SABER: a multiparental tomato population leveraging wild relative diversity for high-resolution QTL mapping

The narrow genetic base of cultivated tomato (Solanum lycopersicum L.) represents a major constraint on crop improvement, necessitating the exploitation of wild relatives to broaden allelic diversity. Here we present SABER (Solanum lycopersicum Allele Biodiversity Enriched Resources), a novel eight-founder Multiparent Advanced Generation Intercross (MAGIC) population that, for the first time, incorporates the Galápagos wild relative Solanum cheesmaniae as a founder alongside seven elite S. lycopersicum lines.

Following a structured crossing scheme and Single Seed Descent (SSD) advancement, F6 recombinant inbred lines were genotyped at 5,850 high-confidence SNP markers using Single Primer Enrichment Technology (SPET). Population structure analyses confirmed low residual heterozygosity, limited substructure among offspring, and successful introgression of S. cheesmaniae alleles across all twelve chromosomes. Mapping performance was validated through three Mendelian traits with known genetic determinants, all of which resolved to genomic positions consistent with the literature. Quantitative Trait Loci (QTL) mapping identified known loci for fruit epicarp and flesh color, and two novel QTLs for days to flowering, number of leaves before flowering, and soluble solids content.

Together, these results demonstrate that SABER is a powerful and reliable platform for high-resolution QTL mapping and candidate gene discovery, and establish a replicable framework for integrating wild germplasm into multiparental tomato breeding resources.