BackgroundTomato mating systems were strongly affected by domestication events. Mutations disrupting self-incompatibility paralleled by changes retracting the stigma position (SP) within the staminal cone conferred strict autogamy and self-fertility to the cultivated forms. Although major genes affecting these changes have been identified, SP control in domesticated forms that retain a constitutive or heat-inducible noninserted SP needs elucidation. To widen the possibility of identifying SP genetic determinants, we analyzed the trait in four populations (two germplasm collections, a multiparental recombinant inbred and a biparental progeny) under different environmental conditions (normal and heat stressed).ResultsOverall, 37 markers significantly associated with the trait were identified. Several colocalizations were found, both among regions first reported in this work and among them and previously reported positions. This finding supported the reliability of the analysis. Three such regions, in the long arms of chromosomes 1, 8 and 11, were validated in an independent segregating population, and candidate genes in confidence intervals were identified among transcription factors and hormone-, stress- and cell wall-related genes.ConclusionOverall, this work supported the hypothesis that the SP phenotype is controlled by different key genes in tomato, paving the way for the identification of novel players and novel mechanisms involved in the regulation of herkogamy.