The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation. In addition, the characterisation of very diversified materials with molecular markers offers a unique opportunity to define significant marker-trait associations of biological and agronomic interest. Here, 50 tomato landraces (mainly collected in central Italy), nine vintage and modern cultivars, and two wild outgroups were grown at two locations in central Italy and characterised for 15 morpho-physiological traits and 29 simple sequence repeat (SSR) loci. The markers were selected to include a group of loci in regions harbouring reported quantitative trait loci (QTLs) that affect fruit size and/or shape (Q-SSRs) and a group of markers that have not been mapped or shown to have a priori known linkage (NQ-SSRs). As revealed by univariate and multivariate analyses of morphological data, the landraces grouped according to vegetative and reproductive traits, with emphasis on fruit size, shape and final destination of the product. Compared to the low molecular polymorphism reported in tomato modern cultivars, our data reveal a high level of molecular diversity in landraces. Such diversity has allowed the inference of the existence of a genetic structure that was factored into the association analysis. As the proportion of significant associations is higher between the Q-SSR subset of markers and the subset of traits related to fruit size and shape than for all of the other combinations, we conclude that this approach is valid for establishing true-positive marker-trait relationships in tomato.

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 variation 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 resistance 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 attributed 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 candidate 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 demonstrated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs.

Increased interest toward traditional tomato varieties is fueled by the need to rescue desirable organoleptic traits and to improve the quality of fresh and processed tomatoes in the market. In addition, the phenotypic and genetic variation preserved in tomato landraces represents a means to understand the genetic basis of traits related to health and organoleptic aspects and improve them in modern varieties. To establish a framework for this approach, we studied the content of several metabolites in a panel of Italian tomato landraces categorized into three broad fruit type classes (flattened/ribbed, pear/oxheart, round/elongate). Three modern hybrids, corresponding to the three fruit shape typologies, were included as reference. Red ripe fruits were morphologically characterized and biochemically analyzed for their content in glycoalkaloids, phenols, amino acids, and Amadori products. The round/elongate types showed a higher content in glycoalkaloids, whereas flattened types had higher levels of phenolic compounds. Flattened tomatoes were also rich in total amino acids and in particular in glutamic acid. Multivariate analysis of amino acid content clearly separated the three classes of fruit types. Making allowance of the very low number of genotypes, phenotype-marker relationships were analyzed after retrieving single nucleotide polymorphisms (SNPs) among the landraces available in the literature. Sixty-six markers were significantly associated with the studied traits. The positions of several of these SNPs showed correspondence with already described genomic regions and QTLs supporting the reliability of the association. Overall the data indicated that significant changes in quality-related metabolites occur depending on the genetic background in traditional tomato germplasm, frequently according to specific fruit shape categories. Such a variability is suitable to harness association mapping for metabolic quality traits using this germplasm as an experimental population, paving the way for investigating their genetic/molecular basis, and facilitating breeding for quality-related compounds in tomato fruits.

A TILLING allele of the tomato Aux/IAA9 gene offers new insights into fruit set mechanisms and perspectives for breeding seedless tomatoes. (2015) Molecular Breeding, vol. 35 (n° 1).

Tomato ( Solanum lycopersicum L.) is one of the most cultivated vegetable in the world and it represents a large source of bioactive compounds, including carotenoids and polyphenols (phenolic acids and flavonoids). However, the concentration of flavonoids in tomato is considered sub-optimal, particularly because anthocyanins are not generally present. Therefore, this crop has been the object of an intense metabolic engineering in order to obtain anthocyanin-enriched tomatoes by using either breeding or transgenic strategies. Some wild tomato species, such as S. chilense and S. cheesmaniae , biosynthesize anthocyanins in the fruit sub-epidermal tissue, and some alleles from those genotypes have been introgressed into a new developed purple tomato line, called “Sun Black” (SB). It is a tomato line with a purple skin color, both in green and in red fruit stages, due to the biosynthesis of anthocyanins in the peel, and a normal red color pulp, with a taste just like a traditional tomato. SB is the result of a breeding programme and it is not a genetically modified (GM) product. We report the chemical characterization and structure elucidation of the attractive anthocyanins found in the peel of SB tomato, as well as other bioactive compounds (carotenoids, polyphenols, vitamin C) of the whole fruit. Using one- and two-dimensional NMR experiments, the two main anthocyanins were identified to be petunidin 3- O -[6″- O -(4 ‴ - O - E - p- coumaroyl-α-rhamnopyranosyl) -β-glucopyranoside]-5- O -β-glucopyranoside (petanin) and malvidin 3- O -[6″- O -(4 ‴ - O - E - p- coumaroyl-α-rhamnopyranosyl)-β-glucopyranoside]-5- O -β-glucopyranoside (negretein). The total anthocyanins in the whole ripe fruit was 1.2 mg/g dry weight (DW); 7.1 mg/100 g fresh weight (FW). Chlorogenic acid (the most abundant phenolic acid) was 0.6 mg/g DW; 3.7 mg/100 g FW. The main flavonol, rutin was 0.8 mg/g DW; 5 mg/100 g FW. The total carotenoid content was 211.3 μg/g DW; 1,268 μg/100 g FW. The total phenolic content was 8.6 mg/g DW; 52.2 mg/100 g FW. The vitamin C content was 37.3 mg/100 g FW. The antioxidant activities as measured by the TEAC and ORAC assays were 31.6 and 140.3 μmol TE/g DW, respectively (193 and 855.8 μmol TE/100 g FW, respectively). The results show the unique features of this new tomato genotype with nutraceutical properties.

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The development of the ovary into a fruit depends on pollination and fertilization. It has been proposed that the restriction of ovary growth before pollination is because of the stamens acting as negative regulators. Accordingly, the silencing of genes responsible for stamen identity has been correlated with parthenocarpy in different species. The tomato (Solanum lycopersicum L.) parthenocarpic fruit (pat) mutation associates autonomous ovary development with homeotic transformation of the anthers and aberrancy of ovules in the ovary. In this study, we tested the hypothesis that stamen aberrations and parthenocarpy in pat are driven by cues coming from the altered expression of class B MADS box genes. The data showed that the Pat locus is not allelic to either of the two tomato mutations putatively involved in the B function, stamenless (sl)-2 and pistillate (pi) or to genes encoding class B transcription factors. Whereas pat pi double mutants were not recovered because of tight linkage, pat sl-2 double mutants showed mainly epistatic effects. The developmental regulation of the Sl DEFICIENS (DEF) gene in the wild-type (WT) at anthesis as well as its differential transcription in the pat ovary suggest that it plays a role in the control of ovary growth. Accordingly, when compared with the WT, the gene was also differentially expressed in the parthenocarpic fruit-2 (pat-2) mutant, that is not allelic to pat and has normal ovule development. Altogether the results indicate that in tomato SlDEF plays a role in the control of ovary growth and that the pat mutation is located upstream of this regulatory cascade.

Parthenocarpy in a broad sense includes those processes that allow the production of seedless fruits. Such fruits are favorable to growers, because they are set independently of successful pollination, and to processors and consumers, because they are easier to deal with and to eat. Seedless fruits however represent a biological paradox because they do not contribute to offspring production. In this work, the occurrence of parthenocarpy in Angiosperms was investigated by conducting a bibliographic survey. We distinguished monospermic (single seeded) from plurispermic (multiseeded) species and wild from cultivated taxa. Out of 96 seedless taxa, 66% belonged to plurispermic species. Of these, cultivated species were represented six times higher than wild species, suggesting a selective pressure for parthenocarpy during domestication and breeding. In monospermic taxa, wild and cultivated species were similarly represented. The occurrence of parthenocarpy in wild species suggests that seedlessness may have an adaptive role. In monospermic species, seedless fruits are proposed to reduce seed predation through deceptive mechanisms. In plurispermic fruit species, parthenocarpy may exert an adaptive advantage under suboptimal pollination regimes, when too few embryos are formed to support fruit growth. In this situation, parthenocarpy offers the opportunity to accomplish the production and dispersal of few seeds, thus representing a selective advantage. Approximately 20 sources of seedlessness have been described in tomato. Excluding the EMS induced mutation parthenocarpic fruit (pat), the parthenocarpic phenotype always emerged in biparental populations derived from wide crosses between cultivated tomato and wild relatives. Following a theory postulated for apomictic species, we argument that wide hybridization could also be the force driving parthenocarpy, following the disruption of synchrony in time and space of reproductive developmental events, from sporogenesis to fruit development. The high occurrence of polyploidy among parthenocarpic species supported this suggestion. Other commonalities between apomixis and parthenocarpy emerged from genetic and molecular studies of the two phenomena. Such insights may improve the understanding of the mechanisms underlying these two reproductive variants of great importance to modern breeding.