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Tomato (Solanum lycopersicum L.) is one of the most important crops worldwide. In this study, we used 7720 genome-wide SNPs to characterize the genetic diversity within a tomato germplasm collection enriched with 64 accessions from southern Italy of the so called "da serbo" type i.e. drought-tolerant and long storage landraces. Notwithstanding the relatively small collection area, 1575 (20.4%) polymorphic SNPs, mostly on Chr11, detected considerable levels of genetic variation. Maximum parsimony analysis of genetic distance revealed four main clusters and clearly separated most "da serbo" landraces from the outgroups. One of the clusters grouped the landraces from the Mount Vesuvius area, though no further indications of a geographic-specific structure were found. STRUCTURE analysis confirmed the presence of four genetic groups within the collection, with admixture between them. A survey of non-synonymous SNPs highlighted several mutations in genes related to stress tolerance and fruit maturation/quality. Overall, our results suggest possible exchange of "da serbo" genetic material between southern Italy regions and indicate that the long storage "da serbo" germplasm could be a promising reservoir of peculiar alleles for traits of interest. [ABSTRACT FROM AUTHOR]

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 65.8M and 56.4M 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. [ABSTRACT FROM AUTHOR]

Polyploidy and hybridization often provide genetic and phenotypic variability upon which evolutionary forces can act and are therefore considered as fundamental evolutionary processes for diversification in vascular plants, resulting in plant adaptation to changing environmental conditions. However, polyploid speciation is a complex process, potentially involving ecological divergence between lineages of different ploidies and/or genetic mixing with parental species. In the present study, we investigated the origins and dynamics of the Sicilian endemic orchid Neotinea commutata and its relationships with putative parental species. Molecular, cytogenetic and morphometric analyses revealed that N. commutata is a tetraploid derived from hybridization between N. tridentata and N. lactea. However, we also found variation in chromosome number and genome content within N. commutata, indicating that other events, including the possible replacement of the diploid progenitor N. tridentata by N. commutata, may have contributed, or still be contributing, to the evolutionary dynamics of this neoendemic taxon, which appears to be partially reproductively isolated from its progenitors. Distributional data indicate that the allopolyploid N. commutata has been able to establish and spread on the island when compared with its putative parents. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 707-720. [ABSTRACT FROM AUTHOR]