Lipid metabolic pathways and the roles of candidate transcription factors identified via lipidomic and transcriptomic analyses at various stages of seed development in Carya illinoinensis

BACKGROUND: Pecan (Carya illinoinensis) is an important woody oilseed tree species, known for its nuts rich in healthy oil. However, the molecular mechanisms and functions of key genes involved in lipid biosynthesis during pecan seed development remain poorly understood. RESULTS: In this study, the oil content of mature seeds from the ‘Nacono’ and ‘Creek’ cultivars was 70.22% and 58.39%, respectively. Untargeted lipidomics identified five major classes of lipid molecules, with the highest proportions of glycerophospholipids and glycerolipids. These lipids contained five distinct fatty acids, with linolenic and lignoceric acids being the most abundant. cDNA libraries were constructed for seeds at 110, 124, 138, and 152 days after flowering (DAF) in both cultivars. A total of 25,099 differentially expressed genes (DEGs) were identified, including 1,695 transcription factor (TF) genes classified into 67 families. Based on transcriptome data, 15 TF genes exhibiting significant trends in fragments per kilobase of transcript per million mapped reads (FPKM) were selected for qRT-PCR validation, and the expression patterns were consistent with the transcriptome analysis. As the DAF increased, the expression levels of CiPaw16G032200-bHLH, CiPaw07G014900-bHLH, and CiPaw06G056900-C2H2 were continuously down-regulated, while CiPaw15G075200-C2H2 was up-regulated, suggesting that these genes may play crucial roles in lipid accumulation during pecan seed development. CONCLUSIONS: This study presentes a comprehensive analysis of lipid accumulation and transcriptional regulation during pecan seed development. The results reveal the molecular and biochemical mechanisms governing lipid deposition and offer valuable insights for the genetic enhancement of oil yield in this economically important species.