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

[EN] We developed a novel eight-way tomato multi-parental advanced generation inter-cross (MAGIC) population to improve the accessibility of tomato relatives genetic resources 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, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof-of-concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. 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. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding. This work was supported by grant PID2020-118627RB-I00 funded by MICIU/AEI/10.13039/501100011033, TED2021-129296B-I00 funded by MCIN/AEI/10.13039/501100011033 and European Union Europea NextGenerationEU/PRTR, CIPROM/2021/020 funded by Conselleria d Innovació, Universitats, Ciència i Societat Digital of the Generalitat Valenciana, the HARNESSTOM innovation action (grant agreement no. 101000716) funded by the European Commission H2020 Research and Innovation P ogramme, and the Horizon Europe PRO-GRACE project (grant agreement no. 10194738). Andrea Arrones is grateful to Spanish Ministerio de Ciencia, Innovación y Universidades for a predoctoral (FPU18/01742) contr