title: Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform.
abstract: 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.
authors.affiliation: Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Adriana
authors.initials: A
authors.lastname: Sacco
authors.affiliation: Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Valentino
authors.initials: V
authors.lastname: Ruggieri
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'Orticoltura, Pontecagnano, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: Parisi
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'Orticoltura, Pontecagnano, Italy.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Festa
authors.affiliation: Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Maria Manuela
authors.initials: MM
authors.lastname: Rigano
authors.affiliation: Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE University of Tuscia, Viterbo, Italy).
authors.forename: Maurizio Enea
authors.initials: ME
authors.lastname: Picarella
authors.affiliation: Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE University of Tuscia, Viterbo, Italy).
authors.forename: Andrea
authors.initials: A
authors.lastname: Mazzucato
authors.affiliation: Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Amalia
authors.initials: A
authors.lastname: Barone
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D005638:Fruit / Q000235:genetics / Q000378:metabolism; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci