Epistatic QTL for yield heterosis in tomato

Controlled population development and genome-wide association studies have proven powerful in uncovering genes and alleles underlying complex traits. An underexplored dimension of such studies is the phenotypic contribution of non-additive interactions between quantitative trait loci (QTL). Capturing such epistasis in a genome-wide manner requires very large populations to represent replicated combinations of loci whose interactions determine phenotypic outcomes. Here, we dissect epistasis using a densely genotyped population of 1400 backcross-inbred lines (BILs) between a modern processing tomato inbred (Solanum lycopersicum) and the Lost Accession of a distant, green-fruited, drought-tolerant wild species, Solanum pennellii. The homozygous BILs, each representing an average of 11 introgressions, and their hybrids with the recurrent parents were phenotyped for tomato yield components. Population-wide mean yield of the BILs was less than 50% of that of their hybrids (BILH), and correspo...