# Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
## 3 Results
### GWAS Analysis  
Table 2 summarizes the GWAS results and Table S6 gives the exhaustive list of associations identified for the 46 VOCs, SSC and fruit weight. The CCI, TCI and TCT panels allowed the identification of 205, 138 and 183 associations, respectively. The CI length ranged from 164 bp to 4 Mbp with an average CI length of 0.2 Mbp across panels. The full list of genes harboured in the CIs is presented in Table S7. The number of genes ranged from one to 73 with an average gene number of 19 across all CIs. Overall, we identified 95, 74 and 118 CGs (Table S7) based on annotations suggested in the literature for the corresponding metabolic pathways, in addition to 142, 118 and 172 TFs in the CI of the CCI, TCI and TCT panels, respectively. Table S3 lists all possible CGs and TFs from the full list of genes provided by the SL4.0 tomato version of the genome and ITAG.4.0 annotation. A total of 36% of the 287 CGs, and 7% of the 432 TFs presented a cis-eQTL in fruit in [51]. The \(\chi^{2}\) test on each metabolic pathway and each panel showed significant enrichment of CG presence in the CI of associations from the three panels for SSC and both benzenoid and phenylalanine-derived VOCs. We found enrichment in CGs for the branched-chain amino acid-derived (resp. carotenoid and terpenoid-derived) metabolic pathway for the TCI (resp. TCT) panel. Both CCI and TCT (resp. CCI and TCI) panels showed associations with significant enrichment of CGs from the lipid-derived (resp. sulphur-derived) metabolic  
pathway. Overall, the MLMM method paired with the definition of narrow CIs allowed us to accurately retrieve CGs. \begin{table}
\begin{tabular}{c c c c c c c c c c c} \hline \hline \multirow{2}{*}{**Met. ID**} & \multirow{2}{*}{**Met. Patch**} & \multirow{2}{*}{**Aroma**} & \multicolumn{3}{c}{**Mean**} & \multicolumn{3}{c}{**h2**} & \multicolumn{3}{c}{**Nb. Assoc**} \\ \cline{3-10}  & & & **FTMV** & **TCT** & **CCI** & **TCT** & **CCI** & **TCT** & **CCI** & **TCT** \\ \hline BENZA & B & + & 1.91 & 1.21 & 0.63 & 0.36 & 0.32 & 1 & 1 & 4 \\ EUGEN & B & \(-\) & 1.33 & 1.18 & 0.63 & 0.75 & 0.76 & 8 & 9 & 11 \\ GUAIA & B & \(\ast\) & 1.60 & 0.68 & 0.86 & 0.76 & 0.74 & 7 & 3 & 3 \\ PCYM & B & \(\ast\) & 0.82 & 1.07 & 0.72 & 0.48 & 0.44 & 4 & 6 & 3 \\ SALI & B & \(-\) & 1.44 & 0.98 & 0.77 & 0.67 & 0.66 & 11 & 2 & 6 \\
1N3 MBUT & BCAA & + & 1.49 & 1.55 & 0.55 & 0.30 & 0.37 & 2 & 5 & 10 \\
2 ISOBUT & BCAA & + & 1.36 & 1.12 & 0.68 & 0.43 & 0.45 & 1 & 2 & 1 \\
3 MBUT & BCAA & \(\ast\) & 1.94 & 1.22 & 0.51 & 0.16 & 0.08 & 4 & 3 & 10 \\
6 MHON & C & + & 1.04 & 1.15 & 0.62 & 0.32 & 0.47 & 4 & 1 & 0 \\ BDAM & C & \(\ast\) & 0.64 & 0.99 & 0.75 & 0.53 & 0.55 & 0 & 6 & 2 \\ BIONO & C & \(\ast\) & 0.91 & 1.18 & 0.41 & 0.18 & 0.35 & 8 & 0 & 2 \\ GRACE & C & \(\ast\) & 1.15 & 1.48 & 0.40 & 0.34 & 0.30 & 4 & 1 & 0 \\ GRIAL & C & \(\ast\) & 1.02 & 1.16 & 0.60 & 0.32 & 0.43 & 6 & 1 & 0 \\ NERAL & C & \(\ast\) & 1.14 & 1.13 & 0.60 & 0.22 & 0.36 & 3 & 0 & 0 \\
1P3 ON & L & + & 0.90 & 1.03 & 0.77 & 0.52 & 0.55 & 4 & 4 & 7 \\
2 EFUR & L & \(\ast\) & 0.99 & 1.04 & 0.32 & 0.38 & 0.46 & 1 & 5 & 0 \\
3 MFUR & L & \(\ast\) & 0.84 & 1.22 & 0.40 & 0.25 & 0.36 & 3 & 4 & 1 \\
3 PONE & L & + & 1.14 & 1.17 & 0.49 & 0.28 & 0.22 & 1 & 3 & 3 \\ E2 HEP & L & + & 0.84 & 1.05 & 0.33 & 0.19 & 0.36 & 1 & 1 & 3 \\ E2 PEN & L & + & 0.88 & 1.12 & 0.65 & 0.45 & 0.56 & 2 & 3 & 5 \\ EE24D & L & \(\ast\) & 0.86 & 1.13 & 0.61 & 0.35 & 0.33 & 4 & 0 & 0 \\ EE24H & L & \(\ast\) & 1.13 & 0.94 & 0.65 & 0.41 & 0.51 & 0 & 2 & 3 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: GWAS summary for SSC and VOCs impacting tomato aroma. Figure 2: PLS-DA on VOC and sugar content in the three genetic groups of the TCT panel. (**a**) F1 hybrid plot. Each colour corresponds to a genetic group in the TCT panel. (**b**) VOCs maximizing the discrimination between the genetic groups on the first axis of the F1 hybrid plot. The colour of the contribution highlights the genetic group which shows enrichment in the corresponding VOC.