Genetic dissection of drought tolerance in the TOMAGIC population

The ToMAGIC population is a Multi-parent Advanced Generation Inter-cross (MAGIC) population consisting of 375 inbred lines developed from a cross between four accessions of Solanum pimpinellifolium (SP) and four of S. lycopersicum var. cerasiforme (SLC). The founders of this population exhibit significant diversity in their adaptation to varied environments, ranging from deserts to tropical forests and altitudes from sea level to over 1500 meters. Developed using a funnel scheme including three cycles of intercrossing, ToMAGIC has undergone extensive recombination of the genomes of the eight founders. A subset of 138 lines, capturing the genetic variance of the population, was screened over two years under drought stress (irrigation halted at two stages) and control conditions in a greenhouse. Ninety-five traits have been phenotyped, including inflorescence traits, leaf characteristics, biometric parameters, yield, fruit quality, and leaf senescence, were collected. Repeated measures statistical analysis revealed that reduced irrigation began to impact inflorescence traits such as fruit number, flower number per inflorescence, and fruit setting starting from the second inflorescence. In contrast, earliness was affected starting from the fifth inflorescence. A genome-wide association study (GWAS) identified eight genomic regions across seven chromosomes (1, 2, 3, 7, 8, 9, and 12) associated with traits linked to drought tolerance. Clusters of genes associated with abscisic acid (ABA) signalling, reactive oxygen species (ROS) regulation, and osmolyte biosynthesis pathways have been identified within each of these genomic regions. Notably, our results indicate that drought tolerance in this population is a combined effect of genomic regions contributed by multiple donors, rather than a single source. This study underscores the importance of integrating diverse genetic contributions to enhance drought tolerance. Further, the best drought predictors have been identified, and a subset of traits including fruit weight, yield, plant height, wilting, total biomass production, fruit setting, and the number of flowers per inflorescence was selected based on their relevance. These traits have been used to perform genomic selection to select lines exhibiting superior drought tolerance and possessing the key genomic regions identified. Two lines exhibited a transgressive phenotype, outperforming all parental lines in both conditions. These lines hold potential for targeted crosses to integrate desirable traits into commercial cultivars.