Diversity Between Italian Landraces and Contemporary Tomato Varieties

Italy is considered one of the secondary center of diversification for cultivated tomato (Solanum lycopersium). Cultivation in this country is still characterized by a wealth of local landraces. Landraces are an essential element of the tomato diversity that has not been explored exhaustively. To increase the efficiency of the characterization and the utilization of cultivated tomato germplasm, we examined patterns of polymorphism in Italian tomato landraces in comparison to commercial varieties. According to the analysis of 214 genotypes with 177 biallelic SNPs, landraces have lower allelic richness, a higher number of rare alleles and a lower number of private alleles when compared to contemporary cultivars. Furthermore, the identification of loci putatively under positive selection implies that adaptation and selection have led to a genomic signature in cultivated landraces. On the other hand, the analysis of 146 genotypes with 14 multi-allelic SSRs did not reveal significant differences between landraces and cultivars in terms of allelic richness. In addition, different private alleles could be identified. Our work indicated that although a good portion of the genetic diversity of tomato landraces may have been captured in the founder lines of contemporary varieties, landraces carry a footprint at the genomic level and have some private alleles. These features provide evidence to encourage a long-term effort for a detailed molecular and phenotypic characterization of cultivated tomato landrace.