QTL pyramiding uncovers epistatic interactions that modify cuticle phenolics in tomato

The plant cuticle plays several roles with agronomic relevance such as controlling water loss or protecting against ultraviolet (UV) radiation and mechanical damage. In tomato fruit cuticle, phenolics are chiefly the flavonoid chalconaringenin and a small portion of phenolic acids. They confer the cuticle mechanical resistance as well as thermal properties and UV photoprotection. Nine QTLs related to the accumulation of cuticle phenolics in tomato fruit were previously detected in a Solanum lycopersicum × S. pimpinellifolium recombinant inbred population. Confocal Raman microscopy has been employed to separate the effect of these cuticle QTLs on the two phenolic fractions, showing that most QTL lines preferentially affected chalconaringenin accumulation, with only two QTL lines (ph8.1 and ph12.1) having an equal effect on both chalconaringenin and phenolic acids. A QTL pyramiding strategy has been employed to study the combined effect of different loci and has revealed a complex array of interactions. Approximately 80% of the double and triple QTL lines displayed significant epistatic interaction. Notably, a QTL combination between chromosomes 5 and 12 that increases the percentage of cuticle phenolics beyond single QTL lines was identified. CHALCONE SYNTHASE (CHS1 and CHS2) expression analyses have shown that CHS1 seems to be the main enzyme responsible for the synthesis of chalconaringenin that is accumulated within the cuticle. Additionally, an S. pimpinellifolium genomic region in chromosome 5 that favors CHALCONE ISOMERASE1 expression in the peel of ripening tomatoes without affecting chalconaringenin accumulation in the cuticle was identified, raising the possibility of an increase in fruit of downstream flavonols without compromising cuticle phenolics.