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.

Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8 M and 56.4 M of 30–150 bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC.

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.