Solanum pennellii introgression population as source of candidate genes for higher phenylpropanoid accumulation in tomato fruit

Introgression lines (ILs) of Solanum pennellii into S. lycopersicon cv. M82 background have been widely used for dissecting genetic variability associated to complex traits [Eshed and Zamir, 1995, Genetics 141:1147-1162]. Among all, ILs enabled the identification of QTLs (Quantitative Trait Loci) for tomato fruit quality including the level of different metabolites having antioxidant activity [Rousseaux et al 2005, TAG 111: 1396–1408]. This is expected to greatly help the breeding work for these traits, which show a continuous variation and are strongly influenced by environmental conditions. However, the fine mechanism controlling antioxidant levels in tomato fruit remain still elusive. Tomatoes are one of the valuable sources of antioxidants such as carotenes, ascorbic acid (AsA), and phenolic compounds (flavonoids and hydroxycinnamic acid derivatives). These secondary metabolites have been proved to be beneficial for humans and animals because their involvement in the prevention of many proliferative and degenerative disease. The aim of this work is to gain greater insights in the genetic control of phenylpropanoid accumulation in tomato fruit by using genomics-based strategies. In order to identify QTLs controlling antioxidant accumulation in tomato fruit we carried out a comparative analysis of Solanum pennellii x S. lycopersicum cv. M82 introgression lines (ILs) over three year trials in greenhouse environment. Among all, IL7-3 showed higher fruit content of total phenolics and the HPLC-UV profile revealed that chlorogenic acid mainly accounted for the higher performance of this line. To investigate in details genetic mechanisms and candidate genes controlling phenols synthesis and accumulation in IL7-3 fruit we performed a comparative transcriptomic analysis in tomato pericarp. In particular, RNA was extracted from pericarp of IL7-3 and M82 parental line and hybridized on a 90k Combimatrix TomatArray 1.0. The experiment was repeated over two consecutive years. The transcriptomic approach allowed to identify 291 differentially expressed transcripts, 149 showing up-rgulation and 142 down-regulation. Based on functional annotation, gene ontology classification and hierarchical clustering, subsets of differentially expressed transcripts were used to develop model networks describing mechanisms controlling accumulation of phenylpropanoids in tomato fruit. The network we draw explains the variation in phenols levels in terms of interactions between ethylene signalling, plant responses to stress and biosynthesis of phenolics. Also, key transcripts of our model were validated by qPCR approach. To functionally characterize candidate genes involved in controlling phenylpropanoid levels in tomato fruit a TILLING (Targeting Induced Local Lesion IN Genomes) approach has being currently used for two transcription factors involved in ethylene response (e.g. ERF1 and EIN3). Characterization of mutants is expected to provide insights on antioxidant control in tomato ripe fruit.