Final Report Summary - SOLANUM (Solanum in Europe: phylogeny and genetic diversity) Solanum is a genus of nearly 1,400 species and only a small portion of them are cultivated. It is obvious that we should aim to use the traits provided by the large and unexplored diversity. This genus is important from an agricultural perspective as well as from an evolutionary standpoint. The genus consists of valuable crops like eggplant, tomato, and especially potato, all economically extremely important in European agriculture. Only a few species of the genus are native in Europe. The most important ones include Solanum dulcamara and S. nigrum belonging of the Dulcamaroid and Morelloid clades. During the Marie Curie Action project we focused on the evolutionary aspects of Solanaceae with special focus on the European species. One of our major findings during the project is the discovery of duplicated copies of the original phenylalanine (trnFGAA) gene in Solanaceae chloroplast genome, which are specific to a larger clade within the Solanoideae subfamily. This Pseudosolanoid clade consists of 29 genera and includes many economically important plants such as potato, tomato, eggplant and pepper. The pseudogenic copies are composed of several highly structured motifs that are partial residues or entire parts of the anticodon, T- and D-domains of the original trnF gene. We also found a common ATT(G)n motif and its modifications were found to border the 5’ of the duplicated regions. The duplications are found after putative promoter motifs (-35 TTGACA/-10 GAGGAT). This feature differs from previous observations reported from other plant families, e.g. Brassicaceae. The evolution of Solanum trnF pseudogene cpDNA copies in contrast to its sister genus Jaltomata is difficult to be explained in a parsimonious way because reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum may be explained by inter- or intrachromosomal recombination in the chloroplast. Our other major findings are related to the application of a recently developed core set of intron-targeting markers and I detected such variation among accessions of the eight different species of black nightshades (Solanum sect. Solanum). Members of this group are important sources of food, mostly in Africa, while others are poisonous weeds with almost global distribution. The tested 29 primers were designed previously for potato based on Solanaceae EST and other genomic databases and targeted 16 different genes. Our results showed that Solanum intron-targeting markers are not very polymorphic and we identified considerable structure among accessions indicating fairly high interspecies differentiation. Further analyses showed that inbreeding is unlikely to be the major driving force in determining the genetic structure of the analyzed species. All phylogenetic analyses resolved the species included in our study as well supported groups, but provided weak information about their relationships. In summary, indel markers would be useful for the assignment of new Solanum germplasm to taxonomic groups or to identify certain taxa. They could also be used to address important question about genetic diversity and should yield results comparable to other markers covering the whole genome. New Intron-targeting (IT) markers were also developed from next generation sequencing (NGS) derived transcript sequencing data from the potato cultivar White Lady. The applicability of the IT markers was analyzed in other potato enotypes, and their transferability was studied in other Solanum species: section Archaesolanum (5 species), European species of sect. Solanum (6 species) and in a Solanum nigrum population (11 genotypes). Out of 250 randomly chosen transcript sequences, 144 intron harboring loci could be identified for which primer pairs were designed on exons flanking the putative introns. The usefulness of the IT primers was experimentally analyzed on a subset of 40 randomly chosen loci. By localizing the detected 17 polymorphic loci 11 of the 12 potato chromosomes could be identified. Specificity of the designed IT primers was tested by sequence analysis of amplified IT fragments in a randomly chosen locus. The observed levels of polymorphisms and genetic diversity suggest that the developed markers are adequate for characterizing genetic variation and provide efficient tools for potato genetic studies, namely DNA fingerprinting, marker-assisted selection, genetic mapping and diversity analysis. Once a comprehensive transcriptome database is generated the number of NGS-derived IT markers that could be utilized for fine mapping and in various types of molecular analysis may rapidly increase.