Lipidomic and comparative transcriptomic analysis of fatty acid synthesis pathway in Carya illinoinensis embryo

Pecan (Carya illinoinensis) is an important oilseed nut and is rich in fatty acids and flavonols. Pecan fatty acid has significantly edible, industrial, and clinical value. To investigate the dynamic patterns and compositions of fatty acid, and the molecular mechanism that controls fatty acid accumulation in pecan, lipidomic and transcriptomic analyses were performed to determine lipid profiles and gene expression in pecan’s fatty acid biosynthesis pathway. In the present study, compared to cultivars ‘Caddo’ and ‘Y-01’, ‘Mahan’ formed larger and heavier embryos and accumulated higher oil content. Lipidomic analysis showed that fatty acid and (O-acyl)-1-hydroxy fatty acid contents were higher in ‘Mahan’ at the mature stage. Based on full-length and comparative RNA-Seq, differential expression gene enrichment analysis revealed that many functional genes participated in the pathways of ‘fatty acid biosynthesis’, ‘fatty acid metabolism’, and ‘linoleic acid metabolism’. High fatty acid accumulation model from ‘Mahan’ demonstrated that key enzyme encoding genes played an important role in regulating fatty acid biosynthesis. Co-expression module analysis indicated that several transcription factors (MYB, TCP, bHLH, Dof, ERF, NAC) were involved in fatty acid accumulation by regulating the expression of functional genes, and real-time quantitative PCR verification proved that these transcription factors had a high correlation with pecan fatty acid accumulation pattern. These findings provided an insight into the molecular mechanism of fatty acid accumulation in C. illinoinensis embryo, which contributes to pecan oil yielding and pecan molecular breeding.