Reciprocal Effects for Fruit Traits in Tomato: Evidence from QTL Mapping in an Interspecific Cross

Abstract

Reciprocal effects (RE) arise when cross direction influences trait expression and may result from maternal, cytoplasmic, or parent-of-origin effects. Here, we evaluated the impact and persistence of RE at both phenotypic and molecular levels in populations derived from an interspecific tomato cross using a classical QTL mapping framework. Reciprocal effects were detected from the F1 to the F2 generations for key fruit quality traits, including fruit diameter (D), height (H), weight (FW), and shelf life (SL). Reciprocal differences were observed in gene action estimates and deviations from the additive–dominant model, but these effects did not persist across generations. Genetic correlations among fruit traits differed between reciprocal F2 populations, revealing cross direction dependent trait relationships among traits. At the molecular level, reciprocal linkage maps showed significant differences in chromosome lengths and recombination patterns, despite conserved marker order. Integration of phenotypic and molecular data revealed pronounced differences in both the number and genomic positions of QTLs detected in the reciprocal F2 populations. Six QTLs associated with D, FW, fruit shape (FS), and color (L) were consistently detected across populations and genetic backgrounds. Validation in F3 families confirmed the persistence of reciprocal effects for H and locule number (LN), as well as pleiotropic effects involving FW, D, and H. Together, these results demonstrated that reciprocal effects shape the genetic architecture of tomato fruit quality traits and highlight the importance of incorporating cross direction into QTL analyses and breeding strategies.