy to reduce the loss from this disease because control using pesticides has been ineffective. Three independent sources of resistance have been identified with quantitative trait loci (QTL) mapping to the centromeric region on chromosome 11. These sources are derived from Hawaii 7998 (QTL-11A), PI 114490 (QTL-11B), and LA2533 (QTL-11C). To determine which QTL introgression from chromosome 11 provides the greatest resistance to multiple species, we developed near-isogenic lines (NILs) using marker-assisted backcrossing. In parallel, we developed an NIL that contains Rx-4/Xv3, which provides major gene resistance to Xanthomonas perforans. Additionally, we combined Rx-4/Xv3 resistance with QTL-11A. These sources of resistance were independently introduced into the susceptible parent, OH88119. During a 3-year period from 2016 to 2018, we evaluated backcross-derived families and NILs from each source in independent field trials inoculated with X. perforans, X. euvesicatoria, or X. gardneri. Our results suggest that both QTL-11C and QTL-11A combined with Rx-4/Xv3 provide effective genetic resistance against multiple Xanthomonas species. In addition, we provide evidence for additive to dominant genetic action for the QTL introgressions.

Progress in Developing Bacterial Spot Resistance in Tomato

Bacterial spot (BS), caused by four species of Xanthomonas: X. euvesicatoria, X. vesicatoria, X. perforans and X. gardneri in tomato (Solanum lycopersicum L.) results in severe loss in yield and quality by defoliation and the appearance of lesions on fruits, respectively. The combined industry standard for BS control (foliar applications Actigard® rotated with copper plus mancozeb) does not offer sufficient protection, especially when weather conditions favor disease spread. Development of tomato cultivars with BS resistance is thus an important measure to minimize losses. Hypersensitive and non-hypersensitive resistance has been identified in different wild accessions and cultivated tomato relatives and has been transferred to cultivated tomato. However, complete resistance is yet to be obtained. With the advent of next generation sequencing and precise genome editing tools, the genetic regions that confer resistance to bacterial spot can be targeted and enriched through gene pyramiding in a new commercial cultivar which may confer higher degree of horizontal resistance to multiple strains of Xanthomonas causing bacterial spot in tomato.

Using forward genetics in Nicotiana benthamiana to uncover the immune signaling pathway mediating recognition of the Xanthomonas perforans effector XopJ4

The immune pathway responsible for perception of the Xanthomonas perforans effector XopJ4 was identified in the plant Nicotiana benthamiana. This pathogen causes significant yield loss in commercial tomato cultivation. Genetic mapping and viral-induced gene silencing were used to identify immune signaling components of the XopJ4 perception pathway in N. benthamiana. Transient complementation assays were performed to determine the functionality of gene variants and co-immunoprecipitation assays were used to gain insight into the molecular mechanism of the pathway. Two N. benthamiana ethyl methanesulfonate (EMS) mutants deficient for XopJ4 perception were identified as having loss-of-function mutations in the gene encoding the nucleotide binding, leucine-rich repeat (NLR) protein NbZAR1. Silencing of a receptor-like cytoplasmic kinase family XII gene, subsequently named XOPJ4 IMMUNITY 2 (JIM2), blocks perception of XopJ4. This study demonstrates the feasibility of conducting mutant screens in N. benthamiana to investigate the genetic basis of the plant immune system and other processes. The identification of NbZAR1 and JIM2 as mediating XopJ4 perception in N. benthamiana supports the model of ZAR1 being involved in the perception of many different pathogen effector proteins with specificity dictated by associated receptor-like cytoplasmic kinases.

Comparison of Marker-Based Genomic Estimated Breeding Values and Phenotypic Evaluation for Selection of Bacterial Spot Resistance in Tomato

Bacterial spot affects tomato crops (Solanum lycopersicum) grown under humid conditions. Major genes and quantitative trait loci (QTL) for resistance have been described, and multiple loci from diverse sources need to be combined to improve disease control. We investigated genomic selection (GS) prediction models for resistance to Xanthomonas euvesicatoria and experimentally evaluated the accuracy of these models. The training population consisted of 109 families combining resistance from four sources and directionally selected from a population of 1,100 individuals. The families were evaluated on a plot basis in replicated inoculated trials and genotyped with single nucleotide polymorphisms (SNP). We compared the prediction ability of models developed with 14 to 387 SNP. Genomic estimated breeding values (GEBV) were derived using Bayesian least absolute shrinkage and selection operator regression (BL) and ridge regression (RR). Evaluations were based on leave-one-out cross validation and on empirical observations in replicated field trials using the next generation of inbred progeny and a hybrid population resulting from selections in the training population. Prediction ability was evaluated based on correlations between GEBV and phenotypes (r_g), percentage of coselection between genomic and phenotypic selection, and relative efficiency of selection (r_g/r_p). Results were similar with BL and RR models. Models using only markers previously identified as significantly associated with resistance but weighted based on GEBV and mixed models with markers associated with resistance treated as fixed effects and markers distributed in the genome treated as random effects offered greater accuracy and a high percentage of coselection. The accuracy of these models to predict the performance of progeny and hybrids exceeded the accuracy of phenotypic selection.

YopJ Family Effectors Promote Bacterial Infection through a Unique Acetyltransferase Activity

Gram-negative bacterial pathogens rely on the type III secretion system to inject virulence proteins into host cells. These type III secreted "effector" proteins directly manipulate cellular processes to cause disease. Although the effector repertoires in different bacterial species are highly variable, the Yersinia outer protein J (YopJ) effector family is unique in that its members are produced by diverse animal and plant pathogens as well as a nonpathogenic microsymbiont. All YopJ family effectors share a conserved catalytic triad that is identical to that of the C55 family of cysteine proteases. However, an accumulating body of evidence demonstrates that many YopJ effectors modify their target proteins in hosts by acetylating specific serine, threonine, and/or lysine residues. This unique acetyltransferase activity allows the YopJ family effectors to affect the function and/or stability of their targets, thereby dampening innate immunity. Here, we summarize the current understanding of this prevalent and evolutionarily conserved type III effector family by describing their enzymatic activities and virulence functions in animals and plants. In particular, the molecular mechanisms by which representative YopJ family effectors subvert host immunity through posttranslational modification of their target proteins are discussed.

Association Analysis for Bacterial Spot Resistance in a Directionally Selected Complex Breeding Population of Tomato

Bacterial spot of tomato is caused by at least four species of Xanthomonas with multiple physiological races. We developed a complex breeding population for simultaneous discovery of marker-trait linkage, validation of existing quantitative trait loci (QTL), and pyramiding of resistance. Six advanced accessions with resistance from distinct sources were crossed in all combinations and their F1 hybrids were intercrossed. Over 1,100 segregating progeny were evaluated in the field following inoculation with X. euvesicatoria race T1 strains. We selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicated field trials inoculated with T1 and T3 (X. perforans) strains. The estimated heritability of T1 resistance was 0.32. In order to detect previously reported resistance genes, as well as novel QTL, we explored methods to correct for population structure and analysis based on single markers or haplotypes. Both single-point and haplotype analyses identified strong associations in the genomic regions known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Accounting for kinship and structure generally improved the fit of statistical models. Detection of known loci was improved by adding kinship or a combination of kinship and structure using a Q matrix from model-based clustering. Additional QTL were detected on chromosomes 1, 4, 6, and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance (P < 0.01). Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.

Xanthomonas euvesicatoria type III effector XopQ interacts with tomato and pepper 14-3-3 isoforms to suppress effector-triggered immunity

Effector-triggered immunity (ETI) to host-adapted pathogens is associated with rapid cell death at the infection site. The plant-pathogenic bacterium Xanthomonas euvesicatoria (Xcv) interferes with plant cellular processes by injecting effector proteins into host cells through the type III secretion system. Here, we show that the Xcv effector XopQ suppresses cell death induced by components of the ETI-associated MAP kinase cascade MAPKKKα MEK2/SIPK and by several R/avr gene pairs. Inactivation of xopQ by insertional mutagenesis revealed that this effector inhibits ETI-associated cell death induced by avirulent Xcv in resistant pepper (Capsicum annuum), and enhances bacterial growth in resistant pepper and tomato (Solanum lycopersicum). Using protein-protein interaction studies in yeast (Saccharomyces cerevisiae) and in planta, we identified the tomato 14-3-3 isoform SlTFT4 and homologs from other plant species as XopQ interactors. A mutation in the putative 14-3-3 binding site of XopQ impaired interaction of the effector with CaTFT4 in yeast and its virulence function in planta. Consistent with a role in ETI, TFT4 mRNA abundance increased during the incompatible interaction of tomato and pepper with Xcv. Silencing of NbTFT4 in Nicotiana benthamiana significantly reduced cell death induced by MAPKKKα. In addition, silencing of CaTFT4 in pepper delayed the appearance of ETI-associated cell death and enhanced growth of virulent and avirulent Xcv, demonstrating the requirement of TFT4 for plant immunity to Xcv. Our results suggest that the XopQ virulence function is to suppress ETI and immunity-associated cell death by interacting with TFT4, which is an important component of ETI and a bona fide target of XopQ.

Fractionation, stability, and isolate-specificity of QTL for resistance to Phytophthora infestans in cultivated tomato (Solanum lycopersicum)

Cultivated tomato (Solanum lycopersicum) is susceptible to late blight, a major disease caused by Phytophthora infestans, but quantitative resistance exists in the wild tomato species S. habrochaites. Previously, we mapped several quantitative trait loci (QTL) from S. habrochaites and then introgressed each individually into S. lycopersicum. Near-isogenic lines (NILs) were developed, each containing a single introgressed QTL on chromosome 5 or 11. NILs were used to create two recombinant sub-NIL populations, one for each target chromosome region, for higher-resolution mapping. The sub-NIL populations were evaluated for foliar and stem resistance to P. infestans in replicated field experiments over two years, and in replicated growth chamber experiments for resistance to three California isolates. Each of the original single QTL on chromosomes 5 and 11 fractionated into between two and six QTL for both foliar and stem resistance, indicating a complex genetic architecture. The majority of QTL from the field experiments were detected in multiple locations or years, and two of the seven QTL detected in growth chambers were co-located with QTL detected in field experiments, indicating stability of some QTL across environments. QTL that confer foliar and stem resistance frequently co-localized, suggesting that pleiotropy and/or tightly linked genes control the trait phenotypes. Other QTL exhibited isolate-specificity and QTL × environment interactions. Map-based comparisons between QTL mapped in this study and Solanaceae resistance genes/QTL detected in other published studies revealed multiple cases of co-location, suggesting conservation of gene function.

A secreted lipolytic enzyme from Xanthomonas campestris pv. vesicatoria is expressed in planta and contributes to its virulence

A recombinase-based in vivo expression technology (RIVET) approach with Xanthomonas campestris pv. vesicatoria (Xcv) revealed that lipA, annotated as putative secreted lipase, is expressed during the interaction between this pathogen and tomato. Here, the tnpR and uidA reporter genes were used to show that lipA is strongly induced in XVM2 minimal medium and during the early stages of tomato infection by Xcv. A mutant strain impaired in lipA was generated by insertional mutagenesis. This mutant grew in a similar manner to the wild-type in rich medium, but its growth was significantly compromised in a medium containing olive oil as a single carbon source. The lipolytic activity of the extracellular fraction of the lipA mutant was reduced significantly relative to that of the wild-type strain, thus confirming that lipA indeed encodes a functional secreted enzyme with lipolytic activity. A plasmid carrying a wild-type copy of lipA complemented the lipA mutant for extracellular lipolytic activity. Dip inoculation experiments with tomato lines Hawaii 7998 (H7998) and Micro Tom showed that the lipA mutant grew to a lesser extent than the wild-type in tomato leaves. Following leaf syringe infiltrations, the mutant strain induced disease symptoms that were less severe than those induced by the wild-type strain, supporting a significant role of lipA in the pathogenicity of Xcv.

Fine mapping and analysis of a candidate gene in tomato accession PI128216 conferring hypersensitive resistance to bacterial spot race T3

Bacterial spot caused by Xanthomonas euvesicatoria, X. vesicatoria, X. perforans and X. gardneri is one of the most destructive diseases in tomatoes (Solanum lycopersicum L.) growing in tropical and subtropical regions. Exploring resistance genes from diverse germplasm and incorporating them into cultivated varieties are critical for controlling this disease. The S. pimpinellifolium accession PI128216 was reported to carry the Rx4 gene on chromosome 11 conferring hypersensitivity and field resistance to race T3. To facilitate the use of marker-assisted selection in breeding and map-based cloning of the gene, an F(2) population derived from a cross between the susceptible variety OH88119 and the resistant accession PI128216 was created for fine mapping of the Rx4 gene. Using 18 markers developed through various approaches, we mapped the gene to a 45.1-kb region between two markers pcc17 and pcc14 on chromosome 11. A NBS-LRR class of resistance gene was identified as the candidate for the Rx4 gene based on annotation results from the International Tomato Annotation Group. Comparison of the genomic DNA sequences of the Rx4 alleles in PI128216 and OH88119 revealed a 6-bp insertion/deletion (InDel) and eight SNPs. The InDel marker was successfully used to distinguish resistance and susceptibility in 12 tomato lines. These results will facilitate cloning the Rx4 gene and provide a useful tool for marker-assisted selection of this gene in tomato breeding programs.

Molecular mapping of hypersensitive resistance from tomato 'Hawaii 7981' to Xanthomonas perforans race T3

Bacterial spot of tomato (Solanum lycopersicum) is caused by four species of Xanthomonas. The disease causes significant yield losses and a reduction in fruit quality. Physiological races have been described with tomato race 3 (T3) corresponding to strains of Xanthomonas perforans. The breeding line Hawaii 7981 (hereafter H7981) shows a hypersensitive reaction (HR) to race T3 strains conditioned by the interaction of the host resistance locus Xv3 and the bacterial effector avrXv3. The Xv3 gene is required for H7981-derived resistance to be effective under field conditions, though its expression is subject to genetic background. The segregation of HR in F(2) populations derived from H7981 crossed to processing tomato parents OH88119 and OH7870 was studied in 331 progeny, with the two independent crosses providing validation. We screened 453 simple-sequence repeat, insertion/deletion, and single-nucleotide polymorphism markers and identified 44 polymorphic markers each for the OH88119 and OH7870 populations covering 84.6 and 73.3% of the genome, respectively, within 20 centimorgans (cM). Marker-trait analysis using all polymorphic markers demonstrated that Xv3-mediated resistance maps to chromosome 11 in the two independent crosses. Allelism tests were conducted in crosses between lines carrying Xv3 derived from H7981, Rx-4 derived from plant introduction (PI) 128216, and resistance derived from PI 126932. These allelism tests suggested that the loci conditioning HR to race T3 strains are linked within 0.1 cM, are allelic, or are the same gene.

The cucurbit pathogenic bacterium Acidovorax citrulli requires a polar flagellum for full virulence before and after host-tissue penetration

Acidovorax citrulli causes seedling blight and bacterial fruit blotch of cucurbits. Previous reports demonstrated the contribution of type IV pili (T4P) to A. citrulli virulence and to systemic infection of melon seedlings. Microfluidic flow-chamber assays demonstrated the involvement of T4P in surface adhesion and biofilm formation, whereas polar flagella did not appear to contribute to either of these features. On the other hand, a transposon mutant impaired in the biosynthesis of polar flagella was identified in screens for reduced virulence of an A. citrulli mutant library. Further characterization of polar flagellum mutants confirmed that A. citrulli requires a polar flagellum for full virulence on melon plants. Foliage and stem inoculation experiments revealed that polar flagella contribute to A. citrulli virulence and growth in planta at both pre- and post-host-tissue penetration. Interestingly, light microscope observations revealed that almost all A. citrulli wild-type cells extracted from the xylem sap of stem-inoculated melon seedlings remained motile, supporting the importance of this organelle in virulence and colonization of the host vascular system. We also report a negative effect of polar flagellum impairment on T4P-mediated twitching motility of A. citrulli and discuss a possible co-regulation of these two motility machineries in this bacterium.

The Xanthomonas campestris pv. vesicatoria citH gene is expressed early in the infection process of tomato and is positively regulated by the TctDE two-component regulatory system

Xanthomonas campestris pv. vesicatoria (Xcv) is the causal agent of bacterial spot disease of tomato and pepper. Previously, we have reported the adaptation of a recombinase- or resolvase-based in vivo expression technology (RIVET) approach to identify Xcv genes that are specifically induced during its interaction with tomato. Analysis of some of these genes revealed that a citH (citrate transporter) homologous gene contributes to Xcv virulence on tomato. Here, we demonstrate that the citH product indeed facilitates citrate uptake by showing the following: citH is specifically needed for Xcv growth in citrate, but not in other carbon sources; the citH promoter is specifically induced by citrate; and the concentration of citrate from tomato leaf apoplast is considerably reduced following growth of the wild-type and a citH-complemented strain, but not the citH mutant. We also show that, in the Xcv-tomato interaction, the promoter activity of the citH gene is induced as early as 2.5h after Xcv is syringe infiltrated into tomato leaves, and continues to be active for at least 96h after inoculation. We identified an operon containing a two-component regulatory system homologous to tctD/tctE influencing citH expression in Xcv, as well as its heterologous expression in Escherichia coli. The expression of hrp genes does not seem to be affected in the citH mutant, and this mutant cannot be complemented for growth in planta when co-inoculated with the wild-type strain, indicating that citrate uptake in the apoplast is important for the virulence of Xcv.

Identification of QTL associated with resistance to bacterial spot race T4 in tomato

Bacterial spot of tomato (Solanum lycopersicum L.), caused by several Xanthomonas sp., is a serious but difficult disease to control by chemical means. Development of resistance has been hindered by emergence of races virulent to tomato, by the quantitative inheritance of resistance, and by a low correlation between seedling assays and resistance in the field. Resistance to multiple races, including race T4, has been described in the S. lycopersicum var. cerasiformae accession PI 114490. We used molecular markers to identify associations with quantitative trait loci (QTL) in an elite inbred backcross (IBC) population derived from OH 9242, PI 114490 and Fla. 7600, a breeding line with tomato accession Hawaii 7998 (H7998) in its pedigree. Race T4 resistance has also been described in the advanced breeding lines Fla. 8233, Fla. 8517, and Fla. 8326, and a selective genotyping approach was used to identify introgressions associated with resistance in segregating progeny derived from crosses with these lines. In the IBC population, loci on chromosomes 11 and 3, respectively, explained as much as 29.4 and 4.8% of resistance variation. Both these loci were also confirmed by selective genotyping: PI 114490 and H7998 alleles on chromosome 11 each provided resistance. The PI 114490 allele on chromosome 3 was confirmed in the Fla. 8517 population, and an allele of undetermined descent was confirmed at this locus in the Fla. 8326 population. A chromosome 12 allele was associated with susceptibility in the Fla. 8517 population. Additional loci contributing minor effects were also implicated in the IBC population or by selective genotyping. Selection for the major QTL in a marker-directed phenotyping approach should significantly improve the efficiency of breeding for resistance to bacterial spot race T4, although as yet undetected QTL would be necessary to carry out strict marker assisted selection.

Tomato MAPKKKε is a positive regulator of cell-death signaling networks associated with plant immunity

Mitogen-activated protein (MAP) kinase cascades are fundamental components of the signaling pathways associated with plant immunity. Despite the large number of MAP kinase kinase kinases (MAPKKK) encoded in the plant genome, only very few of them have an assigned function. Here, we identified MAPKKK gene of tomato (Solanum lycopersicum), SIMAPKKKε, which is required for hypersensitive response cell death and disease resistance against Gram-negative bacterial pathogens. Silencing of SIMAPKKKε compromised tomato resistance to Xanthomonas campestris and Pseudomonas syringae strains, resulting in the appearance of disease symptoms and enhanced bacterial growth. In addition, silencing of NbMAPKKKε in Nicotiana benthamiana plants significantly inhibited the cell death triggered by expression of different R gene/effector gene pairs. Conversely, overexpression of either the full-length SIMAPKKKε gene or its kinase domain in N. benthamiana leaves caused pathogen-independent activation of cell death that required an intact kinase catalytic domain. Moreover, by suppressing the expression of various MAPKK and MAPK genes and overexpressing the SIMAPKKKε kinase domain, we identified a signaling cascade acting downstream of SIMAPKKKε that includes MEK2, WIPK and SIPK. Additional epistasis experiments revealed that SIPKK functions as a negative regulator of SIMAPKKKε-mediated cell death. Our results provide evidence that SIMAPKKKε is a signaling molecule that positively regulates cell death networks associated with plant immunity.

Inheritance of Resistance to Foliar Infection by Xanthomonas axonopodis pv. dieffenbachiae in Anthurium

The inheritance of resistance to the foliar phase of bacterial blight disease, caused by Xanthomonas axonopodis pv. dieffenbachiae, in Anthurium andraeanum was studied using parent-offspring regression analysis. In all, 14 parental cultivars, each represented by 3 plants per replicate, and 12 biparental progenies derived from the parents, each represented by 20 plants per replicate, were evaluated for foliar resistance using a leaf-disc, vacuum infiltration method in a randomized complete block design with three replications over two seasons. Three to five leaf discs (5.6 cm²; stage-2 leaves) obtained from each plant were vacuum infiltrated (15 psi; 10 s) with 10⁸ CFU/ml of inoculum and incubated (30°C) in trays. The time taken for the lesion to cover the entire disc was recorded for each disc. The progeny distributions were normally distributed with considerable transgressive segregation. Midparent/offspring regression analysis showed a high narrow sense heritability of 0.89 ± 0.13. These results indicate that inheritance of foliar resistance to blight is quantitative, with a major role for additive genetic effects. A breeding strategy to combine resistance to bacterial blight at both the foliar and systemic levels is discussed.

A new genetic linkage map of tomato based on a Solanum lycopersicum x S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes

The narrow genetic base of the cultivated tomato, Solanum lycopersicum L., necessitates introgression of new variation from related species. Wild tomato species represent a rich source of useful genes and traits. Exploitation of genetic variation within wild species can be facilitated by the use of molecular markers and genetic maps. Recently we identified an accession (LA2093) within the red-fruited wild tomato species Solanum pimpinellifolium L. with exceptionally desirable characteristics, including disease resistance, abiotic stress tolerance, and high fruit lycopene content. To facilitate genetic characterization of such traits and their exploitation in tomato crop improvement, we developed a new recombinant inbred line (RIL) population from a cross between LA2093 and an advanced tomato breeding line (NCEBR-1). Furthermore, we constructed a medium-density molecular linkage map of this population using 294 polymorphic markers, including standard RFLPs, EST sequences (used as RFLP probes), CAPS, and SSRs. The map spanned 1091 cM of the tomato genome with an average marker spacing of 3.7 cM. A majority of the EST sequences, which were mainly chosen based on the putative role of their unigenes in disease resistance, defense-related response, or fruit quality, were mapped onto the tomato chromosomes for the first time. Co-localizations of relevant EST sequences with known disease resistance genes in tomato were also examined. This map will facilitate identification, genetic exploitation, and positional cloning of important genes or quantitative trait loci in LA2093. It also will allow the elucidation of the molecular mechanism(s) underlying important traits segregating in the RIL population. The map may further facilitate characterization and exploitation of genetic variation in other S. pimpinellifolium accessions as well as in modern cultivars of tomato.

Characterization of hypersensitive resistance to bacterial spot race T3 (Xanthomonas perforans) from tomato accession PI 128216

Bacterial spot of tomato is caused by four species of Xanthomonas. The accession PI 128216 (Solanum pimpinellifolium) displays a hypersensitive reaction (HR) to race T3 strains (predominantely Xanthomonas perforans). We developed an inbred backcross (IBC) population (BC(2)S(5), 178 families) derived from PI 128216 and OH88119 (S. lycopersicum) as the susceptible recurrent parent for simultaneous introgression and genetic analysis of the HR response. These IBC families were evaluated in the greenhouse for HR to race T3 strain Xcv761. The IBC population was genotyped with molecular markers distributed throughout the genome in order to identify candidate loci conferring resistance. We treated the IBC population as a hypothesis forming generation to guide validation in subsequent crosses. Nonparametric analysis identified an association between HR and markers clustered on chromosome 11 (P < 0.05 to 0.0001) and chromosome 6 (0.04 > P > 0.002). Further analysis of the IBC population suggested that markers on chromosome 6 and 11 failed to assort independently, a phenomenon known as gametic phase disequilibrium. Therefore, to validate marker-trait linkages, resistant IBC plants were crossed with OH88119 and BC(3)F(2) progeny were evaluated for HR in the greenhouse. In these subsequent populations, the HR response was associated with the chromosome 11 markers (P < 0.0002) but not with the markers on chromosome 6 (P > 0.25). Independent F(2) families were developed by crossing resistant IBC lines to OH8245, OH88119, and OH7530. These populations were genotyped, organized into classes based on chromosome 11 markers, and evaluated for resistance in the field. The PI 128216 locus on chromosome 11 provided resistance that was dependent on gene dosage and genetic background. These results define a single locus, Rx-4, from PI 128216, which provides resistance to bacterial spot race T3, has additive gene action, and is located on chromosome 11.

Mapping of loci from Solanum lycopersicoides conferring resistance or susceptibility to Botrytis cinerea in tomato

Cultivated tomato (Solanum lycopersicum, syn. Lycopersicon esculentum) is susceptible to the necrotrophic ascomycete and causal agent of gray mold, Botrytis cinerea. Resistance to this fungal pathogen is elevated in wild relatives of tomato, including Solanum lycopersicoides. An introgression line population (IL) containing chromosomal segments of S. lycopersicoides within the background of tomato cv. VF36 was used to screen the genome for foliar resistance and susceptibility to B. cinerea. Based on this screen, putative quantitative trait loci (QTL) were identified, five for resistance and two for susceptibility. Four resistance QTL decreased infection frequency while the fifth reduced lesion diameter. One susceptibility QTL increased infection frequency whereas the other increased lesion diameter. Overlapping chromosomal segments provided strong evidence for partial resistance on chromosomes 1 and 9 and for elevated susceptibility on chromosome 11. Segregation analysis confirmed the major resistance QTL on the long arm of chromosome 1 and susceptibility on chromosome 11. Linkage of partial resistance to chromosome 9 could not be confirmed. The usefulness of these data for resistance breeding and for map-based cloning of foliar resistance to B. cinerea is discussed.

Durability of resistance in tomato and pepper to xanthomonads causing bacterial spot

Both hypersensitive and quantitative forms of resistance to the bacterial spot pathogens (Xanthomonas spp.) occur in pepper and tomato. Five resistance genes involved in hypersensitivity in pepper and four in tomato have been identified so far. The corresponding pathogen avirulence genes have been cloned and characterized, and features, including a propensity for accumulating mutations and at times, loss of plasmid-borne avirulence genes, are known to occur. The frequency of these changes affects race composition among pathogen populations and determines the durability of the corresponding plant resistance. At least four different species of Xanthomonas are known to cause bacterial spot, and these can differ in specific avirulence gene content. Quantitative or multigenic resistance has also more recently been researched and appears to be more durable than the hypersensitive resistance. Two recessive genes have been identified that yield a nonhypersensitive form of resistance in pepper and together can provide strong resistance. More emphasis is being given to transfer of quantitative trait resistance to commercial cultivars of both tomato and pepper.

Identification of a host 14-3-3 Protein that Interacts with Xanthomonas effector AvrRxv

AvrRxv is a member of a family of pathogen effectors present in pathogens of both plant and mammalian species. Xanthomonas campestris pv. vesicatoria strains carrying AvrRxv induce a hypersensitive response (HR) in the tomato cultivar Hawaii 7998. Using a yeast two-hybrid screen, we identified a 14-3-3 protein from tomato that interacts with AvrRxv called AvrRxv Interactor 1 (ARI1). The interaction was confirmed in vitro with affinity chromatography. Using mutagenesis, we identified a 14-3-3-binding domain in AvrRxv and demonstrated that a mutant in that domain showed concomitant loss of interaction with ARI1 and HR-inducing activity in tomato. These results demonstrate that the AvrRxv bacterial effector recruits 14-3-3 proteins for its function within host cells. AvrRxv homologues YopP and YopJ from Yersinia do not have AvrRxv-specific HR-inducing activity when delivered into tomato host cells by Agrobacterium. Although YopP itself cannot induce HR, its C-terminal domain containing the catalytic residues can replace that of AvrRxv in an AvrRxv-YopP chimera for HR-inducing activity. Phylogenetic analysis indicates that the sequences encoding the C-termini of family members are evolving independently from those encoding the N-termini. Our results support a model in which there are three functional domains in proteins of the family, translocation, interaction, and catalytic.

A Solanum lycopersicum x Solanum pimpinellifolium linkage map of tomato displaying genomic locations of R-genes, RGAs, and candidate resistance/defense-response ESTs

We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on an F(2) population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.4 cM of the 12 tomato chromosomes with an average marker distance of 4.0 cM. The length of the map and linear order of the markers were in good agreement with the published maps of tomato. The ESTs were chosen based on their sequence similarities with known resistance or defense-response genes, signal-transduction factors, transcriptional regulators, and genes encoding pathogenesis-related proteins. Locations of several ESTs and RGAs coincided with locations of several known tomato resistance genes and quantitative resistance loci (QRLs), suggesting that candidate-gene approach may be effective in identifying and mapping new R genes. This map will be useful for marker-assisted exploitation of desirable traits in LA2093 and other S. pimpinellifolium accessions, and possibly for utilization of genetic variation within S. lycopersicum.

Transcriptional analysis of the tomato resistance response triggered by recognition of the Xanthomonas type III effector AvrXv3

The type III effector AvrXv3 from Xanthomonas campestris pv. vesicatoria (Xcv) elicits a resistance response in the tomato line Hawaii 7981. To test whether similar genes participate in responses triggered by recognition of different avirulence proteins, we examined the effect of AvrXv3 expression on the plant transcriptome as compared to that of other avirulence proteins. By microarray analysis we monitored expression of approximately 8,600 tomato genes upon inoculation with isogenic Xcv strains differing only by the avrXv3 gene. Changes in transcript levels of 139 genes were observed within 8 h, and a massive shift in expression of 1,294 genes was detected at 12 h. Recognition of AvrXv3 modulated a large number of genes encoding transcription factors and signaling components. In addition, genes involved in defense and stress responses, lipid metabolism, protein degradation, and secondary metabolism were mainly up-regulated. Conversely, genes related to photosynthesis and protein synthesis were generally down-regulated. Many novel genes encoding proteins of unknown function were also identified. A comparison between AvrXv3-modulated genes and those differentially expressed in tomato plants recognizing other bacterial effectors revealed partial overlap and similar distribution in functional classes. The identification of tomato genes modulated by AvrXv3 expression paves the way for dissecting defense networks activated by recognition of this effector in resistant plants.

Identification of genes in Xanthomonas campestris pv. vesicatoria induced during its interaction with tomato

Xanthomonas campestris pv. vesicatoria is the causal agent of bacterial spot disease of tomato and pepper. The disease process is interactive and very intricate and involves a plethora of genes in the pathogen and in the host. In the pathogen, different genes are activated in response to the changing environment to enable it to survive, adapt, evade host defenses, propagate, and damage the host. To understand the disease process, it is imperative to broaden our understanding of the gene machinery that participates in it, and the most reliable way is to identify these genes in vivo. Here, we have adapted a recombinase-based in vivo expression technology (RIVET) to study the genes activated in X. campestris pv. vesicatoria during its interaction with one of its hosts, tomato. This is the first study that demonstrates the feasibility of this approach for identifying in vivo induced genes in a plant pathogen. RIVET revealed 61 unique X. campestris pv. vesicatoria genes or operons that delineate a picture of the different processes involved in the pathogen-host interaction. To further explore the role of some of these genes, we generated knockout mutants for 13 genes and characterized their ability to grow in planta and to cause disease symptoms. This analysis revealed several genes that may be important for the interaction of the pathogen with its host, including a citH homologue gene, encoding a citrate transporter, which was shown to be required for wild-type levels of virulence.

A novel link between tomato GRAS genes, plant disease resistance and mechanical stress response

SUMMARY Members of the GRAS family of transcriptional regulators have been implicated in the control of plant growth and development, and in the interaction of plants with symbiotic bacteria. Here we examine the complexity of the GRAS gene family in tomato (Solanum lycopersicum) and investigate its role in disease resistance and mechanical stress. A large number of tomato ESTs corresponding to GRAS transcripts were retrieved from the public database and assembled in 17 contigs of putative genes. Expression analysis of these genes by real-time RT-PCR revealed that six SlGRAS transcripts accumulate during the onset of disease resistance to Pseudomonas syringae pv. tomato. Further analysis of two selected family members showed that their transcripts preferentially accumulate in tomato plants in response to different avirulent bacteria or to the fungal elicitor EIX, and their expression kinetics correlate with the appearance of the hypersensitive response. In addition, transcript levels of eight SlGRAS genes, including all the Pseudomonas-inducible family members, increased in response to mechanical stress much earlier than upon pathogen attack. Accumulation of SlGRAS transcripts following mechanical stress was in part dependent on the signalling molecule jasmonic acid. Remarkably, suppression of SlGRAS6 gene expression by virus-induced gene silencing impaired tomato resistance to P. syringae pv. tomato. These results support a function for GRAS transcriptional regulators in the plant response to biotic and abiotic stress.

Resistance in Lycopersicon esculentum Intraspecific Crosses to Race T1 Strains of Xanthomonas campestris pv. vesicatoria Causing Bacterial Spot of Tomato

ABSTRACT We used molecular markers to identify quantitative trait loci (QTL) that confer resistance in the field to Xanthomonas campestris pv. vesicatoria race T1, a causal agent of bacterial spot of tomato. An F(2) population derived from a cross between Hawaii 7998 (H 7998) and an elite breeding line, Ohio 88119, was used for the initial identification of an association between molecular markers and resistance as measured by bacterial populations in individual plants in the greenhouse. Polymorphism in this cross between a Lycopersicon esculentum donor of resistance and an elite L. esculentum parent was limited. The targeted use of a core set of 148 polymerase chain reaction-based markers that were identified as polymorphic in L. esculentum x L. esculentum crosses resulted in the identification of 37 markers that were polymorphic for the cross of interest. Previous studies using an H 7998 x L. pennellii wide cross implicated three loci, Rx1, Rx2, and Rx3, in the hypersensitive response to T1 strains. Markers that we identified were linked to the Rx1 and Rx3 loci, but no markers were identified in the region of chromosome 1 where Rx2 is located. Single marker-trait analysis suggested that chromosome 5, near the Rx3 locus, contributed to reduced bacterial populations in lines carrying the locus from H 7998. The locus on chromosome 5 explained 25% of the phenotypic variation in bacterial populations developing in infected plants. An advanced backcross population and subsequent inbred backcross lines developed using Ohio 88119 as a recurrent parent were used to confirm QTL associations detected in the F(2) population. Markers on chromosome 5 explained 41% of the phenotypic variation for resistance in replicated field trials. In contrast, the Rx1 locus on chromosome 1 did not play a role in resistance to X. campestris pv. vesicatoria race T1 strains as measured by bacterial populations in the greenhouse or symptoms in the field. A locus from H 7998 on chromosome 4 was associated with susceptibility to disease and explained 11% of the total phenotypic variation. Additional variation in resistance was explained by plant maturity (6%), with early maturing families expressing lower levels of resistance, and plant habit (6%), with indeterminate plants displaying more resistance. The markers linked to Rx3 will be useful in selection for resistance in elite x elite crosses.

Molecular properties of the Xanthomonas AvrRxv effector and global transcriptional changes determined by its expression in resistant tomato plants

The Xanthomonas campestris pv. vesicatoria avirulence gene AvrRxv specifies resistance on the tomato line Hawaii 7998 by interacting with three nondominant plant resistance genes. AvrRxv molecular properties that impinge on its avirulence activity were characterized and transcriptional changes caused by AvrRxv expression in resistant tomato plants were extensively examined. AvrRxv localized predominantly to the cytoplasm and possibly in association with plasma and nuclear membranes in both resistant and susceptible tomato plants. The AvrRxv cysteine protease catalytic core was found to be essential for host recognition, because introduction of mutations in this domain affected the ability of AvrRxv to elicit a hypersensitive response and the inhibition of bacterial growth in resistant plants. In addition, expression profiles were analyzed for approximately 8,600 tomato genes in resistant plants challenged with X. campestris pv. vesicatoria strains expressing wild-type AvrRxv or a catalytic core AvrRxv mutant. In all, 420 genes were identified as differentially modulated by the expression of a functional AvrRxv, including over 15 functional classes of proteins and a large number of transcription factors and signaling components. Findings of this study allow the development of new hypotheses about the molecular basis of recognition between AvrRxv and the corresponding resistance proteins, and set the stage for the dissection of signaling and cellular responses triggered in tomato plants by this avirulence factor.

Identification and expression profiling of tomato genes differentially regulated during a resistance response to Xanthomonas campestris pv. vesicatoria

The gram-negative bacterium Xanthomonas campestris pv. vesicatoria is the causal agent of spot disease in tomato and pepper. Plants of the tomato line Hawaii 7981 are resistant to race T3 of X. campestris pv. vesicatoria expressing the type III effector protein AvrXv3 and develop a typical hypersensitive response upon bacterial challenge. A combination of suppression subtractive hybridization and microarray analysis identified a large set of cDNAs that are induced or repressed during the resistance response of Hawaii 7981 plants to X. campestris pv. vesicatoria T3 bacteria. Sequence analysis of the isolated cDNAs revealed that they correspond to 426 nonredundant genes, which were designated as XRE (Xanthomonas-regulated) genes and were classified into more than 20 functional classes. The largest functional groups contain genes involved in defense, stress responses, protein synthesis, signaling, and photosynthesis. Analysis of XRE expression kinetics during the tomato resistance response to X. campestris pv. vesicatoria T3 revealed six clusters of genes with coordinate expression. In addition, by using isogenic X. campestris pv. vesicatoria T2 strains differing only by the avrXv3 avirulence gene, we found that 77% of the identified XRE genes were directly modulated by expression of the AvrXv3 effector protein. Interestingly, 64% of the XRE genes were also induced in tomato during an incompatible interaction with an avirulent strain of Pseudomonas syringae pv. tomato. The identification and expression analysis of X. campestris pv. vesicatoria T3-modulated genes, which may be involved in the control or in the execution of plant defense responses, set the stage for the dissection of signaling and cellular responses activated in tomato plants during the onset of spot disease resistance.

Proteomic analysis of resistance mediated by Rcm 2.0 and Rcm 5.1, two loci controlling resistance to bacterial canker of tomato

Two quantitative trait loci from Lycopersicon hirsutum, Rcm 2.0 and Rcm 5.1, control resistance to Clavibacter michiganensis subsp. michiganensis, the causal agent of bacterial canker of tomato. Lines containing Rcm 2.0 and Rcm 5.1 and a susceptible control line were compared at 72 and 144 h postinoculation, using 2-dimensional gel electrophoresis to identify proteins regulated in response to C. michiganensis subsp. michiganensis infection. A total of 47 proteins were subjected to tandem mass spectrometry. Database queries with resulting spectra identified tomato genes for 26 proteins. The remaining 21 proteins were either identified in other species or possessed no homology to known proteins. Spectra were interpreted to deduce peptide amino acid sequences that were then used to query publicly available data. This approach identified tomato genes or expressed sequence tags for 44 of the proteins analyzed. Three superoxide dismutase (SOD) enzymes were differentially regulated among genotypes, and patterns of hydrogen peroxide accumulation were genotype- and tissue-specific, indicating a role for oxidative stress in response to C. michiganensis subsp. michiganensis. Steady-state mRNA and protein levels for SOD, thioredoxin M-type, S-adenosylhomocysteine hydrolase, and pathogenesis-related proteins demonstrated similar patterns of differential regulation. Lines containing Rcm 2.0 and Rcm 5.1 accumulate different proteins and steady-state mRNAs in response to inoculation, suggesting that the two loci may confer resistance through distinct mechanisms.

LeMPK3 is a mitogen-activated protein kinase with dual specificity induced during tomato defense and wounding responses

Mitogen-activated protein (MAP) kinase cascades are readily activated during the response of plants to avirulent pathogens or to pathogen-derived elicitors. Here we show that the tomato MAP kinase LeMPK3 is specifically induced at the mRNA level during elicitation of the hypersensitive response in resistant plants infected by avirulent strains of the phytopathogenic bacteria Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato, as well as upon treatment with the fungal elicitor ethylene-inducing xylanase. LeMPK3 gene expression was also induced very rapidly by mechanical stress and wounding much earlier than upon pathogen infection, but not in response to the defense-related plant hormones ethylene and jasmonic acid. Moreover, in resistant tomato plants infected by X. campestris pv. vesicatoria, transcript accumulation was followed by an increase in LeMPK3 kinase activity. Biochemical characterization of a glutathione S-transferase-LeMPK3 fusion protein revealed that the LeMPK3 MAP kinase autophosphorylates in vitro mainly on tyrosine and less so on threonine and serine, whereas it phosphorylates myelin basic protein on serine and threonine. In vitro phosphorylation of a poly-(Glu-Tyr) copolymer by LeMPK3 demonstrated its capability to phosphorylate tyrosine residues on substrates as well. By mutagenesis and phosphoamino acid analysis, Tyr-201 in the kinase activation domain was identified as the main LeMPK3 autophosphorylation site and as critical for kinase activity. Finally, LeMPK3 autophosphorylation showed a preference for Mn(2+) cations and proceeded via an intramolecular mechanism with an estimated K(m) value for ATP of 9.5 microm. These results define LeMPK3 as a MAP kinase with dual specificity and strongly suggest that it represents a convergence point for different signaling pathways inducing the activation of defense responses in tomato.

A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a Lycopersicon esculentum x Lycopersicon hirsutum cross

A molecular linkage map of tomato was constructed based on a BC1 population (N = 145) of a cross between Lycopersicon esculentum Mill. line NC84173 (maternal and recurrent parent) and Lycopersicon hirsutum Humb. and Bonpl. accession PI126445. NC84173 is an advanced breeding line that is resistant to several tomato diseases, not including early blight (EB) and late blight (LB). PI126445 is a self-incompatible accession that is resistant to many tomato diseases, including EB and LB. The map included 142 restriction fragment length polymorphism (RFLP) markers and 29 resistance gene analogs (RGAs). RGA loci were identified by PCR amplification of genomic DNA from the BC1 population, using ten pairs of degenerate oligonucleotide primers designed based on conserved leucine-rich repeat (LRR), nucleotide binding site (NBS), and serine (threonine) protein kinase (PtoKin) domains of known resistance genes (R genes). The PCR-amplified DNAs were separated by denaturing polyacrylamide gel electrophoresis (PAGE), which allowed separation of heterogeneous products and identification and mapping of individual RGA loci. The map spanned 1469 cM of the 12 tomato chromosomes with an average marker distance of 8.6 cM. The RGA loci were mapped to 9 of the 12 tomato chromosomes. Locations of some RGAs coincided with locations of several known tomato R genes or quantitative resistance loci (QRLs), including Cf-1, Cf-4, Cf-9, Cf-ECP2, rx-1, and Cm1.1 (chromosome 1); Tm-1 (chromosome 2); Asc (chrromosme 3); Pto, Fen, and Prf (chromosome 5); 01-1, Mi, Ty-1, Cm6.1, Cf-2, CF-5, Bw-5, and Bw-1 (chromosome 6); I-1, 1-3, and Ph-1 (chromosome 7); Tm-2a and Fr1 (chromosome 9); and Lv (chromosome 12). These co-localizations indicate that the RGA loci were either linked to or part of the known R genes. Furthermore, similar to that for many R gene families, several RGA loci were found in clusters, suggesting their potential evolutionary relationship with R genes. Comparisons of the present map with other molecular linkage maps of tomato, including the high density L. esculentum x Lycopersicon pennellii map, indicated that the lengths of the maps and linear order of RFLP markers were in good agreement, though certain chromosomal regions were less consistent than others in terms of the frequency of recombination. The present map provides a basis for identification and mapping of genes and QTLs for disease resistance and other desirable traits in PI126445 and other L. hirsutum accessions, and will be useful for marker-assisted selection and map-based gene cloning in tomato.

Xv4-vrxv4: a new gene-for-gene interaction identified between Xanthomonas campestris pv. vesicatoria race T3 and wild tomato relative Lycopersicon pennellii

Strains of tomato race 3 (T3) of Xanthomonas campestris pv. vesicatoria elicit a hypersensitive response (HR) in leaves of Lycopersicon pennellii LA716. Genetic segregation of the resistance exhibited ratios near 3:1 in F2 populations, which confirmed that a single dominant gene controlled the inheritance of this trait. With the aid of a collection of introgression lines, restriction fragment length polymorphism, and cleaved amplified polymorphic sequence markers, the resistance locus was located on chromosome 3 between TG599 and TG134. An avirulence gene named avrXv4 was also isolated by mobilizing a total of 600 clones from a genomic DNA library of the T3 strain 91-118 into the X. campestris pv. vesicatoria strain ME90, virulent on L. pennellii. One cosmid clone, pXcvT3-60 (29-kb insert), induced HR in resistant plants. The avirulent phenotype of pXcvT3-60 was confirmed by comparing growth rates in planta and electrolyte leakages among transconjugants carrying a mutated or intact clone with the wild-type T3 strain 91-118. A 1.9-kb DNA fragment contained within a 6.8-kb active subclone was sequenced and was determined to carry an open reading frame of 1,077 bp. The predicted AvrXv4 protein exhibits high similarity to members of an emerging new family of bacterial proteins from plant and mammalian pathogens comprising AvrRxv, AvrBsT, YopJ, YopP, AvrA, and YL40.

Comparative genetics of disease resistance within the solanaceae

Genomic positions of phenotypically defined disease resistance genes (R genes) and R gene homologues were analyzed in three solanaceous crop genera, Lycopersicon (tomato), Solanum (potato), and Capsicum (pepper). R genes occurred at corresponding positions in two or more genomes more frequently than expected by chance; however, in only two cases, both involving Phytophthora spp., did genes at corresponding positions have specificity for closely related pathogen taxa. In contrast, resistances to Globodera spp., potato virus Y, tobacco mosaic virus, and tomato spotted wilt virus were mapped in two or more genera and did not occur in corresponding positions. Without exception, pepper homologues of the cloned R genes Sw-5, N, Pto, Prf, and I2 were found in syntenous positions in other solanaceous genomes and in some cases also mapped to additional positions near phenotypically defined solanaceous R genes. This detailed analysis and synthesis of all available data for solanaceous R genes suggests a working hypothesis regarding the evolution of R genes. Specifically, while the taxonomic specificity of host R genes may be evolving rapidly, general functions of R alleles (e.g., initiation of resistance response) may be conserved at homologous loci in related plant genera.

Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologues in the genomes of two dicotyledons: tomato and arabidopsis

The presence of a single resistance (R) gene allele can determine plant disease resistance. The protein products of such genes may act as receptors that specifically interact with pathogen-derived factors. Most functionally defined R-genes are of the nucleotide binding site-leucine rich repeat (NBS-LRR) supergene family and are present as large multigene families. The specificity of R-gene interactions together with the robustness of plant-pathogen interactions raises the question of their gene number and diversity in the genome. Genomic sequences from tomato showing significant homology to genes conferring race-specific resistance to pathogens were identified by systematically "scanning" the genome using a variety of primer pairs based on ubiquitous NBS motifs. Over 70 sequences were isolated and 10% are putative pseudogenes. Mapping of the amplified sequences on the tomato genetic map revealed their organization as mixed clusters of R-gene homologues that showed in many cases linkage to genetically characterized tomato resistance loci. Interspecific examination within Lycopersicon showed the existence of a null allele. Consideration of the tomato and potato comparative genetic maps unveiled conserved syntenic positions of R-gene homologues. Phylogenetic clustering of R-gene homologues within tomato and other Solanaceae family members was observed but not with R-gene homologues from Arabidopsis thaliana. Our data indicate remarkably rapid evolution of R-gene homologues during diversification of plant families.

Regulation of expression of avirulence gene avrRxv and identification of a family of host interaction factors by sequence analysis of avrBsT

Resistance in tomato line Hawaii 7998 as well as in several nonhost plants to Xanthomonas campestris pv. vesicatoria tomato strain (XcvT) is mediated in part by the avirulence gene avrRxv. Analysis of growth of wild-type and avrRxv deletion strains indicates that avrRxv plays a crucial role in the ability of XcvT 92-14 to induce resistance on Hawaii 7998. We used avrRxv reporter gene fusions and Northern (RNA) blot analysis to test several growth environments for inductive potential. We found that avrRxv is constitutively expressed at high levels and that growth in planta, in tobacco conditioned medium, and in hrp-inductive medium XVM2 did not affect the high levels of expression. In addition, hrp structural and regulatory mutant backgrounds had no effect. We mutated the bipartite plant inducible promoter (PIP)-box sequence and found that avrRxv activity appears to be independent of an intact PIP-box element. We present the sequence of the avrRxv homologue called avrBsT and align the six AvrRxv host interaction factor family members including mammalian pathogen virulence factors YopJ and YopP from Yersinia spp. and AvrA from Salmonella typhimurium, and open reading frame Y4LO with unknown function from the symbiont Rhizobium sp.

Diversity among xanthomonads pathogenic on pepper and tomato

Xanthomonas campestris pv. vesicatoria, causal agent of bacterial spot of tomato and pepper, had been considered for nearly 70 years to be a relatively homogeneous organism. However, in the past decade this bacterium was determined to be composed of two genetically and phenotypically distinct groups. The two groups, designated A and B, were distinguished based on amylolytic activity, expression of unique protein bands, reaction on differential hosts (tomato races T1 and T2), reaction patterns with monoclonal antibodies, DNA restriction profiles, and DNA:DNA hybridization. The A and B groups were placed into X. axonopodis pv. vesicatoria and X. vesicatoria, respectively. A third group, designated C, was pathogenically (race T3) and serologically distinct from A and B strains, and formed unique DNA restriction profiles. DNA:DNA hybridization data suggest that C is distinct but related to A strains and may represent a subspecies of A. A final group, designated D, consisted of X. gardneri, an organism identified in Yugoslavia in 1957, and also found in Costa Rica. Group D was determined to be genetically distinct from strains within the other two groups; it represents a third Xanthomonas species pathogenic on tomato and pepper.