Conclusions

According to the economic importance of olive oil, the quantity and quality of oil should be improved in parallel based on international standards in commercial cultivars. Technical variation in different experiments and limited number of biological replicates in RNA-seq researches could affect the reproducibility and the statistical power of the experiments. Meta-analysis of RNA-seq data can increase the speed of production of functional data related to the quality of olive oil and produce useful information. The present work would be an effective and useful step in reducing the time of cultivar screening by developing key genes relating to oil quality in olive breeding programs. The IDR index indicated the meta-analysis had good power to identify new differentially expressed genes and identified 155, 473, and 241 differential expressed genes for the first time respectively in the C1, C2, and C3. The identified key genes were investigated in the metabolic pathways related to oil quality and the identified metabolic pathways were also grouped into four groups according to the pathway of oil biosynthesis and the factors affecting its quality. The metabolic pathways that affecting the quality of oil have been examined independently confirming the earlier published results through meta-analysis and contributing to the reproducibility of the results. The galactose metabolism pathway can be further investigated as a source of carbon supply in olive fruit, and due to the increase in the expression of its genes in the S3, it can help to supply carbon in the final stage of growth when the fruit photosynthesis is reduced. Moreover, the production of acetyl-CoA in various ways in different growth stage shows the high efficiency of olive in the production of fatty acids. In the fatty acid biosynthesis pathway FabF and SAD have a critical role in oil quality and second identified pathway is more suitable for production of high oleic acid. Furthermore, the production of TAG by the PDAT probably occurred in the mesocarp and played an important role in the production of TAG and oil in the mesocarp. Also, the results of present study showed biosynthesis of phenolic compounds in olives in terms of growth stages might be in the opposite of the biosynthesis of fatty acids and there are the highest amount of phenolic compounds after fruit formation, while the biosynthesis of oil is at its lowest. The identified and confirmed genes by meta-analysis approach provided a suitable dataset to draw on for future studies in different scientific sectors. The present research can also play a role in cultivar selection by applying potential molecular markers developed in the here individuated key genes, reducing the duration of breeding programs, and helping the genome editing by introducing key and essential genes for the development of healthy compounds.
Authors' contributions
AA.A. collected data, performed all steps of the meta-analysis of RNA-seq, wrote the main draft, and done final revision on the manuscript. V.S. was conceived and designed the project, guide and confirmed the data analysis, and revised and approved the final manuscript. S.M and R.M provided critical advices on the manuscript and revised the manuscript. M.HM revised the final manuscript. The research was co-supervised by M.HM. All authors have read and approved the final manuscript.

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Additional files

Additional file1. Up and down-regulated identified genes of the galactose metabolism pathway in the biosynthesis of raffinose family oligosaccharides.
Additional file 2. Up and down-regulated identified genes of the glycolysis pathway in production of acetyl-CoA.
Additional file 3. Up and down-regulated identified genes of the pyruvate pathway in production of acetyl-CoA.
Additional file 4. Summary of important pathways and identified important genes in the meta-analysis.
Additional file 5. Identification of enriched genes in glycolysis and pentose phosphate pathways.
Additional file 6. Up and down-regulated identified genes in the Fatty acid biosynthesis pathway.
Additional file 7. Up and down-regulated identified genes in the Fatty acid degradation pathway.
Additional file 8. Up and down-regulated identified genes in the glycerolipid metabolism pathway.
Additional file 9. Up and down-regulated identified genes in the terpenoid backbone biosynthesis pathway.
Additional file 10. The results of search strategies and the information of thirty experiments was recorded.