Fatty Acid Profiling of “Mollar de Elche” Pomegranate (Punica granatum L.) Peel and Seeds: Impact of Farming System, Locality, and Interannual Climate Variability

Agronomic practices and interannual climate variability significantly modulate the bioactive composition of agricultural by-products. This study evaluated the effects of farming systems (organic vs. conventional) and geographic locality across two harvest seasons (2022–2023) on the fatty acid (FA) profiles of peel and seeds from the “Mollar de Elche” pomegranate (Punica granatum L.) Protected Designation of Origin (PDO). Gas chromatography (GC-FID) analyses demonstrated that the harvest year, characterized by significantly reduced extreme temperature days in 2023, exerted a dominant, overriding effect on lipid biosynthesis compared to agronomic management. In the seeds, punicic acid was the unequivocal predominant FA, increasing dramatically from an average of ~75,700 mg/kg dry matter (DM) under severe heat stress (2022) to ~150,000 mg/kg DM under milder conditions (2023) (p < 0.001). In the peel, polyunsaturated fatty acid (PUFA) accumulation was strictly dependent on the interaction between localized geographic micro-conditions and climate, rendering the farming system a secondary factor. Crucially, the milder 2023 season significantly enhanced the unsaturated-to-saturated (U/S) ratio in both tissues and markedly improved cardiovascular lipid quality, lowering both the Atherogenic (AI) and Thrombogenic (TI) indices. These findings demonstrate that while organic farming can optimize lipid unsaturation under favorable climatic conditions, severe environmental stress nullifies these agronomic benefits, highlighting the need for climate-resilient strategies to valorize pomegranate by-products.