A seasonal dynamics of free fatty acid content and gene expression provides new insights into the fatty acid metabolism in Acer truncatum seeds

Acer truncatum Bunge (ATB) seed oil has garnered attention in China as a promising edible oil due to its diverse health benefits. The transcriptome and targeted metabolome analyses were conducted on ATB seeds collected from Tongliao, Inner Mongolia (IMTL) between May to September. A total of 36 free fatty acids (FFAs) (like nervonic acid and linolenic acid) were identified, with 12 FFAs showing differential accumulation. Through integrative analysis, Weighted Gene Co-expression Network Analysis (WGCNA), and K -means clustering, key genes involved in conjoint KEGG pathways between differential expressed genes (DEGs) and differential accumulated free fatty acids (DAFFAs) were identified: Atru.chr6.3280 in fatty acid biosynthesis, Atru.chr6.2845 in unsaturated fatty acid synthesis, Atru.chr3.2472_Atru.chr3.2479 in the linoleic acid pathway, Atru.chr4.2824 in very-long-chain fatty acid biosynthesis, Atru.chr6.2603 , Atru.chr2.229 , Atru.chr4.1919 , Atru.chr5.2650 , Atru.chr1.598 , and novel.4789 in cutin, suberin, and wax biosynthesis, novel.4790 , Atru.chr6.2046 , Atru.chr9.2308 , Atru.chr6.3280 and Atru.chr3.305 in cofactor biosynthesis. Notably, six transcription factors (TFs) from the B3, MYB, NAC, AP2/ERF, and bHLH families were found to be strongly correlated with the DAFFAs. This research offers a novel perspective on the molecular mechanisms underlying fatty acid metabolism in ATB seed oil and establishes a basis for future studies on its functional properties. • 12 key differential accumulation free fatty acids (DAFFAs) were detected. • Genes strongly associated with DAFFAs were identified. • Six transcription factors were strongly correlated with DAFFAs. • A potential mechanism linking DAFFAs and related genes was proposed.