ddRAD sequencing-based genotyping in cultivated tomato
we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicum L.) accessions enriched in da serbo (called de penjar in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most da serbo landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5 kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in da serbo materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and JAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the da serbo germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL da serbo germplasm as a promising source of alleles for tolerance to stresses.