There is more to tomato fruit colour than candidate carotenoid genes.

Determining gene sequences responsible for complex phenotypes has remained a major objective in modern biology. The candidate gene approach is attempting to link, through mapping analysis, sequences that have a known functional role in the measured phenotype with quantitative trait loci (QTL) that are responsible for the studied variation. To explore the potential of the candidate approach for complex traits we conducted a mapping analysis of QTL for the intensity of the red colour of the tomato fruit (mainly lycopene) and for probes associated with the well-characterized carotenoid biosynthesis pathway. Seventy-five tomato introgression lines (ILs), each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii delimited 107 marker-defined mapping bins. Three of the bins resolved known qualitative colour mutations for yellow (r) and orange (B and Del) fruits resulting from variation in specific carotenoid biosynthesis genes. Based on trials in different environments, 16 QTL that modified the intensity of the red colour of ripe fruit were assigned to bins. Candidate sequences associated with the carotenoid biosynthesis pathway were mapped to 23 loci. Only five of the QTL co-segregated with the same bins that contained candidate genes - a number that is expected by chance alone. Furthermore, similar map location of a QTL and a candidate is far from a direct causative relationship between a gene and a phenotype. This study highlights the wealth and complexity of the variation present in the genus Lycopersicon that could be employed for basic research and genetic improvement of fruit colour in tomato.