The identified metabolic pathways were grouped according to the biosynthetic cycle of fatty acids and factors affecting oil quality, to provide more details about the most important identified pathways. In the study of oil biosynthesis, attention should be paid to the three key stages of carbon supply in the skeleton of triacylglycerols including the production of fatty acids, the assembly of fatty acids, and finally the formation of complex lipids (Salas et al., 2013).
  1. Pathways related to carbon source: In the first group, there are metabolic pathways that supply carbon for production of fatty acids, and the pathway of galactose metabolism has been identified in this group (Additional file 1). There are several sources of carbon in olive tree (Salas et al., 2013), which are A) Leaves photosynthesis (transfer of photosynthetic products from leaves to other organs) B) Raffinose family oligosaccharides (making of sugar alcohols and oligosaccharides such as mannitol, raffinose, and stachyose along with other photosynthetic materials in separate reactions), and C) Fruit photosynthesis. In olive, biosynthesis of mannitol and sorbitol, which are sugar alcohol, is present, and this pathway was also observed in the Apiaceae family (Sánchez & Harwood, 2002). In addition, the biosynthesis of oligosaccharides such as stachyose and raffinose, which are found in the legumes family, was also observed in olives (Salas et al., 2013). Therefore, it is possible to confirm that making sugar alcohols and oligosaccharides, as observed in other plant families, can be a reliable source of carbon also in olives.
  2. Pathways related to Acetyl-CoA: In the second group, the presence of acetyl-CoA along with two enzymes acetyl-CoA carboxylase (ACCase) and fatty acid synthase (FAS) is necessary to start the biosynthesis of fatty acids (Salas et al., 2013). It was stated that a stable and rapid pathway for the supply of acetyl-CoA is glycolysis and pentose phosphate pathways using pyruvate by the activity of the enzyme pyruvate dehydrogenase (AID in 2012). In the present study, the key metabolic pathways identified for acetyl-CoA biosynthesis were glycolysis (Additional file 2) and pyruvate metabolism (Additional file 3).
  3. Pathways related to fatty acids: In the third group, biosynthesis of the carbon chain of fatty acids, the key metabolic pathways of fatty acid biosynthesis, fatty acid elongation, and biotin metabolism were individuated in the present study. Metabolic pathway glycerolipid metabolism was identified as a key metabolic pathway in the assembling of fatty acids and the formation of complex lipids. In addition, two metabolic pathways alpha-linolenic acid metabolism and linoleic acid metabolism were identified as important pathways in the production of by-products of fatty acid biosynthesis.
  4. Pathways related to non-fatty acids components (minor compound): The fourth group was related to metabolic pathways that have a direct impact on the quality of the oil and its taste. In this group, six key metabolic pathways were observed: terpenoid backbone biosynthesis, phenylpropanoid biosynthesis, flavonoid biosynthesis, limonene and pinene degradation, monoterpenoid biosynthesis, and carotenoid biosynthesis.
The detected metabolic pathways affecting the quality of oil in this study have been investigated independently, and the genes affecting each metabolic pathway have been identified and introduced (Additional file 4).