Tomato resources for functional genomics

Tomato is currently the model species for fleshy fruit development and for Solanaceae species. The recent completion of a high‐quality genome sequence of the inbred tomato (Solanum lycopersicum) cultivar ‘Heinz 1706’ allowed the prediction and in silico annotation of ca 35,000 genes. Assigning a biological function to these genes is among the priorities of the tomato community, especially for genes contributing to fleshy fruit development and quality, and to other major agronomical traits in tomato and Solanaceae. More than a decade of research using genomic tools, mostly transcriptome and metabolome, combined with genetic mapping approaches, provided first cues on the possible function of tomato genes by describing where, when, and with which other gene/metabolite these genes are expressed. Current advances in sequencing technologies now allow the exhaustive inventory of tomato transcripts in various plant organs, tissues and even cell types. To cope with the need to assign biological functions to a large number of genes, tomato mutant resources based on several technologies [T‐DNA and transposon insertional mutants, fast‐neutron, γ‐ray and ethyl methanesulfonate (EMS) mutants] have been developed in the recent years. Among them, the Targeting Induced Local Lesions In Genomes (TILLING) technology, based on the generation by EMS of high density point mutations evenly distributed in the genome and on the subsequent detection of mutations in target genes is presently the most established. The present chapter will describe the main resources, strategies and tools currently available for linking genes to phenotype in tomato