## 3 Results
### Biological Use Case 1: Comparative Genomics to Study Tomato Fruit Shape and Potato Tuber Shape  
For this use case, we used the pbg-ld endpoint (APIs) with a Jupyter Notebook [56] to study the difference in the genetic mechanism underlying fruit shape in tomatoes and tuber shape in potatoes. Both tomato fruits and potato tubers can have a genetically determined wide variation in their shape, for example elongated and round. The candidate gene _Solyc10g076180_ (SIOFP20 is a member of the OVATE Family Protein (OFP)) on chromosome 10 of the reference tomato genome (Heinz 1706) and is one of the determinants of round fruit shape. However, this gene does not have an ortholog in the reference potato genome (DM), which has very elongated tubers [59]. In this use case, first, we query and compare the QTL regions on chromosome 10 in tomato and in potato. This QTL regions are associated with round shape in tomato fruits and predominantly elongated shape in potatoes. We classify these genes in three categories (a) genes that are unique in tomato (b) genes that are unique in potato (c) genes that are common to both species (Table 1). Furthermore, we check the GO annotations as well as orthologs in all these genes. Three genes (_Solyc10g076170.1_, _Solyc10g076190.1_, _Solyc10g076180.1_) are present in class (a) which indicates that they are unique in tomato. Out of these genes, the _Solyc10g076170.1_ gene was removed from the latest UniProt release. _Solyc10g076190.1_ is a peroxidase gene (that is also common in class (b) and class (c)) in Table 1. _Solyc10g076180.1_ is the only unique member of the OVATE family. Genes in class (b) are all peroxidase genes whereas the class (c) contains several genes coding for peroxidadases and one gene involved in lipid transport. According to our analysis the candidate gene _Solyc10g076180.1_ does not have a corresponding ortholog in the potato DM reference genome in the same QTL region on chromosome 10. Therefore, with our tool we explored this further, and retrieve a knowledge network based on homologs of the candidate gene. This network was retrieved with a nested query, in which we first located all paralogs of the _Solyc10g076180.1_ gene in the tomato genome and then we found orthologs of these genes in the potato genome (Figure 6). In this analysis, we found 10 OFP genes (green) in potato and 11 genes (red) in tomato. One less potato gene is due to the missing OFP20 gene in the studied QTL. Figure 6: A network of _Solyc10g076180.1_ homologs in tomato (red) and potato (green) including paralogous (solid) and orthologous relations (dotted). There is no ortholog of OFP20 gene in potato. \begin{table}
\begin{tabular}{l l l l} \hline \hline Tomato genes & \(\mathbf{GO}\) annotations & \ \begin{tabular}{l} Potato orthologs inside the \\ QTL \\ \end{tabular}  & \begin{tabular}{l} Potato orthologs outside \\ QTL \\ \end{tabular}  \\ \hline Soly\(\mathbf{\text{\text{\text{\text{\text{\text{\text{\text{\text  
Out of these OFP genes in potato, PGSC0003 DMG400028155 is located on chromosome 10 in the region 56030393-56031156. However, this region is 6.7 Mb away from the studied QTL region, and thus seems unlikely to harbor the determinant candidate gene. Biological Use Case 2: Prediction of Candidate Genes in Tomato QTL Regions with Functional Annotations and Evolutionary Analysis Using pbg-ld and QTLsearch  
Predicting candidate genes for QTL regions is a key objective in plant genetics and breeding. However, a single QTL region can contain many genes. Mining candidate genes from such a QTL region could be done using existing knowledge of structural and functional gene annotations. In this use case, we aim to develop, illustrate, and analyze a seamlessly integrated workflow that uses linked genomic-data and prioritization pipelines to predict candidate genes within QTL regions for metabolic traits of tomato. Metabolic composition of a tomato is directly associated with its nutritional value, taste, aromas, and quality [60].