Overview of major metabolic pathways involved in the mutant trait formation, as suggested by the interpretation of the GO and MPSS data. Part of the model was modified from Figure 1 of Rodriguez-Concepcion (2006) . The box background in red indicates up-regulated genes, and green indicates down-regulated genes. The genes are designated as TC numbers from TIGR gene index database, and the detailed gene information can be viewed in additional file 6. The TC numbers for LYCb and CCS genes were TC5 and TC5834 respectively. The abbreviations are as follows: 3PGA, glyceraldehyde 3-phosphate; ABA, abscisic acid; DMAPP, dimethylallyl diphosphate; DXP, deoxyxylulose 5-phosphate; DXS, deoxyxylulose 5-phosphate synthase; FPP, farnesyl diphosphate; GPP, geranyl diphosphate; GGPP, geranylgeranyl diphosphate; HDR, hydroxymethylbutenyl 4-diphosphate reductase; HDS, hydroxymethylbutenyl 4-diphosphate synthase; HMG-COA, hydroxymethylglutaryl coenzyme A; IPP, isopentenyl diphosphate; MEP, methylerythritol 4-phosphate; MVA, mevalonic acid.