Integrated transcriptomics and metabolomics analysis unveil flavonoid and anthocyanin metabolism in pink and blue blueberry cultivars

Blueberry is a berry crop with high abundance of bioactive compounds, including flavonoids and anthocyanins, in its fruit. To date, there is limited literature available regarding the molecular mechanism underlying pigment metabolite accumulation and the coloration of blueberry fruit. The aim of this study was to comparatively assess the color difference of the rabbiteye blueberry pink-fruited 'Pink Lemonade' and blue-fruited 'Gardenblue' varieties. During fruit coloring and ripening, the total flavonoid contents gradually decreased, while the anthocyanin content increased significantly. A total of 104 differentially accumulated flavonoid metabolites were identified by untargeted metabolomics. Furthermore, targeted metabolic profiling analysis indicated 48 anthocyanidins that were differentially expressed in their ripening fruits. They each had unique main coloring substances, including malvidin-3-O-glucoside, malvidin-3-O-galactoside, delphinidin-3-O-glucoside in 'Gardenblue' and petunidin-3-O-arabinoside and cyanidin-3-O-arabinoside in 'Pink Lemonade'. Transcriptome sequencing identified 30 structural genes, 11 MYBs and four bHLHs among the differentially expressed genes (DEGs) in the ripening fruits involved in anthocyanin biosynthesis, and partial members were identified by quantitative real-time PCR. Collectively, the integrated multiomics results for the two blueberry fruit varieties not only explain the color difference based on metabolite compositions but also lay the foundation for understanding the blueberry coloration and anthocyanin biosynthesis regulation.