When a QTL is mapped within a genomic region, this implies that there is at least one gene responsible for a fraction of the phenotypic variation. Before trying to identify the gene responsible for the QTL, it first must be precisely characterized at the genetic level. It is critical to determine the number of QTLs segregating within the region. Indeed, several fine-mapping experiments identified several QTLs in regions where a single QTL was detected or where it was assumed that a single gene controlled two related traits (Pater-son et al. 1990; Monforte et al. 2000b; Lecomte et al. 2004b). Several Mendelian mutations in tomato have been characterized by positional cloning, but very few QTLs have been definitively characterized at the molecular level (Paran and Zamir 2003; Salvi and Tuberosa 2005; Price 2006). Direct cloning of a QTL is more difficult than cloning of a major gene because the QTL only partially influences trait variation and its effect can only be appreciated by statistical methods. For this reason, the resources required are more considerable. The first QTL cloned by map-based cloning usuallycorresponds to QTLwithstrongeffects thatare independent of the environment. If nothing is known about the physiological and molecular determinism of a trait, positional cloning is the most straightforward method to characterize a QTL. Alternatively, if genes involved in the expression of the character, or related to developmental processes responsible for a trait (candidate genes) are known, it is possible to test whether polymorphism in one of them can explain variation in the trait. In both cases it is necessary to reduce the interval around the QTL through fine-mapping. The increasing number of molecular tools (Table 5, 16) and online maps (Table 5-7) in tomato will expedite this molecular characterization. Comparison of lines using metabolomic, transcriptomic, or proteomic techniques can help identify genes that can contribute to the phenotype (see Sect. 1.15.3).
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