# Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
## 3 Results
### Breeding for F1 Hybrid Quality  
Table 4 and Figure 3 highlight seven of the most interesting regions for breeding F1 hybrids with improved aromatic quality. For each region, we specified whether the homozygous or heterozygous genotype would be preferable to achieve this flavour improvement. We also described the breeding potential of the CG regions presented in Table 3.  
Figure 3: Circos plot of associations found for VOCs impacting tomato aroma. The outmost lane gives the marker density on the 12 chromosome arms (centromeric region are not displayed). Each successive lane represents a specific metabolic pathway. Association shape depends on the panel in which they were found. An asterisk (*) indicates overlapping associations from the same panel, with only one association plotted in case of overlap. Associations with \(p\) value \(<10^{-6}\) are plotted on the outer end of the lane, otherwise they are plotted on the inner end of the lane. We displayed positions of cloned genes impacting tomato aroma, along with the breeding (blue) and candidate gene (orange) regions we selected on top of the marker lane. Based on the aroma perception of VOCs, a better aroma quality should be obtained when the markers in association in regions \"Breed.2\", \"Breed.3\", \"Breed.9\" and \"Breed.11\", and also those of all CG regions from Table 3, except \"CG.B.8\" are heterozygous. On the contrary homozygosity of the FTMV alleles for the markers associated with regions \"Breed.4\", \"Breed.6\", \"Breed.12\" and \"CG.B.8\" would confer aromatic advantage. \"Breed.3\"--that encompassed \"CG.L.3\" on chromosome 3-- and \"Breed.6\" on chromosome 6 are two regions providing a consistent and overall regulation of lipid-derived VOCs, with associations only found in hybrid panels. Similarly, \"Breed.12\" also carried hybrid specific associations for all terpenoid-derived VOCs on chromosome 12. On chromosome 4, \"CG.B.4\" could contribute to decreasing benzenoid-derived VOC content with associations found in TCI for two VOCs. Targeted breeding for single key VOCs could be achieved with \"CG.L.1\" on chromosome 1, \"CG.B.8\" on chromosome 8 and \"CG.Phe.12\" on chromosome 12 to increase 1P3 ON, BENZA and PHEAC, respectively. Specialized regulation of metabolic pathways could be achieved through \"CG.B.Phe.3\" on chromosome 3 and \"Breed.4\" on chromosome 4: given the overlapping associations we encountered in these two regions, breeders could drive the metabolism of the common phenylalanine precursor to the phenylalanine-derived VOCs, at the expense of the benzenoid-derived VOCs. \"Breed.11\" carried associations TCI specific for all terpenoid-derived VOCs, with specialized regulation of VOCs according to their closeness in the cluster analysis (Figure S3). One could thus increase LIN and \(\alpha\)-terpineol while decreasing (E)-linaloid oxide and (Z)-linaloid oxide. \"Breed.2\" regulated VOCs belonging to different metabolic pathways, and would serve as a lever to decrease the benzenoid-derived EUGEN while increasing the branched-chain amino acid-derived 1N3 MBUT and lipid-derived HEPTAL if the heterozygous allelic combination were to be selected at the markers in association. Finally, \"Breed.9\" gave new insight into the value of the region carrying _Lin5_ where cherry type tomato alleles increased the amount of sugar. Adjacent to _Lin5_, we identified associations highlighted in \"CG.Phe.9\" for three phenylalanine-derived VOCs contributing to consumer liking. Choosing heterozygosity over FTMV homozygosity could thus increase SSC along with key VOCs in this region. However, we found associations for fruit weight within \"Breed.2\" and \"Breed.3\", and near \"Breed.9\" and \"CG.B.4\". The cloned gene _fu2.2_ is located two genes upstream \"Breed.2\". All of these fruit weight associations showed higher fruit weight value for FTMV homozygous genotype.