# Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
## 3 Results
### Candidate Genes for F1 Hybrid Quality  
Apart from cloned genes, two, five and 14 associations found in the CCI, TCI and TCT panel, respectively, carried 17 different CGs previously suggested in [20] (Table S7). Ten CGs belonged to associations for lipid-derived VOCs, three CGs for benzenoid-derived  
\begin{table}
\begin{tabular}{c c c c c c c c c c c} \hline \hline \multirow{2}{*}{**Met. ID**} & \multirow{2}{*}{**Met.**} & \multirow{2}{*}{**Aroma**} & \multicolumn{3}{c}{**Mean**} & \multicolumn{3}{c}{**h2**} & \multicolumn{3}{c}{**Nb. Assoc**} \\ \cline{3-10}  & & & **FTMV** & **TCT** & **CCI** & **TCI** & **TCT** & **CCI** & **TCI** & **TCT** \\ \hline EZ24D & L & * & 0.77 & 1.02 & 0.65 & 0.25 & 0.31 & 3 & 0 & 4 \\ HEPTAL & L & * & 0.97 & 1.10 & 0.30 & 0.19 & 0.02 & 5 & 1 & 5 \\ HEXAL & L & * & 0.92 & 0.96 & 0.51 & 0.25 & 0.56 & 3 & 1 & 3 \\ Z3 HEX & L & * & 1.04 & 0.99 & 0.53 & 0.29 & 0.41 & 3 & 2 & 4 \\ IN2 PHENE & Phe & + & 0.97 & 1.31 & 0.71 & 0.48 & 0.52 & 9 & 4 & 0 \\ BENZY & Phe & + & 1.99 & 1.12 & 0.85 & 0.61 & 0.58 & 9 & 4 & 0 \\ PHEAC & Phe & + & 1.97 & 1.22 & 0.71 & 0.35 & 0.33 & 4 & 3 & 11 \\ PHENE & Phe & + & 1.40 & 1.29 & 0.71 & 0.55 & 0.59 & 4 & 1 & 2 \\ ELINOX & T & * & 0.66 & 1.12 & 0.80 & 0.62 & 0.59 & 5 & 2 & 4 \\ LIN & T & * & 0.94 & 0.99 & 0.03 & 0.32 & 0.30 & 1 & 1 & 4 \\ ZLINOX & T & * & 0.62 & 1.13 & 0.81 & 0.67 & 0.65 & 3 & 5 & 4 \\ SSC & + & 4.70 & 5.88 & 0.82 & 0.77 & 0.73 & 6 & 3 & 2 \\ \hline \hline \end{tabular} We indicated the mean values of the common tester FTMV and the mean values in the overall TCT panel, both measured alongside in 2019. Heritability (h2) is indicated along with the number of associations identified per panel (‘nb.assoc’). VOCs impacting flavour perception are marked with a (*) in column “Aroma.impact” when their odour threshold or abundancy is at stake (reviewed in [56; 57; 58]). VOCs with positive (resp. negative) significant correlation to consumer liking are marked with a (*) (resp. (\(-\))) [8] (adapted from [8]). VOCs abbreviations are specified in “VOC ID” B: ben-zenoid, BCAA: branched-chain amino acid, C: carotenoid, Phe: phenylalanine, T: terpenionid.  
\end{table}
Table 2: _Cont._VOCs and three CGs for phenylalanine-derived VOCs. Six CGs will be further detailed as they belong to the most promising regions where we identified novel CGs. To complete our goals for both fundamental and applied research, we first highlighted the most promising CGs underlying key VOCs, and then we defined candidate regions with potential for multi-VOCs improvement. Whatever the purpose, we filtered our associations based on key criteria, all aimed at improving tomato taste in F1 hybrids: (1) regions carrying associations with \(p\)-values < \(10^{-6}\) for the subset of VOCs impacting tomato aroma; (2) markers in association with balanced Minor Allele Frequency ('MAF') (>0.2) to ensure that both allelic classes were well represented, before estimating FTMV allelic effect on the VOC content; (3) regions displaying overlaps between VOCs belonging to the same metabolic pathway, and with consistent effect of FTMV allelic class on closely related VOCs.  
All CGs identified in the CI of our associations are presented in Table S7. Details about the associations carrying these CGs can be found in Table S6. We selected a subset presented in Table 3 and Figure 3 that gathered the most promising candidates to achieve flavour improvement in F1 hybrids, based on the strategy we defined. We checked the polymorphisms among these CGs in the 47 resequenced lines of the CCI panel. Out of the 33 CGs we suggested in Table 3, 16 presented at least several low (synonymous mutation) to moderate (non-synonymous mutation) effect polymorphisms in their coding region, and six presented high effect (stop gain or loss) polymorphism. Details about these polymorphisms can be found in Table S8.