# Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
## 4 Discussion
### Targeting Appropriate Plant Material to Better Elucidate VOC Genetic Control  
As previous studies highlight [8], the complexity of flavour traits and the lack of suitable markers led to fewer allelic diversity remaining in modern cultivars. This led to loss of flavour, although [58] provided evidence of a considerable increase in allelic diversity in breeding material since the 1970s thanks to numerous introgressions performed from wild related species, mainly for introgression of disease resistance genes and to the commercialization of cherry tomato types due to their interesting flavour. In order to avoid the genetic load carried by wild species, we used small cultivated tomato accessions and SP species (closest wild ancestor of the tomato). We compared the diversity in aroma composition of these plant materials at the line and F1 hybrid levels to better understand flavour inheritance and thus suggest a strategy to breed tastier tomatoes. Taking together the genetic structure analysis (Figure S1) and the PLS-DA on VOC content (Figure 2), we found consistent overlapping patterns of hybrids belonging to different genetic groups in both genetic structure and PLS-DA, suggesting that VOC specificities resulted from allelic specificities, thus ruling out an overall environmental control of VOC abundancy for this study. Furthermore, the correlations calculated between the line (CCI) and hybrid (TCI) panels for similar VOCs were high, with 80% of VOCs displaying R > 0.4 between the two panels. These results suggested a global additivity pattern for most VOC genetic control. Heritabilities were high for most VOC content, although they were generally lower in hybrid panels. Accordingly, we found more associations in the CCI panel compared to the F1 panels, although the TCT panel gathered more phenotypic variability and genetic diversity for some key VOCs leading to more associations despite lower refitabilities. VOCs with high heritabilities offer better response to selection by targeting the genetic loci they rely on. As appeared in PLS-DA when comparing the core collection at the line (CCI) and F1 hybrid (TCI) levels, the hybrid panels still expressed their phenotypic specificities although they shared half of their genotypic information with one another: VOCs discriminating the genetic groups SP and SLC were indeed close to identical (Figure S4) between the CCI and TCI PLS-DA results. Similarly, the cluster analysis on the three panels showed consistent to similar results indicating that being at the line or hybrid level, VOC regulation showed the same patterns, which further supported the additivity hypothesis. Moreover, our clusters matched reviews published on VOC metabolic pathways in tomato fruits [6; 8], and the VOC cluster analysis performed on a biparental population derived from a cross between an SP and an SL accession in [49]. Considering the TCT panel that harboured 44 additional F1 hybrids produced from elite cherry type tomatoes and the common parent FTMV, there is evidence of the emphasis breeders put on creating cherry type tomato varieties with improved aroma composition (Table S4), notably they showedenrichment of the phenylalanine-derived PHEAC, the carotenoid-derived BIONO and BDAM and sugar content, and concomitant reduction of four out of five branched-chain amino acid-derived VOCs and 6C lipid-derived VOCs (Table S5). These compounds are known to impact tomato aroma and were selected, or selected against by breeders without prior quantification. The elite plant material showed enrichment in terpenoid-derived VOCs, which although rarely studied, could also be key VOCs for consumer liking as highlighted in [6]. VOC signatures highlighted in the PLS-DA gave insight into each genetic group specificities, although the heatmap presented in Figure S2 showed that phenotypic diversity could be found back in each genetic group, thus allowing breeders to target donor accessions to improve their breeding plant material.