## 3 Results
### Biological Use Case 1: Comparative Genomics to Study Tomato Fruit Shape and Potato Tuber Shape
\begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Traits of Interest** & **GO Annotations** & **Chromosome** & **Location** & **Candidate Genes** & **References** \\ \hline \multirow{4}{*}{Total soluble solids (Brix)} & GO:0006094, & & & & \\  & GO:00463670, & & & & \\  & GO:0046369, & & 3474710 & Lin5 & [68] \\  & GO:005985, & & & & \\  & GO:0015770 & & & & \\ \hline Carotenoid compounds & GO:0045436, & & & & \\ (Lycopene beta-cyclase activity) & GO:0016117 & 6 & & & \\ \hline \multirow{4}{*}{Polyphenylonic compounds (2-phenylethylhanol, phenylacetaldehyde)} & GO:0016747, & & & & \\  & GO:00102387, & & & & \\  & GO:0018449, & & & & \\  & GO:0004029, & & & & \\  & GO:0008957, & & & & \\  & GO:1990055, & & & & \\  & GO:0050177, & & & & \\  & GO:0018814 & & & & \\ \hline \multirow{4}{*}{Terpenoid compounds} & GO:003677, & & & & \\  & GO:0045893 & & & & \\ \hline Volatile compounds & GO:0046568, & & & & \\ (3-methylbuthanal, & GO:001845, & & & & \\ 3-methylbuthanol) & GO:0052676 & & & & \\ \hline \hline \end{tabular}
\end{table} 
Table 2: A selected set of five QTLs for metabolic traits in tomatoes. These QTLs are used as test cases to analyse the prediction power of the underlying workflow. and has a score significantly higher than all other genes. Here also, we can conclude that our workflow performed as expected. Phenolic derivative compounds like 2-phenylethanol and phenylacetaldehyde have a great impact on the aroma of a tomato [70]. Several QTL locations related to phenolic compounds have been identified in the past out of which, a major QTL region on chromosome 8 mapped by the markers, TG330-CT77 and TG330-CT148 is associated with the accumulation of 2-phenylethanol and phenylacetaldehyde (having genomic coordinates 55068565-63267130) [75]. Additionally, two putative proteins, 2-phenylacetaldehyde reductases proteins (LePAR1 and LePAR2) are known candidates, which catalyze the conversion of 2-phenylacetaldehyde to 2-phenylethanol [76]. Both these proteins are members of a reductase/dehydrogenase family. Table 3 shows the top three genes predicted from our pipeline for these phenolic compounds on chromosome 8. _Solyc08g068190.2_ was the top predicted gene related to this trait. Although we are not sure if this gene is the same as LePAR1 and LePAR2, this gene belongs to the same aldehyde dehydrogenase family. Therefore, our workflow could detect the causal gene within this QTL region. A major QTL related to Terpenoids has been mapped on chromoasome 1 with the genomic coordinates of 86142248-86467672 [77]. Proteins of the Terpene synthase (TPS) family and TPS gene are the expected candidate genes associated with Terpenoids. Five of the TPS-a subclade genes (TPS31, TPS32, TPS33, and TPS35) occur in close proximity within this QTL. Table 3 highlights the top tree genes predicted from our pipeline for this QTL. Our results suggest that the gene _Solyc01g095030.2_, which is a MYB transcription factor, is the causal gene for this QTL region. This is possibly the wrong prediction. The reason for our pipeline to give a wrong prediction here could be that there is no term present in the GO ontology that directly related to Terpenoids. Further, because of this missing GO annotation terms, Terpene synthase is not been well annotated with its function, which makes it difficult for our workflow to detect it as a high ranking gene for the Terpenoids trait. Volatile compounds like 3-methylbuthanal and 3-methylbuthanol influence the flavor, sensory changes, and defense mechanism of tomato fruits [78]. A major QTL related to the volatile compounds (3-methylbuthanal, 3-methylbuthanol) has been mapped on chromosome 3 with the genomic coordinates of 69685329-71362039 [79]. However, it is not known which candidate gene in this QTL is responsible for changes in the concentration of these volatile compounds. Our results suggest that the lactate dehydrogenase (LDH) gene is possibly a candidate gene for this trait.