Integrated metabolome and transcriptome analysis of castor oil accumulation during seed development in Ricinus communis

Ricinoleic acid is a high-value hydroxy fatty acid with broad industrial applications, which is the main composition of castor oil (approximately 87%). Elucidating the molecular mechanisms underlying seed oil synthesis and identifying key candidate genes are essential for increasing ricinoleic acid production. In this study, we employed an integrated metabolomic and transcriptomic approach to investigate the dynamic synthesis of castor oil during seed development in <i>Ricinus communis</i> (<i>R. communis</i>). A total of 790 structurally identified metabolites were detected across 5 distinct developmental stages. These differentially abundant metabolites (DAMs) were classified into 19 clusters based on their expression trends throughout seed development. Annotation results highlighted three key DAMs, i.e., hydroxy ricinoleic acid, ricinoleic acid methyl ester and ricinoleic acid, associated with ricinoleic acid, all of which exhibited a gradual increase in abundance as seed development progressed. Transcriptomic analysis identified 9,940 differentially expressed genes (DEGs), which were grouped into five distinct clusters. Among these, 30 enzyme genes related to fatty acid biosynthesis and six oil body-related genes were screened as candidate genes, with the majority predominantly enriched in clusters I and II. Co-expression network analysis of transcription factors (TFs) and oil-related genes in these two clusters further identified candidate key TFs potentially involved in oil synthesis, including <i>WRI1</i>, <i>DREB</i>, <i>LOB</i> and eight other families. Integrated metabolomic and transcriptomic analysis revealed that the co-upregulation of five candidate genes with three dominant accumulated metabolites (hydroxy ricinoleic acid, ricinoleic acid methyl ester and ricinoleic acid), including an enzyme gene (<i>FAH12</i>) directly involved in ricinoleic acid biosynthesis and four oil body-associated protein genes (<i>OLEs</i> and <i>PXG</i>) associated with oil accumulation and storage. Candidate alternative splicing events were identified during seed development, notably within lipid metabolism genes (<i>SCAD</i>, <i>LACS1</i>, <i>SBH2</i> and <i>LIP1P</i>) and transcription factor <i>ARF2</i>. This study provides a theoretical foundation and valuable reference for future high-oil breeding and metabolic engineering efforts aimed at optimizing ricinoleic acid production.