Metabolomic and Transcriptomic Analysis Reveals the Mechanisms Underlying the Difference in Anthocyanin Accumulation in Apple Fruits at Different Altitudes

Abstract

The red color of apple peel is an important phenotypic and economic trait mainly attributed to anthocyanin accumulation. Apples show a deeper red color at higher altitudes than at lower ones; however, the molecular regulatory network underlying color variation along altitudinal gradients has not been investigated. In this study, the effects of environmental conditions associated with low (124 m) and high (1901 m) altitudes on peel color were assessed through physiological, metabolomic, transcriptomic, and qRT-PCR analyses in Huashuo apple and its sister line, Huarui apple. The content of cyanidin-3-O-galactoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-xyloside was abundant in the high-altitude environment and may contribute to the deeper red color. Transcript levels of structural genes in the anthocyanin synthesis pathway, especially MdCHI, MdCHS, MdANS, and MdDFR, in apple peel were significantly higher at high altitude than at low altitude. Based on the protein interaction prediction and correlation analyses, four transcription factors (MDP0000127691, MDP0000284922, MDP0000758053, and MDP0000074681) could interact with anthocyanin synthesis-related proteins, showing high correlation with anthocyanin accumulation. Therefore, the abovementioned four genes and four transcription factors were predicted to account for the color differences between high and low altitudes. These results provide genetic resources and a theoretical basis for color-oriented fruit improvement.