Combined metabolomic and transcriptomic analysis reveals variation in phenolic acids and regulatory networks in the peel of sweet orange 'Newhall' (C. sinensis) after grafting onto two different rootstocks

Grafting plays a significant role in the biosynthesis of secondary metabolites in plants. In our study, we examined the impact of grafting on the phenolic acid biosynthesis in sweet orange 'Newhall' peel. Through transcriptome-metabolome analysis, we observed notable differences in total phenolic acid content between the two rootstocks [Poncirus trifoliata (ct) and C. junos Siebold ex Tanaka (cj)]. Total phenolic acid content reached its highest level during the later fruit expansion stage (347.27 µg · g−1 FW) in ct. The metabolome analysis identified 270 phenolic acids, out of which 24 were found to be influenced by rootstock grafting. The transcriptome analysis identified 8,562 differentially expressed genes (DEGs). Further analysis using KEGG and GO enrichment revealed that 36 structural genes enriched in the phenolic acid biosynthesis pathway and showed differential expression in ct and cj. Co-expression analysis indicated that the AP2/ERF-ERF and MYB family members exhibited the highest number of differences in ct and cj, suggesting their potential involvement in phenolic acid biosynthesis. Our findings provide insights into the differential accumulation mechanism of phenolic acids in sweet orange 'Newhall' peel after grafting with different rootstocks. These results enhance our understanding of the regulatory mechanisms underlying phenolic acid biosynthesis and offer valuable information for the effective utilization of citrus peel.