Different coloration patterns between the red- and white-fleshed fruits of malus crabapples

• The complex molecular mechanism underlying distinct patterns of flavonoid accumulation is proposed.
• The mechanism relies on changes in differential content and distribution of flavonoid branches.
• MYB TFs regulating structural gene expression showed tissue-specific feature.
• Shading treatment affect the expression profiles of genes related to the flavonoid biosynthesis.

The red crabapple is a rare type of fruit in the malus family that is important for apple breeding because it contains large amounts of anthocyanins/flavonoids. However, the molecular mechanism underlying anthocyanin/flavonoid accumulation in the red peels and flesh of the fruits has not been fully explored. Here, we analyzed flavonoid accumulation and the transcript levels of the main structural genes and transcription factors in fruits under sun-exposed and shaded conditions in two crabapple varieties with different coloration characteristics. Our results show that varietal differences in the flavonoid pathway mainly affect the accumulation of anthocyanins and flavanols. Shading treatment induced a significant decrease in the concentration of anthocyanins but increased the levels of flavanols. Quantitative real-time PCR analysis shows that the transcript levels of the primary structural genes, except for McF3′H and McANR, were higher in the ever-fleshed fruits than in the white-fleshed fruits. Additionally, several MYB TFs have been suggested to be involved in the regulation of the coloration patterns in response to shading. Data analysis indicated that changes in the flavonoid accumulation were associated with the transcription of the structural genes regulated by MYB transcription factors, providing new insights into horticultural plant breeding.