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The global increasing demand of lettuce is pushing farmers to boost their production through several technical means, including mulching and nitrogen fertilization. However, from an environmental protection perspective, the role of scientific research is to limit the excessive use of some chemical approaches. This research aims to evaluate the possible effects of two mulching films (black polyethylene, PE, and brown photoselective film, BF) and two treatments with a plant growth-promoting product, containing Trichoderma spp., (non-treated, - Control and treated with RYZO PEP UP, - TR), on the productive and qualitative traits of lettuce grown under four regimes of nitrogen (0, 30, 60 and 90 kg ha&minus, 1, N0, N30, N60, and N90, respectively). The marketable yield increased at higher nitrogen levels, but without differences between the N60 and N90 doses. The photoselective film elicited marketable yield, with an 8% increase over PE. N fertilization also improved photochemical efficiency (higher Soil Plant Analysis Development and chlorophyllous pigments biosynthesis), as well as antioxidant activities (lipophilic&mdash, LAA and hydrophilic&mdash, HAA) and bioactive compounds (phenols and total ascorbic acid&mdash, TAA). Interestingly, Trichoderma spp. had a positive effect on these qualitative parameters, especially when combined with mulching films, where the increase generated by PE-TR treatment over the all other treatments was 16.3% and 16.8% for LAA and HHA, respectively. In all treatments, the nitrate leaves content was consistently always within the legal limit imposed by the European community. Overall, although Trichoderma spp. did not engender a marked effect on yield, probably due to the short crop cycle, its positive effect on some quality traits is an interesting starting point for further research.

Nitrogen is the primary technical means responsible for food production increase, but on the other hand, wise management is needed because its excessive use can have a negative impact on the environment and on green leafy vegetable quality, such as that rocket. Rocket has the characteristics of accumulating nitrate in leaves with possible impacts on human health. In order to overcome this issue, researchers are focusing their attention on the use of alternative means, such as plant biostimulant application. The scope of this study was to assess the effect of legume-derived protein hydrolysate(LDPH) and tropical plant extract(TPE), combined with various doses of nitrogen (0 kg ha&minus, 1 non-fertilized, N0), 60 kg ha&minus, 1 (sub-optimal, N1), 80 kg ha&minus, 1 (optimal, N2), and 100 kg ha&minus, 1 (supra-optimal, N3)), in order to reduce nitrogen use, boost yield, and enhance the chemical and nutritional value of leaves without significantly accumulating nitrate. Both vegetal-based plant biostimulants enhanced plant growth, boosted the marketable yield (especially at N0 and N1 levels, by 38.2% and 28.2%, respectively, compared to the non-treated control), and increased the SPAD (Soil Plant Analysis Development) index and leaf pigments content, such as chlorophyll and carotenoids, especially in treated-LDPH rocket. The plant-based biostimulants also produced a major amplification in lipophilic antioxidant activity (+ 48%) and total ascorbic acid content (average + 95.6%), especially at low nitrogen fertilization levels, and maintained nitrate content under the legal European Comission limits.

The present study investigated the transcriptomic and metabolomic changes elicited in tomato plants (Solanum lycopersicum cv. Micro-Tom) following treatments with the biocontrol agent T. harzianum strain M10 or its secondary metabolite harzianic acid (HA), in the presence or absence of the soil-borne pathogen Rhizoctonia solani. Transcriptomic analysis allowed the identification of differentially expressed genes (DEGs) that play a pivotal role in plant growth, development and resistance to biotic stress. Overall, the results support the ability of T. harzianum M10 to activate defense responses in infected tomato plants. We observed an induction of hormone-mediated signaling, as shown by the up-regulation of genes involved in the ethylene and jasmonate (ET/JA) biosynthesis. Further, the protective action of T. harzianum on the host was revealed by the over-expression of genes able to detoxify cells from reactive oxygen species (ROS). Moreover, the over-expression of genes involved in glycolysis, tricarboxylic acid cycle (TCA) and photosynthesis help to understand how this strain promotes plant growth and development. On the other hand, HA treatment also stimulated tomato response to the pathogen by inducing the expression of several genes involved in different defense mechanisms (including protease inhibitors, resistance proteins like CC-NBS-LRR) and activating ET/JA- and salicylic acid (SA)-mediated signaling pathways. The accumulation of steroidal glycoalkaloids caused by either T. harzianum or purified HA, as determined by metabolomic analysis, confirmed the complexity of the plant response to beneficial microbes in terms of secondary metabolism involved in defense mechanisms against pathogens.

Phenolics are antioxidants present in tomato fruit that confer healthy benefits and exhibit crucial roles for plant metabolism and response to environmental stimuli. An approach based on two genomics platforms was undertaken to identify candidate genes associated to higher phenolics content in tomato fruit. A comparative transcriptomic analysis between the S. pennellii Introgression Line 7-3, which produced an average higher level of fruit phenolics, and the cultivated variety M82, revealed that their differences are attributed to genes involved in phenolics accumulation into the vacuole. The up-regulation of genes coding for one MATE-transporter, one vacuolar sorting protein and three GSTs supported this hypothesis. The observed balancing effect between two ethylene responsive factors (ERF1 and ERF4) was also hypothesized to drive the transcriptional regulation of these transport genes. In order to confirm such model a TILLING platform was explored. A mutant was isolated harbouring a point mutation in the ERF1 cds that affects the protein sequence and its expected function. Fruits of the mutant exhibited a significant reduced level of phenolics than the control variety. Changes in the expression of genes involved in sequestration of phenolics in vacuole also supported the hypothesized key-role of ERF1 in orchestrating these genes.

Background The environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sensorial attributes. We used a systems biology approach to elucidate the complex interacting mechanisms regulating the plasticity of sensorial traits. To investigate environmentally challenged transcriptomic and metabolomic remodeling and evaluate the organoleptic consequences of such variations we grown three tomato varieties, Heinz 1706, whose genome was sequenced as reference and two ?local? ones, San Marzano and Vesuviano in two different locations of Campania region (Italy). Results Responses to environment were more pronounced in the two ?local? genotypes, rather than in the Heinz 1706. The overall genetic composition of each genotype, acting in trans, modulated the specific response to environment. Duplicated genes and transcription factors, establishing different number of network connections by gaining or losing links, play a dominant role in shaping organoleptic profile. The fundamental role of cell wall metabolism in tuning all the quality attributes, including the sensorial perception, was also highlighted. Conclusions Although similar fruit-related quality processes are activated in the same environment, different tomato genotypes follow distinct transcriptomic, metabolomic and sensorial trajectories depending on their own genetic makeup. Electronic supplementary material The online version of this article (doi:10.1186/s12870-017-1008-4) contains supplementary material, which is available to authorized users.

Endophytic fungi have a great influence on plant health and growth, and are an important source of bioactive natural compounds. Organic extracts obtained from the culture filtrate of an endophytic strain of Talaromyces pinophilus isolated from strawberry tree (Arbutus unedo) were studied. Metabolomic analysis revealed the presence of three bioactive metabolites, the siderophore ferrirubin, the platelet-aggregation inhibitor herquline B and the antibiotic 3-O-methylfunicone. The latter was the major metabolite produced by this strain and displayed toxic effects against the pea aphid Acyrthosiphon pisum (Homoptera Aphidiidae). This toxicity represents an additional indication that the widespread endophytic occurrence of T. pinophilus may be related to a possible role in defensive mutualism. Moreover, the toxic activity on aphids could promote further study on 3-O-methylfunicone, or its derivatives, as an alternative to synthetic chemicals in agriculture.

The tomato is a model species for fleshy fruit development and ripening, as well as for genomics studies of others Solanaceae. Many genetic and genomics resources, including databases for sequencing, transcriptomics and metabolomics data, have been developed and are today available. The purpose of the present work was to uncover new genes and/or alleles that determine ascorbic acid and carotenoids accumulation, by exploiting one Solanum pennellii introgression lines (IL7-3) harboring quantitative trait loci (QTL) that increase the content of these metabolite in the fruit. The higher ascorbic acid and carotenoids content in IL7-3 was confirmed at three fruit developmental stages. The tomato genome reference sequence and the recently released S. pennellii genome sequence were investigated to identify candidate genes that might control ascorbic acid and carotenoids accumulation. First of all, a refinement of the wild region borders in the IL7-3 was achieved by analyzing CAPS markers designed in our laboratory. Afterwards, six candidate genes associated to ascorbic acid and one with carotenoids metabolism were identified exploring the annotation and the Gene Ontology terms of genes included in the region. Variants between the sequence of the wild and the cultivated alleles of these genes were investigated for their functional relevance and their potential effects on the protein sequences were predicted. Transcriptional levels of candidate genes in the introgression region were extracted from RNA-Seq data available for the entire S. pennellii introgression lines collection and verified by Real-Time qPCR. Finally, seven IL7-3 sub-lines were genotyped using 28 species-specific markers and then were evaluated for metabolites content. These analyses evidenced a significant decrease in transcript abundance for one 9-cis-epoxycarotenoid dioxygenase and one L-ascorbate oxidase homolog, whose role in the accumulation of carotenoids and ascorbic acid is discussed. Comprehensively, the reported results demonstrated that combining genetic and genomic resources in tomato, including bioinformatics tools, was a successful strategy to dissect one QTL for the increase of ascorbic acid and carotenoids in tomato fruit.

Fruit quality is a major focus for most conventional and innovative tomato breeding strategies, with particular attention being paid to fruit antioxidant compounds. Tomatoes represent a major contribution to dietary nutrition worldwide and a reservoir of diverse antioxidant molecules. In a previous study, we identified two Solanum pennellii introgression lines (IL7-3 and IL12-4) harbouring quantitative trait loci (QTL) that increase the content of ascorbic acid (AsA), phenols and soluble solids (degrees Brix; _Bx) in tomato fruit. The purpose of the present work was to pyramid into cultivated varieties the selected QTL for enhanced antioxidant and _Bx content. To better understand the genetic architecture of each QTL, the two ILs were crossed to the recurrent parent M82 (ILH7-3 and ILH12-4) and between them (ILH7-3?12-4). F1 hybrids (ILH7-3?12-4) were then selfed up to obtain F3 progenies in order to stabilize the favourable traits at the homozygous condition. Species-specific molecular markers were identified for each introgressed region and allowed us to select four F2 genotypes carrying both introgressions at the homozygous condition. The F3 double homozygous plants displayed AsA, total phenols and _Bx content significantly higher than M82. Therefore, they may represent suitable genetic material for breeding schemes aiming to increase antioxidant content in tomato fruit.

During its evolution and domestication Solanum lycopersicum has undergone various genetic ‘bottlenecks’ and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape var- iation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resis- tance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attrib- uted to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit weight and locule number. Genotyping was carried out using the tomato array platform SolCAP able to interrogate 7,720 SNPs. In the whole collection 87.1% markers were polymorphic but they decreased to 44–54% when considering groups of genotypes with different origin. The neighbour-joining tree analysis clustered the 123 genotypes into two main branches. The STRUCTURE analysis with K = 3 also divided the population on the basis of fruit size. A genomic-wide association strategy revealed 36 novel markers associated to the variation of 15 traits. The markers were mapped on the tomato chromosomes together with 98 candi- date genes for the traits analyzed. Six regions were evidenced in which candidate genes co-localized with 19 associated SNPs. In addition, 17 associated SNPs were localized in genomic regions lacking candidate genes. The identification of these markers demon- strated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs.

Tomato (Solanum lycopersicum) is a crucial component of the hu- man diet because of its high nutritional value and the antioxidant content of its fruit. As a member of the Solanaceae family, it is considered a model species for genomic studies in this family, especially since its genome has been completely sequenced. Among genomic resources available, Solanum pennellii introgres- sion lines represent a valuable tool to mine the genetic diversity present in wild species. One introgression line, IL12-4, was previously selected for high ascorbic acid (AsA) content, and a transcriptomic analysis indicated the involvement of genes control- ling pectin degradation in AsA accumulation. In this study the integration of data from different “omics” platforms has been ex- ploited to identify candidate genes that increase AsA belonging to the wild region 12-4. Thirty-two genes potentially involved in pathways controlling AsA levels were analyzed with bioinformatic tools. Two hundred-fifty nonsynonymous polymorphisms were detected in their coding regions, and 11.6% revealed deleterious effects on predicted protein function. To reduce the number of genes that had to be functionally validated, introgression sublines of the region 12–4 were selected using species-specific polymor- phic markers between the two Solanum species. Four sublines were obtained and we demonstrated that a subregion of around 1 Mbp includes 12 candidate genes potentially involved in AsA accumulation. Among these, only five exhibited structural delete- rious variants, and one of the 12 was differentially expressed between the two Solanum species. We have highlighted the role of three polymorphic pectinesterases and inhibitors of pectinester- ases that merit further investigation.

Water deficit strongly affects plant yield and quality. However, plants can minimize drought injury by adaptation me-chanisms that have evolved to escape harmful conditions. The response to water deprivation is a complex trait con-trolled by several genes. In order to gain a deeper understanding of drought response mechanisms in tomato, a collec-tion of 27 genotypes was studied under different water deficit conditions. Since developmental stages might be differ-ently influenced by drought, analyses were carried out on young plantlets during fruit setting. The only genotype that showed good performances both as water retention and fruit production was the ecotype Siccagno. All the genotypes were analyzed at molecular level with the aim of detecting structural polymorphisms in selected stress-responsive genes. In addition, the expression level of a number of these genes was measured in the genotypes more tolerant to water defi-cit. Many polymorphisms were detected in six stress-responsive genes, and some could imply significant modifications in the protein structure. Furthermore, the expression analysis by RT-qPCR of three stress-responsive genes allowed ar-guing that a higher level of expression of the gene erd15 might be related to the better response to water deficit exhib-ited by Siccagno. Similarly, the lower expression of eight genes in the same genotype analysed through a microarray experiment confirmed the involvement of these stress-related genes in the tomato response to drought. Further investi-gations are required for a better comprehension of the mechanisms underlying response to water deficit in tomato by exploiting the genetic resource identified as more tolerant. The use of new technologies able to globally analyze struc-tural polymorphism and expression level of genes will succeed to identify crucial genes involved in stress response in the ecotype Siccagno grown under different water regimes.

Tomato is one of the most important vegetable crop worldwide with a total production of around 141 million tons on a cultivated area of around 5 million hectares (FAOSTAT, 2009, http://faostato.fao.org). Among the most representative countries, Italy contributes with more than 6 million tons to the world production, on a cultivated area of around 117.000 hectares, both in open fields and greenhouses (FAOSTAT, 2009). This crop represents also one of the major products of the food industry worldwide and Italy ranks first for processing tomato production among Countries of the Mediterranean Region (World Processing Tomato Council, 2009, www.wptc.to). Indeed, the high variability of tomato fruits, ranging from the cherry type to the big round or elongated berry, supplies both fresh market and processing products, such as paste, juice, sauce, powder or whole. In the last years, tomato consumption has further increased since it was demonstrated that tomato fruit could protect against diseases, such as cancer and cardiovascular disorders, due to its antioxidant properties (Rein et al., 2006). Tomato fruits are particularly rich of nutritional compounds such as lycopene and alfa-carotene, vitamin C, flavonoids and hydroxycinnamic acid derivatives whose intake would account for health benefits. The cultivated tomato (Solanum lycopersicum) belongs to the Solanaceae family that includes more than 3.000 species, among which 12 represent tomato wild relatives. These species exhibit a wide variety of adaptation to diverse habitats, plant morphology, fruit size and colour, the latter varying from green to white, yellow, pink, red, brown, depending mainly on the metabolites fruit content. The wild related tomato species represent a potential reservoir of useful genes that have been greatly used in breeding programs (Bai & Lindhout, 2007; Gur & Zamir, 2004). Indeed, this vegetable is one of the most investigated crop both at genetic and genomic level not only because of its economic importance but also because it is one of the best characterized plant systems. It has diploid genetics (24 somatic chromosomes), a small genome size (950 Mb per haploid nucleus), is self-pollinated, has a short generation time, is easily reproduced by seed and vegetative propagation and is crosscompatible with many wild species. All these characteristics make it amenable to genetic analysis.

Background Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits. Results Here, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars. Conclusions The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.

Increased levels of antioxidants such as ascorbic acid (AsA) and phenols in tomato fruit provide health benefits to consumers through a higher intake in the diet. In fact, antioxidants are involved in the prevention of proliferative and degenerative diseases, such as cancer and cardiovascular ones. Although the metabolism of major antioxidants has been characterized in detail, knowledge on regulatory mechanisms of their content in tomatoes remains still elusive. The aim of the work was to identify genetic and molecular mechanisms controlling AsA and phenol accumulation in ripe tomatoes. In order to identify QTLs controlling antioxidant accumulation in tomato fruit we carried out a comparative analysis of Solanum pennellii x S. lycopersicum cv.M82introgression lines (ILs) over three year trials in greenhouse environment. Also, to dissect QTLs in candidate genes we performed a comparative transcriptomic analysis in tomato pericarp, total RNA from the IL12-4, IL7-3, IL10-1 and M82was hybridized on a combimatrix TomatArray 1.0 over two consecutive years. Among ILs, the IL12-4 showed higher AsA accumulation than M82, the IL 7-3 higher AsA and phenols accumulation and the IL 10-1 lower accumulation of AsA. The transcriptomic approach allowed to identify 253 differentially expressed transcripts in the IL12-4, 260 in the IL 7-3 and 239 in the IL 10-1. Based on functional annotation, gene ontology classification and hierarchical clustering, subsets of differentially expressed transcripts were used to develop model networks describing mechanisms controlling accumulation of antioxidant in tomato fruit. The models we identified explain variations in AsA and phenols levels in terms of metabolic flux and alternative pathways, precursor availability, demand for antioxidants, abundance of reactive oxygen species and ethylene signalling. Currently, efforts are focusing on the development of new molecular markers and innovative breeding approach designs are in progress aimed at pyramiding QTLs for nutritional quality in modern cultivars.

Background High levels of ascorbic acid (AsA) in tomato fruits provide health benefits for humans and also play an important role in several aspects of plant life. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. The transcriptional control of AsA levels in fruits can be investigated by combining the advanced genetic and genomic resources currently available for tomato. A comparative transcriptomic analysis of fruit tissues was carried out on an introgression line containing a QTL promoting AsA accumulation in the fruit, using a parental cultivar with lower AsA levels as a reference. Results Introgression line IL 12-4 (S. pennellii in a S. lycopersicum background) was selected for transcriptomic analysis because it maintained differences in AsA levels compared to the parental genotypes M82 and S. pennellii over three consecutive trials. Comparative microarray analysis of IL 12-4 and M82 fruits over a 2-year period allowed 253 differentially-expressed genes to be identified, suggesting that AsA accumulation in IL 12-4 may be caused by a combination of increased metabolic flux and reduced utilization of AsA. In particular, the upregulation of a pectinesterase and two polygalacturonases suggests that AsA accumulation in IL12-4 fruit is mainly achieved by increasing flux through the L-galactonic acid pathway, which is driven by pectin degradation and may be triggered by ethylene. Conclusions Based on functional annotation, gene ontology classification and hierarchical clustering, a subset of the 253 differentially-expressed transcripts was used to develop a model to explain the higher AsA content in IL 12-4 fruits in terms of metabolic flux, precursor availability, demand for antioxidants, abundance of reactive oxygen species and ethylene signaling.

In recent years, interest in tomato breeding for enhanced antioxidant content has increased as medical research has pointed to human health benefits from antioxidant dietary intake. Ascorbate is one of the major antioxidants present in tomato, and little is known about mechanisms governing ascorbate pool size in this fruit. In order to provide further insights into genetic mechanisms controlling ascorbate biosynthesis and accumulation in tomato, we investigated the fruit transcriptome profile of the Solanum pennellii introgression line 10-1 that exhibits a lower fruit ascorbate level than its cultivated parental genotype. Our results showed that this reduced ascorbate level is associated with an increased antioxidant demand arising from an accelerated oxidative metabolism mainly involving mitochondria, peroxisomes, and cytoplasm. Candidate genes for controlling ascorbate level in tomato fruit were identified, highlighting the role of glycolysis, glyoxylate metabolism, and purine breakdown in modulating the ascorbate pool size. Electronic supplementary material The online version of this article (doi:10.1007/s10528-012-9531-3) contains supplementary material, which is available to authorized users.

Background Genome Wide Association Studies (GWAS) have been recently used to dissect complex quantitative traits and identify candidate genes affecting phenotype variation of polygenic traits. In order to map loci controlling variation in tomato marketable and nutritional fruit traits, we used a collection of 96 cultivated genotypes, including Italian, Latin American, and other worldwide-spread landraces and varieties. Phenotyping was carried out by measuring ten quality traits and metabolites in red ripe fruits. In parallel, genotyping was carried out by using the Illumina Infinium SolCAP array, which allows data to be collected from 7,720 single nucleotide polymorphism (SNP) markers. Results The Mixed Linear Model used to detect associations between markers and traits allowed population structure and relatedness to be evidenced within our collection, which have been taken into consideration for association analysis. GWAS identified 20 SNPs that were significantly associated with seven out of ten traits considered. In particular, our analysis revealed two markers associated with phenolic compounds, three with ascorbic acid, β-carotene and trans-lycopene, six with titratable acidity, and only one with pH and fresh weight. Co-localization of a group of associated loci with candidate genes/QTLs previously reported in other studies validated the approach. Moreover, 19 putative genes in linkage disequilibrium with markers were found. These genes might be involved in the biosynthetic pathways of the traits analyzed or might be implied in their transcriptional regulation. Finally, favourable allelic combinations between associated loci were identified that could be pyramided to obtain new improved genotypes. Conclusions Our results led to the identification of promising candidate loci controlling fruit quality that, in the future, might be transferred into tomato genotypes by Marker Assisted Selection or genetic engineering, and highlighted that intraspecific variability might be still exploited for enhancing tomato fruit quality. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0337-9) contains supplementary material, which is available to authorized users.

Background Tomato is an economically important crop with fruits that are a significant source of bioactive compounds such as ascorbic acid and phenolics. Nowadays, the majority of the enzymes of the biosynthetic pathways and of the structural genes controlling the production and the accumulation of antioxidants in plants are known; however, the mechanisms that regulate the expression of these genes are yet to be investigated. Here, we analyzed the transcriptomic changes occurring during ripening in the fruits of two tomato cultivars (E1 and E115), characterized by a different accumulation of antioxidants, in order to identify candidate genes potentially involved in the biosynthesis of ascorbic acid and phenylpropanoids. Results RNA sequencing analyses allowed identifying several structural and regulator genes putatively involved in ascorbate and phenylpropanoids biosynthesis in tomato fruits. Furthermore, transcription factors that may control antioxidants biosynthesis were identified through a weighted gene co-expression network analysis (WGCNA). Results obtained by RNA-seq and WGCNA analyses were further confirmed by RT-qPCR carried out at different ripening stages on ten cultivated tomato genotypes that accumulate different amount of bioactive compounds in the fruit. These analyses allowed us to identify one pectin methylesterase, which may affect the release of pectin-derived D-Galacturonic acid as metabolic precursor of ascorbate biosynthesis. Results reported in the present work allowed also identifying one L-ascorbate oxidase, which may favor the accumulation of reduced ascorbate in tomato fruits. Finally, the pivotal role of the enzymes chalcone synthases (CHS) in controlling the accumulation of phenolic compounds in cultivated tomato genotypes and the transcriptional control of the CHS genes exerted by Myb12 were confirmed. Conclusions By using transcriptomic analyses, candidate genes encoding transcription factors and structural genes were identified that may be involved in the accumulation of ascorbic acid and phenylpropanoids in tomato fruits of cultivated genotypes. These analyses provided novel insights into the molecular mechanisms controlling antioxidants accumulation in ripening tomato fruits. The structural genes and regulators here identified could also be used as efficient genetic markers for selecting high antioxidants tomato cultivars. Electronic supplementary material The online version of this article (10.1186/s12864-019-5428-4) contains supplementary material, which is available to authorized users.