High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor and cuticle properties. Firmness is a complex polygenic trait involving the co-regulation of many genes and has proved especially challenging to unravel. In this study a Quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir S. pennellii interspecific introgression (IL) lines and fine mapped in a population consisting of 7500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct sub-peaks, Firs.p.QTL2.1-2.5 and an effect on a distal region of IL 2-4 that was non-overlapping with IL 2-3. All these effects were located within an 8.6 Mb region. Using genetic markers, each sub-peak within this combinatorial locus was mapped to a physical location within the genome and an ethylene response factor (ERF) underlying Firs.p.QTL2.2 and a region contain three pectin methylesterase (PME) genes underlying Firs.p.QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the non-overlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. QRT-PCR was used to quantify expression of each candidate gene. The ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus