Transcriptome and metabolome profiling provides insight into the regulatory network of fruit coloration in Coffea arabica L

Coffee is the most popular beverage in the world with exceptional flavor and taste. Fruit color is known as the prime quality attribute that influences the nutritional quality and health benefits of coffee. The molecular mechanism underlying the diversity of fruit coloration is still unclear in C. arabica. A network of key genes and metabolites involved in coffee fruit coloration was constructed. The analysis of transcriptome and metabolic was performed by using six contrast-colored fruits. The results revealed that the differential metabolites and genes were enriched in the anthocyanin biosynthesis and carotenoid biosynthetic pathways in C. arabica fruits. In total, 31 differentially accumulated anthocyanins, 34 differentially accumulated carotenoid and 75 differentially expressed genes were identified. In addition, the difference in composition and concentration of carotenoids influenced the diversity of fruit coloration. The results of combined metabolome and transcriptome data showed a strong relationship between differentially expressed genes and accumulated metabolites. After conjoint analysis of transcriptome and metabolome, we found 13 anthocyanidins associated DEGs had a strong linkage with nine compounds and 16 carotenoids annotated DEGs displayed a strong connection with nine carotenoid compounds. This study identified the expression of key genes and the abundance of metabolites, and biosynthesis pathways, which provided the regulatory mechanism of fruit coloration in C. arabica. This study further supported the analysis for genetic control of fruit color in C. arabica.