SABER: enhancing genetic diversity in tomato breeding through a multiparental population

Tomato (Solanum lycopersicum L.) ranks among the world’s most important vegetable crops, with diverse breeding targets shaped by its intended use, whether fresh market or processing. Breeders must address diversified demands from consumers, producers, and environmental challenges, including pest pressures exacerbated by climate change. Achieving these goals necessitates access to broad genetic diversity, alongside improved breeding lines and reliable molecular markers linked to key agronomic traits for marker-assisted selection. Multiparental Advanced Generation Intercross (MAGIC) populations represent a cutting-edge strategy to capture extensive biodiversity and accelerate genetic gains in breeding programs. In tomato, SABER (Solanum lycopersicum Allele Biodiversity Enriched Resource) is a MAGIC population developed by intercrossing seven domesticated tomato lines and a wild Solanum cheesmaniae accession (LA1407). The eight founder genotypes were systematically crossed in a stepwise design, from two-way to fourway and finally eight-way hybrids, followed by several generations of selfing in order to produce a recombinant population of 445 sister lines, currently at generation 13 (G13). Preliminary genotypic characterization of 350 G9 progenies was conducted in 2023, and it is now followed by a second round of characterization using GBS sequencing of G11 lines. Sequencing reads were aligned to the tomato reference genome and filtered for minor allele frequency (MAF > 0.05), missingness for individuals and sites, both at >0.2. Linkage disequilibrium pruning (r² > 0.8) yielded a high-quality dataset comprising 383 individuals and 4,278 single nucleotide polymorphisms (SNPs). These markers were evenly distributed across all 12 chromosomes, although certain regions, particularly on chromosomes 4, 6, and 9, showed elevated marker density; a pattern consistent with the previous genetic characterization study. Phenotypic evaluation focused on key agronomic and quality traits is currently ongoing thus enabling the conduction of associations studies to understand the genetic basis of traits of agronomic relevance. These initial findings underscore SABER’s value as a reservoir of genetic and phenotypic diversity, poised to enhance tomato breeding efforts. The combined genotypic and phenotypic datasets generated from this multiparental MAGIC population will facilitate detailed genetic dissection of complex traits and enable the development of molecular markers to improve selection efficiency in breeding pipelines.