Transcriptomic and metabolomic analyses reveal the potential mechanism of pigment composition and oil quality in the fruit of four colored Idesia polycarpa

As a woody oil tree species with substantial potential for development, Idesia polycarpa Maxim. (I. polycarpa) displays a wide range of fruit colors at maturity, representing the most direct and easily observed phenotype in the field. Nevertheless, the fundamental relationship between fruit coloration and fatty acid (FA) composition has remained insufficiently characterized. In this study, I. polycarpa fruits exhibiting four distinct color phenotypes namely, yellow fruits (YF), orange fruits (OF), red fruits (RF), and crimson fruits (CF), were systematically examined using integrated physiological, biochemical, metabolomic, and transcriptomic analyses. The findings indicated that CF contained the highest oil levels, whereas RF were characterized by the greatest enrichment of unsaturated fatty acids. Metabolomics and transcriptomics analyses further demonstrated that differential accumulation of carotenoids, flavonoids, and anthocyanin compounds constituted the principal metabolites governing fruit coloration. Moreover, these metabolites are suggestive of substrate allocation tradeoffs with the FA synthesis pathway. Multiple key transcription factors (MYB8, ABF-2, and MYC2–10) were identified from the transcriptional regulatory network constructed using weighted gene co-expression network analysis, which may modulate the allocation of carbon flow towards pigment and FA biosynthesis. Additionally, jasmonic acid and abscisic acid were found to participate in this regulatory process. This study clarified the mechanistic association between fruit coloration and oil quality in I. polycarpa, providing a theoretical framework and molecular targets for future breeding of high-yield and high-quality I. polycarpa germplasm.