# Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
## 3 Results
### Candidate Genes for F1 Hybrid Quality
#### 3.5.2 Phenylalanine and Benzenoid-Derived VOCs
\begin{table}
\begin{tabular}{c c c c c c c c c} \hline
**ID** & **VOCs** & **Solyc. ID** & **Function** & **Exp** & **eQTL** & **Low** & **Mod** & **High** \\ \hline CG.L.1 & 1P3 ON & Solyc01g099160 & Lipoxygenase & + & – & 7 & 19 & 0 \\ CG.L.1 & 1P3 ON & Solyc01g099170 & Lipoxygenase & + & – & 1 & 5 & 1 \\ CG.L.1 & 1P3 ON & Solyc01g099190 & Lipoxygenase B & + & – & 6 & 7 & 0 \\ CG.L.1 & 1P3 ON & Solyc01g099200 & Lipoxygenase & + & – & 3 & 2 & 0 \\ CG.L.1 & 1P3 ON & Solyc01g099210 & Lipoxygenase & + & – & 3 & 5 & 1 \\ CG.L.3 & 3 PONE-E2 HEX-E2 PEEN-EE24H- & & Solyc03g083370 & CDSL esterase/lipase & + & – & 8 & 10 & 0 \\  & EE24 HEPT-E224 HEPT-23 HEX & & Solyc03g118120 & Glycostransferase & + & + & 3 & 4 & 0 \\ CG.B.Phe.3 & EUGEN-PHEAC & Solyc03g118190 & Transcription factor & + & + & 0 & 0 & 0 \\ CG.B.Phe.3 & EUGEN-PHEAC & Solyc03g118230 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.Phe.3 & EUGEN-PHEAC & Solyc03g118310 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.4 & EUGEN-CUAIA & Solyc04g074480 & DAHP synthase 2 & + & + & 2 & 1 & 0 \\ CG.B.8 & BENZA & Solyc08g006110 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006190 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g00620 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006210 & Transcription factor & + & + & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006230 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006240 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006270 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006280 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006320 & Transcription factor & + & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006330 & Glycosyltransferase & + & + & 14 & 14 & 1 \\ CG.B.8 & BENZA & Solyc08g006350 & Glycosyltransferase & + & + & 10 & 15 & 1 \\ CG.B.8 & BENZA & Solyc08g006360 & Glycosyltransferase & + & + & 7 & 4 & 0 \\ CG.B.8 & BENZA & Solyc08g006370 & Glycosyltransferase & + & + & 1 & 9 & 1 \\ CG.B.8 & BENZA & Solyc08g006390 & Glycosyltransferase & \(-\) & – & 2 & 6 & 1 \\ CG.B.8 & BENZA & Solyc08g00640 & Glycosyltransferase & \(-\) & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006410 & Glycosyltransferase & \(-\) & – & 0 & 0 & 0 \\ CG.B.8 & BENZA & Solyc08g006483 & Transcription factor & \(-\) & – & 0 & 0 & 0 \\ CG.Phe.9 & PHEAC-1N2 PHENE-PHENE & Solyc09g01109 & Glycosyltransferase & \(-\) & – & 4 & 5 & 0 \\ CG.Phe.9 & PHEAC-1N2 PHENE-PHENE & Solyc09g01110 & Transcription factor & \(+\) & – & 0 & 0 & 0 \\ CG.Phe.12 & PHEAC & Solyc12g010170 & Transcription factor & \(+\) & – & 0 & 0 & 0 \\ CG.Phe.12 & PHEAC & Solyc12g010200 & Hexosyltransferase & \(+\) & – & 3 & 2 & 0 \\ \hline \end{tabular}  
* The function of each gene is given according to the ITAC4.0 annotation. Associations carrying candidate gene regions can be retrieved in Table 8 column ‘association_status’ along with the FTMV genotype at the corresponding markers. ‘exp’ represents expression data based on the fruit transcriptome analysis from [41]. ‘eQTL’ indicates genes for which [51] found a cis regulation eQTL. The number of polymorphisms detected in the coding region of the genes are indicated according to their effect (High: stop codon; Mod: non-synonymous mutation; Low: synonymous mutation). GDSL: named after the conserved motif ‘Gly-Asp-Ser-Leu’, DAHP: 3-Deoxy-D-Arabino-heptubinsonic acid 7-phosphate,+: gene expressed in tomato fruit/gene with a cis-regulation eQTL, –: gene not expressed in tomato fruit / gene with no known cis-regulation eQTL.  
\end{table} 
Table 3: Candidate genes and transcription factors identified in regions defined over associations for VOCs involved in tomato aroma.