Solanum lycopersicoides Introgression Lines Used as Rootstocks Uncover QTLs Affecting Tomato Morphological and Fruit Quality Traits

Tomato (Solanum lycopersicum) is the most important vegetable crop globally; however, its production is often hindered by soil-borne biotic and abiotic stresses. The use of rootstocks provides an effective strategy to mitigate these soil-related challenges. Hence, the development of new rootstock cultivars remains crucial to meet the demands of rapidly changing environmental conditions. Wild tomato species represent valuable genetic resources for rootstock improvement and are increasingly utilized in rootstock breeding programs. Nevertheless, the genetic mechanisms, particularly quantitative trait loci (QTL), underlying rootstock–scion interaction, remain poorly understood. In this study, 38 introgression lines (ILs) derived from S. lycopersicoides were used as rootstock and grafted with the commercial cultivar ‘Torry F1’ to evaluate their effects on morphological and fruit quality traits under greenhouse conditions. The evaluations included assessments of morphological and fruit quality traits for QTL analysis. A total of 19 QTLs were identified, associated with 11 traits such as yield, antioxidant capacity, flavonoid content, and fruit color parameters (L*, a*, b*, C*, h°), with the phenotypic variance explained ranging from 12% to 61%. Of these QTLs, seven favorable alleles originated from S. lycopersicoides, notably including a major yield-associated locus (Fy5.1). In addition, the identification of a QTL for scion stem thickness (Tsc3.1) highlights the genetic contribution of the rootstock to scion development. This study represents the first evaluation of the rootstock potential of S. lycopersicoides ILs and provides novel insights into the genetic basis of rootstock–scion interaction in tomato. The identified QTLs offer valuable information for future breeding efforts aimed at developing improved rootstock cultivars for sustainable tomato production.