Integrated multi-omics analysis identifies candidate genes and proteins associated with oleic acid accumulation in...

Oil palm (Elaeis guineensis Jacq.) is one of the world's most important woody oil crops, with the mesocarp serving as the primary site of palm oil accumulation. Oleic acid (C18:1), an important monounsaturated fatty acid in palm oil, directly affects palm oil quality through changes in its abundance. Although seedless oil palm exhibits relatively high oleic acid levels, the molecular processes associated with its accumulation remain poorly understood. In this study, seedless oil palm mesocarp samples collected at 95 (FL1), 125 (FL2), and 185 (FL3) days after pollination were subjected to integrated metabolomic, proteomic, and transcriptomic analyses, followed by qRT-PCR analysis of selected candidate genes. Metabolomic and proteomic analyses included two biological replicates per developmental stage, whereas transcriptomic analysis was based on one biological sample per stage and qRT-PCR analysis included three biological replicates. The relative LC-MS/MS signal of oleic acid increased markedly during the late developmental stage (FL3). Multi-omics analyses revealed developmental changes in pathways associated with fatty acid biosynthesis, fatty acid metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, carbon metabolism, and glycerolipid/glycerophospholipid metabolism. Proteomic KEGG analysis further showed significant enrichment of several carbon- and fatty-acid-related pathways after multiple-testing correction. Among the candidate genes and proteins identified, PDH E1α, DLAT, and ACC1 were mainly associated with precursor supply, including pyruvate-to-acetyl-CoA conversion and malonyl-CoA formation; KAS-related candidates, FabG-like, and FabZ were associated with chain elongation, reduction, and dehydration reactions in the fatty acid biosynthetic cycle; and LACS4, PLS1, and PLD1 were associated with fatty acid activation and downstream glycerolipid/glycerophospholipid metabolism. FAD2-like was further associated with the downstream desaturation of C18:1 to C18:2, linking oleic acid formation with subsequent C18-unsaturated fatty acid metabolism. Integrated analysis prioritized several candidate genes and proteins associated with oleic acid accumulation. qRT-PCR confirmed significant developmental differences for SAD, FATB1, and FabZ, whereas PKp2, PFPα, PDH E1α, KAS12, ACC1, and EgCEK2-like were supported mainly by pathway position and descriptive multi-omics patterns; FabG-like, DLAT, LACS4, PLS1, and PLD1 were not examined by qRT-PCR. Among these candidates, SAD was associated with the C18:0-ACP-to-C18:1-ACP desaturation step, and its qRT-PCR expression showed a pronounced increase at FL3, consistent with the late-stage increase in the oleic-acid-associated LC-MS/MS signal. Collectively, this study identified metabolic pathways, candidate genes, and proteins associated with oleic acid accumulation in seedless oil palm mesocarp at the metabolite, transcript, and protein levels, providing candidate targets for subsequent functional validation.