Molecular characterization of QTLs consists of identifying the corresponding genes and the variation of either DNA sequence or gene expression explaining trait variation. High throughput genomic approaches can facilitate this by providing candidate genes for QTLs based on gene function. High throughput methods (transcriptomics, proteomics, metabolomics) allow the identification of changes in the content of mRNAs, proteins or metabolites by comparing two or more samples. First applied in Arabidopsis thaliana, these methods are now available in tomato. Initial results of their application to characterize QTLs controlling tomato fruit quality traits at the molecular level have been reported (see below). Traditionally, however, classical positional cloning has allowed the identification of genes corresponding to QTLs.
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