Genotype × Environment Shapes Fig Seed Oil Metabolic Fingerprinting

Background/Objectives: Fig (Ficus carica L.) seed oil represents an underexplored by-product with considerable nutraceutical potential. However, systematic evaluation of genotype × environment (G × E) interactions affecting its biochemical composition remains limited. This study assessed compositional variability across fig varieties, identified metabolic trade-offs, and developed rapid authentication protocols using FTIR-ATR spectroscopy to support predictive G × E models and marker-assisted selection. Methods: Thirty-seven fig varieties were evaluated across two consecutive harvest years (2023–2024) in Morocco. Conventional biochemical analyses measured total phenolic content (TPC), total flavonoid content (TFC), DPPH and ABTS antioxidant activities, and oil yield. FTIR-ATR spectroscopy characterized spectral variations, with ANOVA assessing effects of year, variety, and G × E interactions. Principal Component Analysis (PCA) discriminated genotypes and years. Results: TPC varied substantially (16.5–115.1 mg GAE/100 g oil), declining 36% from 2023 (48.7 ± 16.6 mg GAE/100 g) to 2024 (31.2 ± 16.6 mg GAE/100 g; F = 1372.84, p < 0.001), with TFC showing parallel trends (15.6 vs. 11.8 mg QCE/100 g). DPPH activity increased 34% in 2024 (58.5% vs. 43.7%), while ABTS activity decreased 18.6% from 32.34 ± 14.28% to 26.31 ± 6.10% (p < 0.001). Oil yield decreased from 26.7% to 21.2% and negatively correlated with phenolic accumulation (r = −0.49, p < 0.001). FTIR-ATR identified diagnostic peaks (e.g., 3012, 2928 cm−1), with significant G × E effects (p < 0.001). PCA captured 75.4–84.5% variance, discriminating genotypes and years. Stable high-value cultivars included ‘Dottato Perguerolles’, ‘VCR 276/49’, and ‘Ferqouch Jmel’. Conclusions: Genotypic differences and year-to-year environmental conditions significantly influence fig seed oil composition. The observed negative correlation between oil yield and phenolic content indicates a trade-off between lipid biosynthesis and secondary metabolism. FTIR-ATR spectroscopy coupled with multivariate analysis enables reliable variety discrimination and year differentiation, supporting the development of stable cultivars for nutraceutical applications.