Opportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. In this frame, large panels of tomato varieties represent a valuable resource of traits of interest to consider for the improvement of varieties addressed for sustainable cultivation systems. Here we report comprehensive genotyping, phenotyping and genome-wide association studies (GWAS) using over 37K high quality SNPs obtained through double digest restriction-site associated DNA (dd-RADseq): a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, 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. The rest of the materials originated from different countries and included landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Model ancestry population structure and non-parametric hierarchical clustering have been inferred. Six genetic subgroups were revealed, clearly separating most LSL landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on the 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 LSL 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. For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we grew the collection under organic field trials.
A wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most of the traits. A variable level of heritability was observed with values up to 69% for morphological traits while among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has a more complex genetic control. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits.
Results of this study highlight the presence of a genetic footprint of the ‘da serbo’/LSL germplasm selected in the Mediterranean basin giving new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions. Moreover, we provide novel insights on LSL ‘da serbo’ germplasm as a promising source of alleles for tolerance to stresses providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.
Pasquale Tripodi received a Ph.D. in genetic and horticultural improvement at the Faculty of Agriculture of Portici (NA) and has been a researcher confirmed at the Research Centre for Horticulture, Pontecagnano (SA) since 2012.