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To investigate the genome-wide spatial arrangement of R loci, a complete catalogue of tomato (Solanum lycopersicum) and potato (Solanum tuberosum) nucleotide-binding site (NBS) NBS, receptor-like protein (RLP) and receptor-like kinase (RLK) gene repertories was generated. Candidate pathogen recognition genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution. NBS genes frequently occur in clusters of related gene copies that also include RLP or RLK genes. This scenario is compatible with the existence of selective pressures optimizing coordinated transcription. A number of duplication events associated with lineage-specific evolution were discovered. These findings suggest that different evolutionary mechanisms shaped pathogen recognition gene cluster architecture to expand and to modulate the defence repertoire. Analysis of pathogen recognition gene clusters associated with documented resistance function allowed the identification of adaptive divergence events and the reconstruction of the evolution history of these loci. Differences in candidate pathogen recognition gene number and organization were found between tomato and potato. Most candidate pathogen recognition gene orthologues were distributed at less than perfectly matching positions, suggesting an ongoing lineage-specific rearrangement. Indeed, a local expansion of Toll/Interleukin-1 receptor (TIR)-NBS-leucine-rich repeat (LRR) (TNL) genes in the potato genome was evident. Taken together, these findings have implications for improved understanding of the mechanisms of molecular adaptive selection at Solanum R loci.

Tomato (Solanum lycopersicum) is one of the world’s most important vegetable crops. Managing the health of this crop can be particularly challenging; crop resistance may be overcome by new pathogen races while new pathogens have been introduced by global agricultural markets. Tomato is extensively used as a model plant for resistance studies and much has been attained through both genetic and biotechnological approaches. In this paper, we illustrate genomic methods currently employed to preserve resistant germplasm and to facilitate the study and transfer of resistance genes, and we describe the genomic organization of R-genes. Patterns of gene activation during disease resistance response, identified through functional approaches, are depicted. We also describe the opportunities offered by the use of new genomic technologies, including high-throughput DNA sequencing, large-scale expression data production and the comparative hybridization technique, whilst reporting multifaceted approaches to achieve genetic tomato disease control. Future strategies combining the huge amount of genomic and genetic data will be able to accelerate development of novel resistance varieties sustainably on a worldwide basis. Such strategies are discussed in the context of the latest insights obtained in this field.

Tomato (Solanum lycopersicum L.) has served as an important model system for studying the genetics and molecular basis of resistance mechanisms in plants. An unprecedented challenge is now to capitalize on the genetic and genomic achievements obtained in this species. In this study, we show that information on the tomato genome can be used predictively to link resistance function with specific sequences. An integrated genomic approach for identifying new resistance (R) gene candidates was developed. An R gene functional map was created by co-localization of candidate pathogen recognition genes and anchoring molecular markers associated with resistance phenotypes. In-depth characterization of the identified pathogen recognition genes was performed. Finally, in order to highlight expressed pathogen recognition genes and to provide a first step in validation, the tomato transcriptome was explored and basic molecular analyses were conducted. Such methodology can help to better direct positional cloning, reducing the amount of effort required to identify a functional gene. The resulting candidate loci selected are available for exploiting their specific function.

The evolutionary diversity of wild potato species makes them excellent materials for improving the narrow genetic basis of the cultivated potato Solanum tuberosum. Understanding their genetic diversity is important not only to choose the best parents for breeding, but also to design proper crossing schemes and selection strategies. The objectives of this study were to determine the resistance response to Ralstonia solanacearum, Potato virus Y and low temperatures of 21 clones of 12 potato species, and to determine their genetic diversity through simple sequence repeat (SSR) markers. Sources of resistance have been found for all the investigated traits, with high resistance variability not only between but also within species. Combined resistances were also identified, with positive implications for efficient breeding. SSR analysis allowed the detection of 12 loci and 46 alleles across all genotypes, with an average value of 3.8 alleles per locus. Both unique and rare alleles useful for marker-assisted selection were found. SSR-based cluster analysis revealed that resistant genotypes were distributed among all clusters, suggesting that genetically different resistant genotypes were identified. The information obtained in this study is discussed from a breeding perspective.

Native to South America, the tomato is now grown almost worldwide. During its domestication and improvement, important selection signatures were fixed in certain agronomic and adaption traits. Such traits include fruit morphology, which became a major target for selection over the centuries. However, little is known about precisely when some mutations arose and how they spread through the germplasm. For instance, elongated fruit variants, originating both via mutations in SUN and OVATE genes, may have arisen prior to domestication or during tomato cultivation in Europe. To gain insights into the tomato admixture and selection pattern, the genome of two tomato herbarium specimens conserved in the Herbarium Porticense (PORUN) was sequenced. Comparison of the DNA of herbarium samples collected in Italy between 1750 and 1890 with that of living tomato accessions yielded insights into the history of tomato loci selection. Interestingly, the genotype of the more recent sample (LEO90), classified in 1890 as the oblungum variety, shows several private variants in loci implicated in fruit shape determination, also present also in wild tomato samples. In addition, LEO90, sampled in the nineteenth century, is genetically more distant from cultivated varieties than the SET17 genotype, collected in the eighteenth century, suggesting that elongated tomato varieties may originate from a cross between a landrace and a wild ancestor. Findings from our study have major implications for the understanding of tomato migration patterns and for the conservation of allelic diversity and loci recovery.

Fruit flavour of traditional tomato ecotypes differs from that of modern varieties, the latter being often blamed for lack of flavour. To respond to consumer complaints breeders should know the range of genetic variability available in tomato resources, including local ecotypes, for improving flavour. For this purpose, multitrait characterization, including biochemical, sensorial and molecular analyses, was performed on 12 Italian tomato ecotypes that belong to different types (San Marzano, Sorrento, and Vesuvio). The ecotypes showed a significant variation both in glucose and citric acid content. As for amino acid determination, lysine, aspartic acid and serine showed significant variation among the three types analyzed. Sensory analysis clearly evidenced differences among genotypes: the San Marzano ecotypes revealed sensory profiles that differ from the control processing variety in perception of sweetness and sourness, whereas the Sorrento and Vesuvio ecotype profiles were similar to the fresh market control. In particular, Vesuvio genotypes exhibited a good intensity of tomato aroma and sweetness and an intermediate level of acidity. Finally, molecular characterization performed through AFLP markers provided evidence for a very high level of polymorphism: an ecotype-specific AFLP pattern was identified for at least 11 genotypes, thus defining their molecular fingerprints.

A breeding scheme based on the production of progenies with odd ploidy was followed to introduce useful genes from the wild Solanum commersonii (cmm) into S. tuberosum (tbr) genome. Hybrids from 5x x 4x crosses were characterized for traits of interest, and selection was assisted by amplified fragment length polymorphism (AFLP) analysis. As expected, most of the hybrids were aneuploids, with a trend towards a low degree of aneuploidy. Despite the fact that aneuploidy has often been associated with a reduction in male and female fertility, most of the hybrids were fertile following crosses with tbr, making it possible to produce viable offspring. A screening for resistance traits deriving from cmm was also carried out. With respect to freezing resistance, the killing temperatures of cold-acclimated genotypes were distributed between the wild and cultivated parental values, with some hybrids displaying an acclimation capacity higher than 3 degrees C. A wide variability was also found for tuber soft rot resistance, and hybrids with high levels of resistance were identified. Selection of hybrids was based on a two-stage scheme that consisted of conventional phenotypic selection followed by an estimation of the wild genome content still present in order to identify hybrids combining noteworthy traits with a low wild genome content. Previously selected cmm-specific AFLPs were used to monitor the degree of wild genome content still present in each hybrid. The percentage of cmm-specific markers ranged from 59% to 91%, with an average value of 75%. AFLP analysis was employed to assist in the selection of valuable hybrids for further breeding efforts.

Twenty-one (near) pentaploid hybrids between sexually incompatible Solanum commersonii [2x(1EBN)] and cultivated S. tuberosum [4x(4EBN)] were characterized for tuber traits and fertility. A number of genotypes resembled the S. tuberosum type in terms of stolon length and eye depth and produced tubers under long day conditions. Tuber yields were not as high as expected, probably due to lack of adaptation of the S. commersonii genome to the environmental conditions in southern Italy (on average 325 g·pt⁻¹ and 285 g·pt⁻¹ in 2003 and in 2004, respectively). Compared to 2004, in the summer of 2003, characterized by extremely high temperatures, hybrids gave a higher tuber yield than the S. tuberosum control, suggesting that in our environmental conditions the wild S. commersonii genome, rather than resulting in heterosis for tuber yield, provides better adaptation to harsh environments. Although aneuploidy has often been associated with reduced fertility, several hybrids were fertile in crosses with S. tuberosum when used as female parents. In particular, the average berry set and number of seeds per berry were 38.2% and 31.8%, respectively. Based on significant relationships between ploidy levels and all yield and fertility data measured, the presence of extra chromosome affected the parameters considered: tuber yield in 2003 and 2004, percentage of fruit set, number of seeds per berry and number of seeds per pollinated flower. Regression analysis also indicated that “Residuals” were significant for all parameters measured. Therefore, additional factors (e.g. the genetic makeup of hybrids) may be key to fertility and yield.

Tomato is a food of great relevance both due to its large-scale consumption and its richness in bioactive components. It is an important component of the traditional Mediterranean diet as well as of other diets. Nowadays, concerns about human health and environment preservation have changed the objectives of tomato breeding. In this study, eight tomato F 1 hybrids and their parental lines were analyzed for nutritional properties and agronomic traits using a new selection method that combines biochemical and agronomic evaluation. Eight traits contributing to the nutritional quality of tomato (lycopene, β-carotene, other carotenoids, flavonoids, phenolic acids, vitamins C and E, dry residue) and average yield were assessed in fifteen tomato genotypes. Furthermore the pathogen resistances possessed from these genotypes were, also, considered. In order to select valuable tomato hybrids, a nutritional index (I QUAN ) and an agronomic index (AI) were calculated. Our results suggested that the I QUAN nutritional index may be very useful to forecast the nutritional value of F 1 hybrids based on parental performance. Combining the use of the I QUAN and AI indexes, we were able to select two hybrids (MR 48 and MR 47) that contain considerable amounts of antioxidants and acceptable parameters for commercial production.

2n gametes are the result of meiotic mutations occurring during micro–and mega-sporogenesis. They have been identified in several plant species of different taxa. The potato is probably the crop plant where they have been most intensively studied and also more appropriately used for the genetic improvement of cultivated genotypes. This paper reviews how 2n gametes allow potato breeders to broaden the genetic basis of the cultivated Solarium tuberosum, introducing both new genes for the improvement of traits of interest and allelic diversity to maximize heterozygosity. We provide molecular and breeding evidence that, in the potato, 2n gametes represent a unique tool to transfer target genes from wild forms to the cultivated tetraploid gene pool. In fact, species directly crossable to S. tuberosum haploids can be exploited through sexual polyploidization crossing schemes. For those which have developed cross-ability barriers, specific crossing schemes based on ploidy bridges can be designed. In this paper we also give possible hypotheses to explain conflicting results on the genetic control and meiotic mutations responsible for 2ngamete formation in the potato.