Metabolites derived from bitter fennel serve as flavoring and healing agents in the pharmaceutical, food, and cosmetic sectors. Previously, we developed three fennel breeding populations (Early, Medium, and Late Maturity Synthetic Cultivars) with the potential to produce higher seed yield. This investigation aimed to assess the quality and quantity of the important metabolites in these three cultivars alongside their elite parental populations. Our results showed that the highest amounts of essential oil yield and seed yield were produced by, two breeding populations, Medium and Late Maturity Synthetic Cultivars. These cultivars showed positive seed yield heterosis rates of 28% and 20%, respectively, above the averages of their parental populations. GC-MS analysis of the essential oil samples identified 24 components in total. The major compounds in all genotypes were trans-anethole (34.09–77.84%), limonene (4.99–12.66%), methyl chavicol (1.35–38.69%), and fenchone (6–13.07%). The highest amount of trans-anethole belonged to Fasa and the Medium Maturity Synthetic with 77.84 % and 73.10%, respectively. The analysis of fatty acid compositions in the genotypes was conducted using GC-FID, which revealed the presence of 19 unique fatty acids, of which ten were saturated, and nine were unsaturated fatty acids. Petroselinic acid (67.11–78.44%), and linoleic acid (9.14–11.60%) were the major unsaturated fatty acids in fennel seeds. The Early Maturity Synthetic exhibited the least saturated fatty acid content (7.24%), while the highest levels of unsaturated fatty acids were found in both the Early Maturity Synthetic (89%) and Hashtgerd (88.55%). The genotypes were categorized into four groups using a heat map analysis with hierarchical clustering. Overall, the results showed that the three synthetic cultivars of fennel have outperformed the elite parental populations for seed and essential oil yields, concentration of the major industrial secondary metabolites such as trans-anethole, and higher proportions of unsaturated fatty acids. These cultivars show potential for usage in the pharmaceutical and healthcare industries.
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