## 3 Results
### Biological Use Case 1: Comparative Genomics to Study Tomato Fruit Shape and Potato Tuber Shape
Out of the five QTLs, our workflow performed significantly well in detecting candidate genes for the QTLs of soluble solids, lycopene beta-cyclase activity, and phenolic compounds. Our workflow did not perform well in the detection of candidate genes within the QTL for terpenoids on chromosome 1. This is most probably due to the fact that this QTL region is not well annotated, and there are no GO terms related to Terpenoids. Lastly, our workflow predicts a candidate gene called LDH, for the previously unknown QTL region associated with volatile compounds. QTLSearch, a prediction pipeline for candidate genes in QTL regions, is based on existing knowledge and evolutionary data (orthologs and paralogs). While the performance of QTLSearch is high with well-annotated data, it fails to perform well in detecting candidate genes for QTL regions where little is known. Hence, it is still very challenging to infer about candidate genes in a poorly annotated QTL region. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Gene ID** & **Alias** & **UniProt ID** & **Protein Description** & **Chromosome Number** & **Location** & **Prioritization Score** \\ \hline \multicolumn{6}{c}{**Metabolic Trait 1: Brix/soluble solids**} \\ \hline SolyC9g010090.2 & LIN7 & Q8 LAN2 & Cell-wall invertase & 9 & 3480545-3484159 & 0.202943 \\ SolyC9g010080.2 & lin5 & Q9 LD97 & Beta-fractroturainosidase insoluble isoenzyme 1 & 9 & 3475480-3479343 & 0.172502 \\ SolyC9g010020.2 & - & K4 CR31 & 1-aminoyclopropane-1 carboxylate oxidase & 9 & 3447416-3449839 & 0.043606 \\ \hline \multicolumn{6}{c}{**Metabolic Trait 2: lycopene beta-cyclase**} \\ \hline SolyC9g074240.1 & NSY & K4C9E2 & Chromoplast-specific lycopene beta-cyclase & 6 & 45898227-45899723 & 7.39091 \\ SolyC9g073570.2 & 101245261 & K4C976 & Cytochrome P450 & 6 & 45361777-45364885 & 0.554559 \\ SolyC9g076160.2 & 101248306 & K4C9X6 & Cytochrome P450 & 6 & 47289151-47291972 & 0.471375 \\ \hline \multicolumn{6}{c}{**Metabolic Trait 3: 2-phenylethanol/phenylacetaldehyde**} \\ \hline SolyC9g086190.2 & 101257095 & K4 CM43 & Aldehyde dehydrogenase & 8 & 57303048-5730002 & 3.702432 \\ SolyC9g076790.2 & 101246651 & K4 CN39 & Cinnamyl-CoA reductase-like protein & 8 & 60704895-60707948 & 0.009002 \\ SolyC9g0866800.2 & 101264847 & K4 CM83 & Decarboxylase family protein & 8 & 57730921-57733032 & 0.004473 \\ \hline \multicolumn{6}{c}{**Metabolic Trait 4: terpenids**} \\ \hline SolyC10g05030.2 & 101257705 & K4 AZ73 & MYB transcription factor & 1 & 86401425-86409205 & 20.423493 \\ SolyC10g04820.2 & K4 AZM2 & ARID/BRIGHT DNA-binding domain-containing protein & 1 & 86227211-86231284 & 3.715449 \\ SolyC10g04800.2 & 101245796 & K4 AZM0 & Chromodomain-helicase-DNA-binding protein 1 & 1 & 86208090-86220086 & 1.800694 \\ \hline \multicolumn{6}{c}{**Metabolic Trait 5: Volatile compounds**} \\ \hline SolyC03g122130.2 & K4 BN11 & L-lactate dehydrogenase & 3 & 70079537-70082001 & 0.008994 \\ SolyC03g122140.2 & 101255867 & K4 BN12 & L-lactate dehydrogenase & 3 & 70082466-70085406 & 0.008994 \\ SolyC03g122170.2 & K4 BN15 & L-lactate dehydrogenase & 3 & 70091655-70095510 & 0.008994 \\ \hline \end{tabular}
\end{table} 
Table 3: Top three candidate genes found for the five selected metabolic traits (Brix/soluble solids, lycopene beta-cyclase activity and 2-phenylethanol/phenylacetaldehyde).