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The wild tomato species Solanum chilense is divided in geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype vs. pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance properties can be observed between but also within populations at the level of individual plants. Data also did not reveal clear indications for complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggest that quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is likely not the result of specific adaptations of hosts to the pathogen but of basal defence responses that depend on the host genotype and are pathogen isolate-unspecific.

Flavonoids are natural pigments occurring in plants and are present in fruits, leaves, stems, roots, and flowers. Tobacco plants transformed with an MYB regulatory gene from either Solanum chilense (Sc) or S. lycopersicum (Sl) demonstrate that ScANT1 induces a higher level of anthocyanin accumulation in comparison to SlANT1 and that this gene is sufficient to promote increased anthocyanin levels. We compared the aptitude of ScANT1 protein to induce anthocyanin accumulation to that of SlANT1 protein in tobacco plants. We also tested the effect of amino acid substitutions in ScANT1 and SlANT1. We examined these synthetic alleles' effect following the over-expression of additional anthocyanin synthesis regulators, such as the tomato bHLH (SlJAF13) protein. Our results show that the amino acid changes that differentiate ScANT1 from SlANT1 are the main contributors to the advantage that ScANT1 has over SlANT1 in anthocyanin accumulation per transcript unit. We further demonstrated that altering the amino acid composition of SlANT1 could increase anthocyanin accumulation, while reciprocally modifying ScANT1 lowers the anthocyanin level. These results confirm the increased anthocyanin level in tobacco is attributed to the amino acid differences between ScANT1 and SlANT1. We also show that the co-expression of SlJAF13 with SlANT1 in tobacco plants represses the anthocyanin production.

Salinity intrusion is one of the biggest problems in the context of sustainable agricultural practices. The major concern and challenge in developing salt-resistance in cultivated crops is the genetic complexity of the trait and lack of natural variability for stress-responsive traits. In this context, tomato wild relatives are important and have provided novel alleles for breeding abiotic stress tolerance including salt tolerance. We provide here a case study, involving tomato wild relative Solanum chilense and cultivated variety Solanum lycopersicum, carried out under high salt stress to investigate comparative transcriptional regulation mediating ROS homeostasis and other physiological attributes. Salt dependent oxidative stress in S. lycopersicum was characterized by a relatively higher H2O2 content, generation of O2• ─, electrolytic leakage and lipid peroxidation whereas reduced content of both ascorbate and glutathione. On the contrary, the robust anti-oxidative system in the S. chilense particularly counteracted the salt-induced oxidative damages by a higher fold change in expression profile of defense-related salt-responsive genes along with the increased activities of anti-oxidative enzymes. We conclude that S. chilense harbours novel genes or alleles for salt stress-related traits that could be identified, characterized, and mapped for its possible introgression into cultivated tomato lines.

Isomerization of 9,15,9′-tri-cis-ζ-carotene mediated by 15-cis-ζ-carotene isomerase Z-ISO is a critical step in the biosynthesis of carotenoids, which define fruit color. The tomato clade (Solanum section Lycopersicon) comprises the cultivated tomato (Solanum lycopersicum) and 12 related wild species differing in fruit color and, thus, represents a good model for studying carotenogenesis in fleshy fruit. In this study, we identified homologous Z-ISO genes, including 5′-UTRs and promoter regions, in 12 S. lycopersicum cultivars and 5 wild tomato species (red-fruited Solanum pimpinellifolium, yellow-fruited Solanum cheesmaniae, and green-fruited Solanum chilense, Solanum habrochaites, and Solanum pennellii). Z-ISO homologs had a highly conserved structure, suggesting that Z-ISO performs a similar function in tomato species despite the difference in their fruit color. Z-ISO transcription levels positively correlated with the carotenoid content in ripe fruit of the tomatoes. An analysis of the Z-ISO promoter and 5′-UTR sequences revealed over 130 cis-regulatory elements involved in response to light, stresses, and hormones, and in the binding of transcription factors. Green- and red/yellow-fruited Solanum species differed in the number and position of cis-elements, indicating changes in the transcriptional regulation of Z-ISO expression during tomato evolution, which likely contribute to the difference in fruit color.

Summary Positive Darwinian selection is the driving force underpinning local (in space) and temporal (in time) adaptation, and leaves footprints of selective sweeps at the underlying major genes. These two adaptive processes are classically considered independently, so that most genomic selection scans uncover only recent sweeps underpinning spatial adaptation. However, understanding if these adaptive processes are intermingled and share common genetic bases is crucial to predict a species’ evolutionary potential, for example in response to changing environmental conditions. We use whole genome data from six populations across three different habitats of the wild tomato species Solanum chilense, to 1) infer the past demographic history, and 2) search for genes under strong positive selection. We then correlate the demographic history, allele frequencies in space and time, the age of selection events and the reconstructed historical ecological distribution of the species over five main climatic periods spanning 150,000 years. We find evidence for several selective sweeps targeting regulatory networks involved in root hair development in low altitude, and response to photoperiod and vernalization in high altitude populations. These sweeps occur in a concerted fashion in a given regulatory gene network and only at particular time periods, thereby underpinning temporal local adaptation. These genes under positive selection provide subsequently the basis for spatial local adaptation to novel habitats when new ecological niches become available. Our results reveal the importance of jointly studying spatial and temporal adaptations in species during habitat colonization.

Within the tomato clade, Solanum chilense is considered one of the most promising sources of genes for tomato (S. lycopersicum) selection to biotic and abiotic stresses. In this study, we compared the effects of drought, high temperature, and their combination in two cultivars of S. lycopersicum and six populations of S. chilense, differing in their local habitat. Plants were grown at 21/19 °C or 28/26 °C under well-watered and water-stressed conditions. Plant growth, physiological responses, and expression of stress-responsive genes were investigated. Our results demonstrated strong variability among accessions. Differences in plant growth parameters were even higher among S. chilense populations than between species. The effects of water stress, high temperature, and their combination also differed according to the accession, suggesting differences in stress resistance between species and populations. Overall, water stress affected plants more negatively than temperature from a morpho-physiological point of view, while the expression of stress-responsive genes was more affected by temperature than by water stress. Accessions clustered in two groups regarding resistance to water stress and high temperature. The sensitive group included the S. lycopersicum cultivars and the S. chilense populations LA2931 and LA1930, and the resistant group included the S. chilense populations LA1958, LA2880, LA2765, and LA4107. Our results suggested that resistance traits were not particularly related to the environmental conditions in the natural habitat of the populations. The expression of stress-responsive genes was more stable in resistant accessions than in sensitive ones in response to water stress and high temperature. Altogether, our results suggest that water stress and high temperature resistance in S. chilense did not depend on single traits but on a combination of morphological, physiological, and genetic traits.

Carotenoids are pigments with important nutritional value in the human diet. As antioxidant molecules, they act as scavengers of free radicals enhancing immunity and preventing cancer and cardiovascular diseases. Moreover, α-carotene and β-carotene, the main carotenoids of carrots (Daucus carota) are precursors of vitamin A, whose deficiency in the diet can trigger night blindness and macular degeneration. With the aim of increasing the carotenoid content in fruit flesh, three key genes of the carotenoid pathway, phytoene synthase (DcPSY2) and lycopene cyclase (DcLCYB1) from carrots, and carotene desaturase (XdCrtI) from the yeast Xanthophyllomyces dendrorhous, were optimized for expression in apple and cloned under the Solanum chilense (tomatillo) polygalacturonase (PG) fruit specific promoter. A biotechnological platform was generated and functionally tested by subcellular localization, and single, double and triple combinations were both stably transformed in tomatoes (Solanum lycopersicum var. Microtom) and transiently transformed in Fuji apple fruit flesh (Malus domestica). We demonstrated the functionality of the S. chilense PG promoter by directing the expression of the transgenes specifically to fruits. Transgenic tomato fruits expressing DcPSY2, DcLCYB1, and DcPSY2-XdCRTI, produced 1.34, 2.0, and 1.99-fold more total carotenoids than wild-type fruits, respectively. Furthermore, transgenic tomatoes expressing DcLCYB1, DcPSY2-XdCRTI, and DcPSY2-XdCRTI-DcLCYB1 exhibited an increment in β-carotene levels of 2.5, 3.0, and 2.57-fold in comparison with wild-type fruits, respectively. Additionally, Fuji apple flesh agroinfiltrated with DcPSY2 and DcLCYB1 constructs showed a significant increase of 2.75 and 3.11-fold in total carotenoids and 5.11 and 5.84-fold in β-carotene, respectively whereas the expression of DcPSY2-XdCRTI and DcPSY2-XdCRTI-DcLCYB1 generated lower, but significant changes in the carotenoid profile of infiltrated apple flesh. The results in apple demonstrate that DcPSY2 and DcLCYB1 are suitable biotechnological genes to increase the carotenoid content in fruits of species with reduced amounts of these pigments.

Natural plant populations are highly polymorphic and often show intraspecific quantitative, variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on the perception of conserved pathogen-associated molecular patterns (PAMPs). To dissect and understand such variation, we evaluated the diversity of responses induced by laminarin (representing a general glucan elicitor of plant immune responses) in the wild tomato species Solanum chilense. We confirm considerable overlap of the plant9s global transcriptional responses to laminarin and to the oomycete pathogen Phytophthora infestans. We further measured key components of basal defence responses such as reactive oxygen species (ROS) production and levels of diverse phytohormones and their derivatives upon elicitation with laminarin in 83 plants originating from nine natural populations of S. chilense from distinct geographic origin. We found high diversity in these components at basal and elicitor-induced levels. We generated generalised linear mixed models (GLMMs) with these components to explain the observed resistance phenotype against P. infestans in the plants and found that additive effects of multiple components best explain resistance at the species level. For individual components, we observed the strongest positive correlation between the resistance phenotype and ethylene (ET) production upon laminarin elicitation. The strength of this correlation differed between individual populations. Chemical inhibition of ET production in individuals from a population, in which ET production was associated with resistance, provoked more severe disease symptoms. Our findings reveal high diversity in the strength of induced defence responses within a species and in the basal levels of other stress-related phytohormones. We show the involvement of multiple components with a quantitatively different contribution of individual components to resistance in geographically separated populations of S. chilense against P. infestans.

Crosses between the wild tomato species Solanum peruvianum and Solanum chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin dependent expression of alleles, is perturbed in the hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA (sRNA) expression levels. We identified 2,295 genes and 387 sRNA clusters as differentially expressed when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both hybrid cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resemble the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; differentially expressed sRNAs exhibit reduced transcript abundance in hybrid seeds of both cross directions. Moreover, sRNAs map to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that appear to be targets of sRNA-mediated gene silencing; in these cases, reduced sRNA abundance is concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species., Genome Biology and Evolution, 13 (8), ISSN:1759-6653

PREMISE Common taxonomic practices, which condition species' descriptions on diagnostic morphological traits, may systematically lump outcrossing species and unduly split selfing species. Specifically, higher effective population sizes and genetic diversity of obligate outcrossers are expected to result less reliable phenotypic diagnoses. Wild tomatoes, members of Solanum sect. Lycopersicum, are commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although the section experienced significant early work, which continues presently, the taxonomic status of many wild species has undergone a number of significant revisions and remains uncertain. Species in this section vary in their breeding systems, notably the expression of self-incompatibility, which determines individual propensity for outcrossing METHODS: Here, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced-representation sequencing (RAD-seq), a range of phylogenetic and population genetic analyses, as well as analyses of crossing and morphological data. RESULTS Overall, each of our analyses provides a considerable weight of evidence that the Pacific coastal populations and Andean inland populations of the currently described Solanum chilense represent separately evolving populations, and conceal at least one undescribed cryptic species. CONCLUSIONS Despite its vast economic importance, Solanum sect. Lycopersicon still exhibits considerable taxonomic instability. A pattern of under-recognition of outcrossing species may be common, not only in tomatoes, but across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference.

Members ofSolanumsect.Lycopersicumare commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although it experienced significant early and ongoing work, the taxonomic status of many wild species in this section has undergone a number of significant revisions, and remains uncertain.Here, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced-representation sequencing (RAD-seq), a range of phylogenetic and population genetic analyses, crossing data, and morphological data.Overall, each of our analyses provides some weight of evidence that the Pacific coastal populations and Andean inland populations of the currently describedS. chilenserepresent separately evolving populations.Despite its vast economic importance,Solanumsect.Lycopersiconstill exhibits considerable taxonomic instability. A pattern of under-recognition of outcrossing species may be common across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference.

Natural plant populations encounter strong pathogen pressure and defense-associated genes are known to be under different selection pressure dependent on the pressure by the pathogens. Here we use wild tomato Solanum chilense populations to investigate natural resistance against Cladosporium fulvum, a well-known pathogenic fungus of domesticated tomatoes. We show that populations of S. chilense differ in resistance against the pathogen. Next, we explored the underlying molecular processes in a species wide-context. Then, focusing on recognition of the two prominent avirulence factors secreted by C. fulvum (Avr4 and Avr9) in central and northern populations of S. chilense we observed high complexity in the cognate homologues of Cladosporium resistance (Hcr9) locus underlying the recognition of these effectors. Presence of canonical genomic regions coding for Cf-4 and Cf-9, two major dominant resistance genes in the Hcr9 locus recognizing Avr4 and Avr9, respectively, does not meet prediction from Avr response phenotypes. We find both genes in varying fractions of the plant populations and we show possible co-existence of two functionally active resistance genes, previously thought to be allelic. Additionally, we observed the complete local absence of recognition of additional Avr proteins of C. fulvum. In the southern populations we attribute this to changes in the coregulatory network. As a result of loss of pathogen pressure or adaptation to extreme climatic conditions. This may ultimately explain the observed pathogen susceptibility in the southern populations. This work puts major gene mediated disease resistance in an ecological context.

This assay is based on luminol and horseradish peroxidase-dependent chemiluminescence detection of reactive oxygen species (ROS) production in plant leaf discs with some modification to make it suitable for tomato, specifically for wild tomato Solanum chilense. We tried non-buffered (Water) and buffered systems (MES and MOPS) to evaluate the robustness to detect ROS production in S. chilense leaf discs. Buffering the leaf discs with 20mM MOPS at pH 7.5 during the assay resulted in the best outputs with high reproducibility.

The rhizosphere microbiome is key in survival, development, and stress tolerance in plants. Salinity, drought, and extreme temperatures are frequent events in the Atacama Desert, considered the driest in the world. However, little information of the rhizosphere microbiome and its possible contribution to the adaptation and tolerance of plants that inhabit the desert is available. We used a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the rhizosphere of Baccharis scandens and Solanum chilense native plants from the Atacama Desert. Our results showed that the fungal phyla Ascomycota and Basidiomycota and the bacterial phyla Actinobacteria and Proteobacteria were the dominant taxa in the rhizosphere of both plants. The linear discriminant analysis (LDA) effect size (LefSe) of the rhizosphere communities associated with B. scandens showed the genera Penicillium and Arthrobacter were the preferential taxa, whereas the genera Oidiodendron and Nitrospirae was the preferential taxa in S. chilense. Both plant showed similar diversity, richness, and abundance according to Shannon index, observed OTUs, and evenness. Our results indicate that there are no significant differences (p = 0.1) between the fungal and bacterial communities of both plants, however through LefSe, we find taxa associated with each plant species and the PCoA shows a separation between the samples of each species. This study provides knowledge to relate the assembly of the microbiome to the adaptability to drought stress in desert plants.

[EN] In previous studies, the FGB lab have shown that when a fragment from Chromosome 6 of Solanum chilense (which contains Ty1-3 resistance genes) is introgressed into tomato (Solanum lycopersicum), the fruit volatile profile is affected. Our working hypothesis is that a S. chilense FAD gene located next to the Ty gene is also introgressed -causing a higher expression of FAD, which is translated into a higher synthesis in fruit of volatiles produced from double-bond Fatty Acids through the Lipoxygenase Pathway. The objective of this thesis is to analyse further the effect of this S. chilense introgression by 1) determining if the change in volatiles production is restricted to tomato fruit or affects also leaves, 2) defining the differences at the genomic level between the FAD gene from tomato and S. chilense, and 3) performing a literature review to check on the extent linkage drag has on tomato breeding. We first analysed the VOCs present leaves of Solanum lycopersicum cv. Muchamiel and De la Pera traditional varieties, that either contain or not the Ty resistance gene introgression from S. chilense. We performed a SPME-HeadSpace Gas Chromatography-Mass Spectrometry analysis in order to capture, separate and quantify the volatiles present in our samples. We conducted a Targeted Metabolic Analysis to analyse possible differences in 15 specific compounds and an Untargeted Analysis to analyse all chromatograms¿ data. Results indicate no changes in the Fatty Acids-derived volatiles in leaves, indicating that the effect of the introgression could be restricted to fruit. Moreover, we performed a molecular analysis of the FAD gene sequence in both tomato and S. chilense, concluding that there is a 700bp-long repetitive element present in the promoter of the FAD gene in tomato which is absent in S. chilense species. In order to assess which alterations in the promotor sequence cause the FAD gene to present a higher expression in S. chilense than in tomato, we performed a bioinformatic analysis using the PLACE database and the informatic programs Nsite-PL and NsiteM-PL from the RegSite Database. While this repetitive element disrupts a couple of regulatory domains of the promoter, additional reasons for downregulation could be the hypermethylation of the promoter region in tomato. As this FAD gene is also required for the synthesis of Jasmonate phytohormones, aliquots of our samples are ready for future hormone analysis, since these are important for induction of defense systems in the plant. In order to assess this aspect, our samples were punctured with the zoophytophagous mirid bug Nesidiocoris tenuis and will then be compared with the control samples. Literature review identified a number of cases in tomato breeding where introgression of disease resistance genes has an effect on other traits of the plant due to linkage drag. A review of the most cultivated tomato F1 hybrids indicated that most of them carry more than three introgressions from wild relative species and are, therefore, likely to be affected regarding other traits, either beneficially or not, which ultimately affects consumer liking., [CA] S’ha observat en estudis realitzats anteriorment al laboratorio de FGB de l’IBMCP que, quan s’introgressa un fragment del Cromosoma 6 de l’espècie silvestre Solanum chilense (el qual conté els gens de resistència Ty1-3) en el genoma de la tomaca (Solanum lycopersicum), a més de conferir resistència, s’altera el perfil de compostos volàtils en el fruit. La nostra hipòtesi actual és que un gen FAD de S. Chilense que es localitza pròxim al gen de resistència Ty també s’introgressa amb aquest últim -generant una major expressió de FAD, i provocant finalment una major síntesi en fruit de volàtils produïts a partir d’Àcids Grassos de doble enllaç, a través de la Ruta de la Lipoxigenasa. L’objectiu d¿aquest treball és analitzar amb més profunditat l’efecte que té aquesta introgressió de S. Chilense en tomaca; primer, determinant si el canvi en la producció de volàtils està limitat al fruit o també afecta a les fulles; segon, indicant les diferències que hi ha a nivell genòmic entre el gen FAD en tomaca i en S. chilense; i, tercer, realitzant una revisió bibliogràfica per a determinar fins a quin punt l’esdeveniment de linkage drag afecta al cultiu de la tomaca. En primer lloc, vam analitzar els compostos volàtils (COVs) de fulles de Solanum lycopersicum de les varietats tradicionals Muchamiel i De la Pera, les quals presentaven o no la introgressió del gen Ty de S. chilense. Vam realitzar una anàlisi metabolòmica mitjançant el mètode de Microextracció en Fase Sòlida-Espai de cap-Cromatografia de Gases-Espectrometria de Masses per a capturar, separar i identificar els volàtils presents en les nostres mostres. Vam dur a terme una Anàlisi Metabòlica Dirigida per a determinar les possibles diferències en 15 compostos específics i una Anàlisi No dirigida per a extraure tota la informació dels cromatogrames. Els resultats mostren que no hi ha canvis en els volàtils procedents d’Àcids Grassos en les fulles de tomaca, indicant que els efectes de la introgressió es limiten únicament al fruit. A més a més, vam realitzar una anàlisi molecular de la seqüència del gen FAD en tomaca i en S. chilense, confirmant que hi ha un element repetitiu de 700 pb localitzat en el promotor d’aquest gen en tomaca i no en S. chilense. Amb l’objectiu d’avaluar quins canvis en la seqüència del promotor podrien estar implicats en que aquest gen presente una major expressió en S. chilense que en tomaca, vam portar a terme una anàlisi bioinformàtica utilitzant la base de dades PLACE i els programes Nsite-PL i NsiteM-PL de la base de dades RegSite. Vam concloure que aquest element repetitiu no sols es troba en la seqüència interrompent dos dominis de regulació del promotor, sinó que proposem a més altres motius que expliquen aquesta regulació negativa de FAD en tomaca, com podria ser la hipermetilació de la regió del promotor. Com aquest gen FAD també participa en la síntesi de jasmonat i aquesta hormona és important per a estimular els sistemas de defensa de la planta en resposta a la interacción amb diferents agents biòtics, hem preparat alíquotes de les nostres mostres per a realitzar una anàlisi d’hormones en el futur. Per a avaluar aquesta possibilitat, s’analitzaran mostres de fulles apicals les quals havien sigut picades per l’heteròpter zoofitòfag Nesidiocoris tenuis i es compararan amb les mostres control. Vam realitzar una revisió bibliogràfica sobre l’efecte de creuaments inter-específics en tomaca i vam identificar diversos casos en els que la introgressió de gens de resistència a malalties afectava també altres característiques de la planta, a causa de l’esdeveniment de linkage drag. D’altra banda, una anàlisi bibliogràfica de les F1 híbrides de tomaca més cultivades ens va demostrar que la majoria d’aquestes espècies posseeixen més de tres introgressions procedents d’espècies silvestres, i, per tant, és molt probable que també presenten altres.

The effects of salt on the quality of fruits were investigated in order to compare the impact of salt on key fruit properties of the cultivated domesticated tomato species (Solanum lycopersicum) and its wild halophyte relative Solanum chilense. To this end, cherry tomato plants (S. lycopersicum var. cerasiforme) and from accession LA4107 (S. chilense) were maintained for 112 days in the absence or presence of NaCl (40 and 80 mM) in nutrient solution. Among others, salinity decreased fruit weight and increased total soluble solid (TSS) in S. lycopersicum but not in S. chilense. The fruit antioxidant capacity estimated by ferric reducing antioxidant power (FRAP) analysis was higher in S. chilense than in S. lycopersicum and increased in the former while it decreased in the latter in response to NaCl. Salinity increased the lycopene (LYC) content but decreased &szlig, carotene (b-CAR) concentration in the fruits of S. lycopersicum, while these compounds were not detected in the wild halophyte S. chilense. The oxidative status of salt-treated fruits was more tightly regulated in S. chilense than in S. lycopersicum. The two considered species, however, possess complementary properties and interspecific crosses may therefore be considered as a promising option for the improvement of salt-stress resistance in tomatoes.

Natural plant populations encounter strong pathogen pressure and defense-associated genes are known to be under selection dependent on the pressure by the pathogens. Here we use populations of the wild tomato Solanum chilense to investigate natural resistance against Cladosporium fulvum, a well-known ascomycete pathogen of domesticated tomatoes. Host populations used are from distinct geographical origins and share a defined evolutionary history. We show that distinct populations of S. chilense differ in resistance against the pathogen. Screening for major resistance gene mediated pathogen recognition throughout the whole species showed clear geographical differences between populations and complete loss of pathogen recognition in the south of the species range. In addition, we observed high complexity in a homologues of Cladosporium resistance (Hcr) locus, underlying the recognition of C. fulvum, in central and northern populations. Our findings show that major gene mediated recognition specificity is diverse in a natural plant-pathosystem. We place major gene resistance in a geographical context that also defined the evolutionary history of that species. Data suggest that the underlying loci are more complex than previously anticipated, with small-scale gene recombination being possibly responsible for maintaining balanced polymorphisms in the populations that experience pathogen pressure.,Additional data for the manuscript "Population studies in the wild tomato species Solanum chilense reveal maintenance and loss of resistance at geographically distinct locations" Contains: METADATA MICROSCOPY jpg and xml metadata files for the microscopy images used in our study SNP DATA Alignment files (fasta) for the genes mentioned in the study 3chil*.fa Intermediate files used for the generation of above fasta files Coreceptors* Solanum lycopersicum gene sequences used in the analysis above Solyc*.fa Description of the pipeline used to identify the coreceptors and their mutations Pipeline_fv.txt OTHERS R scripts used for graphs *.R Tables with raw qPCR data as used in the study qpcrdata.csv Details on the populations used in this study Population-details.ods Details on the populations used in this study Avrmix.csv Dualfigure.csv

Tomato (Solanum lycopersicum L.) is one of the most important and popular vegetables worldwide. A wide range of tomato cultivars with different colored fruits is presently available. The purple peel of tomato fruit is due to the accumulation anthocyanin pigments, which are beneficial to both plants and humans. Cultivated tomatoes normally do not make anthocyanin in their fruit peel, but there are some wild relatives of cultivated tomato like Solanum chilense, S. habrochaites, S. cheesmanii, and S. lycopersicoides that do produce anthocyanins in their fruits. In this study, the purple fruit color was obtained by crossing ‘OSU blue’ (blue fruit) and ‘Purple mini’ (brown fruit) and subsequent self-pollination. Anthocyanins are produced via the flavonoid pathway and are regulated by the transcriptional complex of MYB, bHLH, and WD40 repeats transcription factors. We determined the expression profiles of genes related to anthocyanin biosynthesis in tomato genotypes with distinct fruit colors by qRT-PCR. Both the early and late biosynthetic genes of the anthocyanin pathway were up-regulated in the peels of purple tomato fruits, except Sl5GT. Moreover, the expression of the regulatory genes SlANT1 and SlAN1 was dramatically increased in the peels of purple tomato fruits. These results indicate that SlANT1 and SlAN1 might play an important role on anthocyanin biosynthesis in the peels of purple-fruited tomatoes via up-regulation of structural genes in the anthocyanin pathway.

Background and AimsDefective hybrid seed development in angiosperms might mediate the rapid establishment of intrinsic post-zygotic isolation between closely related species. Extensive crosses within and among three lineages of wild tomatoes (Solanum section Lycopersicon) were performed to address the incidence, developmental timing and histological manifestations of hybrid seed failure. These lineages encompass different, yet fairly recent, divergence times and both allopatric and partially sympatric pairs.MethodsMature seeds were scored visually 2 months after hand pollinations, and viable-looking seeds were assessed for germination success. Using histological sections from early-developing seeds from a sub-set of crosses, the growth of three major seed compartments (endosperm, embryo and seed coat) was measured at critical developmental stages up to 21 d after pollination, with a focus on the timing and histological manifestations of endosperm misdevelopment in abortive hybrid seeds.Key ResultsFor two of three interspecific combinations including the most closely related pair that was also studied histologically, almost all mature seeds appeared ‘flat’ and proved inviable; histological analyses revealed impaired endosperm proliferation at early globular embryo stages, concomitant with embryo arrest and seed abortion in both cross directions. The third interspecific combination yielded a mixture of flat, inviable and plump, viable seeds; many of the latter germinated and exhibited near-normal juvenile phenotypes or, in some instances, hybrid necrosis and impaired growth.ConclusionsThe overall results suggest that near-complete hybrid seed failure can evolve fairly rapidly and without apparent divergence in reproductive phenology/biology. While the evidence accrued here is largely circumstantial, early-acting disruptions of normal endosperm development are most probably the common cause of seed failure regardless of the type of endosperm (nuclear or cellular).

Physiological responses of plants to salinity stress requires the coordinated activation of many genes. A salt-induced gene was isolated from roots of the wild tomato species Solanum chilense and named SchRabGDI1 because it encodes a protein with high identity to GDP dissociation inhibitors of plants. These proteins are regulators of the RabGTPase cycle that play key roles in intracellular vesicular trafficking. The expression pattern of SchRabGDI1 showed an early up-regulation in roots and leaves under salt stress. Functional activity of SchRabGDI1 was shown by restoring the defective phenotype of the yeast sec19-1 mutant and the capacity of SchRabGDI1 to interact with RabGTPase was demonstrated through BiFC assays. Expression of SchRabGDI1 in Arabidopsis thaliana plants resulted in increased salt tolerance. Also, the root cells of transgenic plants showed higher rate of endocytosis under normal growth conditions and higher accumulation of sodium in vacuoles and small vesicular structures under salt stress than wild type. Our results suggest that in salt tolerant species such as S. chilense, bulk endocytosis is one of the early mechanisms to avoid salt stress, which requires the concerted expression of regulatory genes involved in vesicular trafficking of the endocytic pathway.

Salicylic acid (SA) is involved in the salt-resistance of the halophyte plant species Solanum chilense. The SA analog 2,6-dichloroisonicotinc acid (INA) is commonly used to elicit SA signal transduction in response to biotic stress and is frequently used to confirm the SA involvement in plant response to pathogens. Data are lacking concerning its impact on plant response to salinity, especially in the halophyte species. Solanum chilense was cultivated in the absence or presence of 125 mM NaCl in nutrient solution and exposed to 0.01 mM exogenous SA or sprayed with 0.5 mM INA. Exogenous SA increased the shoot dry weight while INA did not. Exogenous INA, in contrast to SA, increased the shoot Na+ concentration in NaCl-treated plants and decreased the root K+ concentration. In the absence of salt, both SA and INA induced an increase in H2O2 which was not due to ascorbate peroxidase (EC 1.11.1.11) inhibition. In salt-treated plants, SA stimulated the ascorbate peroxidase activity while INA did not. Exogenous SA increased the root putrescine and spermidine concentrations while INA significantly decreased the concentration of these protecting compounds. It is concluded that exogenous SA and INA do not have similar impacts on the plant behavior and that the difference between these compounds may be influenced by NaCl. The use of INA as a reliable SA analog should therefore be considered with caution in halophyte plant species.

Tomato powdery mildew (Pseudoidium neolycopersici (syn. Oidium neolycopersici)) is one of the most devastating diseases of cultivated tomatoes worldwide. Although the first epidemics were recorded nearly 30 years ago, many aspects of the host-pathogen interaction are still not well understood. Detailed morphological and molecular studies of the anamorphs confirmed that P. neolycopersici is phylogenetically close to Erysiphe aquilegiae var. ranunculi. Host range is rather broad; apart from the family Solanaceae, hosts were found in very distant plant families. Screening of wild Solanum sect. Lycopersicon spp. (previous Lycopersicon spp.) germplasm revealed valuable sources of resistance (Solanum habrochaites, Solanum pennellii, Solanum cheesmaniae, Solanum chilense, Solanum peruvianum). The main resistance mechanism was found to be a hypersensitive response (HR), in some cases followed by limited development of the pathogen. However, there is a broad variation in resistance response at the histological and cytological levels. Biochemical studies focusing on production of reactive oxygen species (ROS), reactive nitrogen species (RNS) and corresponding enzymes during infection of P. neolycopersici showed that all these play a crucial role in activation of defense responses in genotypes of wild Solanum sect. Lycopersicon.

Tomato (Solanum lycopersicum) fruits are typically red at ripening, with high levels of carotenoids and a low content in flavonoids. Considerable work has been done to enrich the spectrum of their health-beneficial phytochemicals, and interspecific crosses with wild species have successfully led to purple anthocyanin-colored fruits. The Aft (Anthocyanin fruit) tomato accession inherited from Solanum chilense the ability to accumulate anthocyanins in fruit peel through the introgression of loci controlling anthocyanin pigmentation, including four R2R3 MYB transcription factor-encoding genes. Here, we carried out a comparative functional analysis of these transcription factors in wild-type and Aft plants, and tested their ability to take part in the transcriptional complexes that regulate the biosynthetic pathway and their efficiency in inducing anthocyanin pigmentation. Significant differences emerged for SlAN2like, both in the expression level and protein functionality, with splicing mutations determining a complete loss of function of the wild-type protein. This transcription factor thus appears to play a key role in the anthocyanin fruit pigmentation. Our data provide new clues to the long-awaited genetic basis of the Aft phenotype and contribute to understand why domesticated tomato fruits display a homogeneous red coloration without the typical purple streaks observed in wild tomato species., The Anthocyanin fruit (Aft) tomato line accumulates anthocyanins in fruit peel through the introgression of R2R3 MYB genes from Solanum chilense. A comparative functional analysis of these genes revealed important differences for one of them, SlAN2like, between wild-type and Aft plants. Remarkably, splicing mutations in the wild-type allele determine a loss of function of the protein, explaining why domesticated tomato does not synthesize anthocyanins in its fruits.

Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense, a wild relative of cultivated tomato (Solanum lycopersicum L.), is known to have exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the mechanism to salinity stress tolerance by S. chilense can be accomplished by comprehensive gene expression studies. In this study 1-month-old seedlings of S. chilense and S. lycopersicum were subjected to salinity stress through application of sodium chloride (NaCl) solution. Through RNA-sequencing here we have studied the differences in the gene expression patterns. A total of 386 million clean reads were obtained through RNAseq analysis using the Illumina HiSeq 2000 platform. Clean reads were further assembled de novo into a transcriptome dataset comprising of 514,747 unigenes with N50 length of 578 bp and were further aligned to the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 265,158 genes that were differentially expressed in response to salt treatment, 134,566 and 130,592 genes were significantly up and down-regulated, respectively. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca2+ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and up-regulation of multiple genes involved in various biological processes in chilense under salinity were identified. Through pathway analysis of DEGs, “Wnt signaling pathway” was identified as a novel pathway for the response to the salinity stress. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transporters, osmotic regulation, defense and stress response, homeostasis and transcription factors were not only salt-induced but also showed higher expression in S. chilense as compared to S. lycopersicum. Thus indicating that these genes may have an important role in salinity tolerance in S. chilense. Overall, the results of this study improve our understanding on possible molecular mechanisms underlying salt tolerance in plants in general and tomato in particular.

RabGTPase activating proteins (RabGAP) are responsible for directing the deactivation of vesicular trafficking master regulators associated to plant development, the RabGTPase proteins. Recently, RabGAPs were identified in Arabidopsis and rice, but studies were not yet reported in tomato. Herein, we identified 24 RabGAP-encoding genes in cultivated tomato (Solanum lycopersicum) and its wild relative genomes (Solanum pimpinellifolium and Solanum pennellii). We analyzed them based on their exon-intron structures, conserved protein motifs, putative subcellular localizations, phylogenetic and gene duplications analyses, interaction networks, and gene expression patterns in tomato. Phylogenetic relationship analysis also indicated that RabGAP family is classified into seven subclasses, of which subclasses I and II are plant-exclusive. Furthermore, segmental duplication events and positive evolutionary forces are associated with the maintenance of the number and function of their members. On the other hand, the protein&ndash, protein interaction networks on tomato suggested that members of subclasses I, II, and III could be associated to endocytic traffic routes. In addition, the qRT-PCR experiments in S. lycopersicum and Solanum chilense exposed to a salt stress treatment validated the differential expression patterns of 20 RabGAP genes in different tissues, development stages, and stress conditions obtained through extensive microarray-based analyses. This work suggests the critical role of RabGAP family in the context of intracellular vesicular trafficking in tomato, particularly under conditions of abiotic stress. It also contributes to the breeding programs associated with the development of crops tolerant to salt stress.

Intracellular vesicular trafficking ensures the exchange of lipids and proteins between the membranous compartments. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) play a central role in membrane fusion and they are key factors for vesicular trafficking in plants, including crops economically important such as tomato (Solanum lycopersicum). Taking advantage of the complete genome sequence available of S. lycopersicum, we identified 63 genes that encode putative SNARE proteins. Then, phylogenetic analysis allowed the classification of SNAREs in five main groups and recognizing their possible functions. A structure analysis of the genes, their syntenic relationships and their location in the chromosomes were also carried out for their characterization. In addition, the expression profiles of SNARE genes in different tissues were investigated using microarray-based analysis. The results indicated that specific SNAREs had a higher induction in leaf, root, flower and mature green fruit. S. lycopersicum is characterized for being a crop sensitive to saline stress unlike its wild relatives, such as Solanum pennellii, Solanum pimpinellifolium, Solanum habrochaites or Solanum chilense, which are tolerant. In this context, we analyzed different microarrays and evaluated and validated the transcript levels through qRT-PCR experiments. The results showed that SlGOS12.2, SlVAMP727 and SlSYP51.2 could have a positive relationship with salt stress and probably an important role in their tolerance. All these data increase our knowledge and can also be utilized to identify potential molecular targets for conferring tolerance to various stresses in tomato.

Nucleotide binding site, leucine-rich repeat receptors (NLRs) are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonization of novel habitats in a model tomato species, Solanum chilense. We used R-gene enrichment sequencing to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonization by resequencing whole genomes from three S. chilense plants from three key populations and performing approximate Bayesian computation using data from the 14 populations. Using these parameters, we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution and identified small subsets of outlier NLRs exhibiting signatures of selection across populations. NLRs under selection between habitats are more often helper genes, whereas those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R-gene adaptation during colonization of different habitats.