Study on the dynamics of fruits color related genes and metabolites during the fruit development of Zanthoxylum bungeanum ‘Hanyuan’

BACKGROUND: Anthocyanins play a crucial role in determining the coloration of plant fruits and are essential for enhancing their economic traits. However, studies on anthocyanin biosynthesis in Zanthoxylum bungeanum 'Hanyuan' fruit have yet to be reported. RESULTS: In this study, the patterns of anthocyanin synthesis in fruit through phenotypic analysis and total anthocyanin measurements across 13 development stages were traced. The results indicated that the pericarp of Z. bungeanum 'Hanyuan' exhibited a gradual transition in color from light red to dark red between 64 d AF and 100 d AF, with the highest total anthocyanin content recorded at 64 d AF. Based on this conclusion, five key stages were selected for the transcriptome and anthocyanin-targeted metabolome analysis to further elucidate the molecular mechanisms underlying anthocyanin synthesis. Metabolomic analysis identified eight metabolites that influence the formation of red color in fruit: Cyanidin-3-O-rutinoside, cyanidin-3-O-xyloside, naringenin, peonidin-3-O-rutinoside, cyanidin-3-O-(6-O-malonyl-beta-D-glucoside), petunidin-3-O-sambubioside, petunidin-3-O-(6-O-p-coumaroyl)-glucoside, and delphinidin-3-O-(6-O-malonyl-beta-D-glucoside). These metabolites exhibited the highest concentrations at 64 d AF, 86 d AF, and 100 d AF. Transcriptome analysis, WGCNA analysis, and correlation analysis indicate that ZbFLS11 and ZbCYP98A32 positively regulate the biosynthesis of cyanidin-3-O-xyloside, petunidin-3-O-(6-O-p-coumaroyl) glucoside, and petunidin-3-O-sambubioside. Zb4CL1 exhibits a positive correlation with petunidin-3-O-(6-O-p-coumaroyl)-glucoside and naringenin. Additionally, the upregulation of five genes (ZbCHS1, ZbCHS2, ZbCHS3, ZbCHS4, and ZbCHS5), ZbC4H2, and ZbC4H3 expressions at 64 d AF and 86 d AF was associated with the accumulation of delphinidin-3-O-(6-O-malonyl-beta-D-glucoside) during the development stages of Z. bungeanum 'Hanyuan' fruit. Furthermore, it was found that MYB113 interact with the structural genes Zb4CL1, ZbCYP98A32, and ZbFLS11, thereby regulating the biosynthesis of petunidin-3-O-(6-O-p-coumaroyl)-glucoside. Additionally, bHLH6 exhibits a positive regulatory relationship with the five genes (ZbCHS1, ZbCHS2, ZbCHS3, ZbCHS4, and ZbCHS5), ZbC4H2, and ZbC4H3, which influence the biosynthesis of delphinidin-3-O-(6-O-malonyl-beta-D-glucoside). CONCLUSION: In summary, the findings of this study elucidate the molecular mechanisms underlying color development in Z. bungeanum 'Hanyuan' fruit across various development stages. This research offers valuable insights for future investigations into the intricate molecular network governing anthocyanin biosynthesis in Z. bungeanum 'Hanyuan' fruit.