Integrated metabolomics and transcriptomics reveal the differences in fruit quality of the red and white Fragaria pentaphylla morphs

Fragaria pentaphylla is a perennial herb with two morphs that produce either white or red fruit. A combined metabolomic and transcriptomic analysis of the red and white fruits was conducted to reveal the different accumulated metabolites and differentially expressed genes between the red and white fruits. Red fruits of F. pentaphylla had higher quality with abundant flavonoids, free amino acids, and vitamins, compared with white fruits. Four anthocyanins, one procyanidin and 15 flavonoids in red morphs were significantly higher than in white morphs. The low level of pelargonin O-hexosyl-O-hexoside, pelargonidin O-hexoside and petunidin O-rutinoside might contribute to the white color of the F. pentaphylla flesh. Eighteen amino acids, except glycine or glutamine, were found in both the red and white morphs. Red fruits had a higher content of amino acids than white fruits. No DEG was involved in the pathway for amino acids synthesis, indicating that the higher levels of amino acids in red fruits than in white were not due to an increased amino acid biosynthesis. Integrated metabolomic and transcriptomic data suggested that COR , CHI , DFR , PKS and COMT genes might be related to the synthesis of flavonoids. Besides, 7OMT and PKS genes were shown to be closely associated with alkaloid and polyphenol synthesis. These results provide new insights into the molecular mechanisms of the color and nutrients in strawberries. • The white flesh of F. pentaphylla has low levels of flavonoids and anthocyanins. • The red fruits of F. pentaphylla are rich in free amino acids and vitamins . • No DEG is involved in amino acids biosynthesis.