A novel tomato inter-specific (Solanum lycopersicum var. cerasiforme and S. pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm

We developed a novel eight-way tomato multi-parental advanced generation inter-cross (MAGIC) population to improve the accessibility of the genetic resources of tomato relatives to geneticists and breeders. The inter-specific MAGIC population (ToMAGIC) was obtained by inter-crossing four accessions each of Solanum lycopersicum var. cerasiforme (SLC) and S. pimpinellifolium (SP), which respectively are the weedy relative and the ancestor of cultivated tomato. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines which were genotyped using a new 12k tomato Single Primer Enrichment Technology (SPET) panel and yielded 6,488 high-quality SNPs. The genotyping data revealed a high degree of homozygosity (average 93.69%), an absence of genetic structure, and a balanced representation (11.62% to 14.16%) of the founder genomes. To evaluate the potential of the ToMAGIC population for tomato genetics and breeding, a proof-of-concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness traits. Genome-wide association studies (GWAS) identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato breeding. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.