Deciphering the Genetic Control of Tomato Fruit Composition in Flavonoids in the Resequencing Era

Identifying the genes controlling the variation of quantitative traits is a key goal for breeders. Genetic variations underlying quantitative traits (QTL) have been mapped by linkage mapping for years and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of genetic background on QTL effect has been underlined. Multi-allelic Advanced Generation Inter-Cross (MAGIC) populations allow a wide range of variability to be analyzed.

We have constructed a MAGIC population by crossing 8 tomato lines, representing a wide range of genetic diversity within the species. The large range of phenotypic variability represented by these lines was then characterized at different scales, metabolomic, proteomic and transcriptomic. The whole genomes of the 8 founder lines were resequenced identifying more than 4 millions SNPs when mapped onto the reference genome. A set of 1536 SNPs markers was then selected to genotype the MAGIC population and used to construct a linkage map. A large increase in recombination frequencies compared to bi-parental populations was shown. QTLs for fruit composition traits were mapped and related to the variations detected at the genome sequence and expression levels in the parental lines. QTL for flavonoid compounds were mapped and candidate genes identified will be presented.