Integrated transcriptomic and metabolomic analysis provides insights into lipid metabolism during seed development in Chionanthus retusus

Chionanthus retusus Lindl. & Paxton (Chinese fringe tree), a traditional native tree species in China, holds potential for development as a novel woody oil tree. To investigate the characteristics of seed oil accumulation and the molecular mechanisms underlying fatty acid biosynthesis, a systematic analysis of phenotype, transcriptome, and metabolome was conducted on kernels from high-oil (T-5) and low-oil (T-8) individuals at three critical stages of seed development (60, 74, and 91 days after flowering, DAF). The results showed that the oil contents of T-5 and T-8 reached 40.6% and 32.8%, respectively, at 91 DAF, and the two individuals exhibited different fatty acid accumulation patterns. At 91 DAF, C18:3 and C16:1 predominated in T-5, whereas C18:0 and C18:3 were the major fatty acids in T-8. This divergence was associated with the sustained high expression of desaturase genes (FAD2 and FAD3 ) in T-5 and their downregulation in T-8. Transcriptomic analysis identified 2931 genes in the “blue” module highly correlated with oil accumulation. Among them, KASIII , which encodes the key rate-limiting enzyme catalyzing the initial condensation reaction of fatty acid synthase, was highly expressed during the rapid oil accumulation phase and occupied a core position in the gene co-expression network. CrKASIII overexpression significantly remodeled the fatty acid composition of tobacco seeds, increasing the concentrations of major C16/C18 saturated and unsaturated fatty acids, indicating that KASIII acts as a crucial node driving carbon chain elongation from the initial step and shaping fatty acid composition. This study provides the first systematic elucidation of molecular mechanisms underlying seed oil accumulation in C. retusus and offers clear molecular targets and a theoretical foundation for improving oil quality in woody oil plants.