High-resolution mapping and epistatic QTL of tomato fruit metabolism

Tomato wild relatives are valuable genetic resources for trait discovery and understanding the genetic basis of fruit metabolism and quality. Yet, only a fraction of naturally occurring variation has been exploited. Here, we performed metabolite profiling of two large Backcross Inbred Line populations derived from crosses between the wild species S. pennellii accession LA5240 (Lost) and cultivated genotypes LEA (determinate) and TOP (indeterminate), including [~]1400 and [~]500 lines, respectively. High-resolution mapping identified enormous metabolic quantitative trait loci (mQTL), including a new locus on chromosome 12 associated with fruit sucrose accumulation that harbours INVERTASE INHIBITOR 3 (SlINVINH3) protein. Comparative analysis indicated that SlINVINH3 is highly expressed in wild S. pennellii 0716 fruit, whereas a six-amino acid deletion is present in its coding sequence compared with S.pennellii LA5240 and S. lycopersicum. We further demonstrated that in SlINVINH3-overexpressing tomato plants, only the S. pennellii LA5240 allele led to increased sucrose, accompanied by reduced fructose and glucose levels. Furthermore, the large population size enabled us to assess the epistatic interactions, with approximately 40% of interactions being more-than-additive and 60% less-than-additive. Our results demonstrate the power of permanent exotic populations to reveal hidden metabolic diversity and provide an approach for improving fruit quality through targeted breeding and metabolic engineering.