Sweet cherries are economically important fruit trees, and their quality changes during development need to be determined. The mechanism of fruit quality changes in sweet cherries were determined by analyzing sweet cherry fruits at 12 developmental stages. The results showed that the soluble sugar, anthocyanin content, and hormones of sweet cherries all changed drastically during the color transition. Therefore, the fruits at the beginning of color conversion, at the end of color conversion, and at the ripening state were selected for the comprehensive analysis of their metabolome and transcriptome. Different sugars, such as D-glucose, sucrose, and trehalose, were identified in the metabolome. Dihydroquercetin, delphinidin-3-glucoside, cyanidin-3-rutincoside, and other flavonoid species were also identified. D-glucose and cyanidin-3-rutinoside were among the most important components of sweet cherry soluble sugars and anthocyanins, respectively. The transcriptional analysis identified key structural genes and nine transcription factors involved in the ABA, sugar, organic acid, and anthocyanin synthesis pathways, with the following specific regulatory patterns. NAC71, WRKY57, and WRKY3 regulate fruit sugar accumulation mainly by acting on INV, SPS, and SUS. MYC2 is involved in the synthesis of anthocyanin precursors by activating PAL and C4H, whereas TCP7 mainly regulates CHI and F3H. WRKY3, NAC71, and WRKY57 have important positive regulatory significance on anthocyanin accumulation, mainly by activating the expression of DFR, ANS, and 3GT.

In the production process of sweet cherry, there are unreasonable planting densities and tree shape selections. With increasing tree age, the crown of the tree continues to expand and the tree body is prone to canopy closure, which leads to the inability to efficiently use space and light energy. Low-light has become a major limiting factor in the quality of sweet cherry. Therefore, we analyzed the changes of various physiological indicators and the transcriptome of ‘Hongdeng’ sweet cherry under shading treatment in this study to investigate the effects of low-light stress on the photosynthetic characteristics of sweet cherry leaves and fruit physiology and biochemistry. The results showed that shading significantly reduces the light capture capacity of leaves, damages the photosystem, reduces carbon assimilation capacity, and consumes the majority of the captured light energy as photochemical energy, thereby restricting the growth and development of leaves and reducing the accumulation of nutrients in fruits. Shading significantly reduced fruit weight, sugar content, and vitamin C content at maturity and significantly increased acid content. Transcriptomic data demonstrated that low-light stress produces a large number of differential genes related to carbon metabolism, organic acid metabolism, and stress resistance, thereby suggesting that low-light stress may affect the expression of these related genes and inclusions in the fruit. The results of this study will provide theoretical and technical support for the physiological response mechanism of low-light tolerance in sweet cherry, the selection and breeding of low-light tolerant sweet cherry varieties, and the cultivation of sweet cherry in facilities.

The color of sweet cherry fruits is an important indicator of their appearance and quality. That influences the purchasing desires of consumers. We performed a multi-omics analysis of two different colors of sweet cherry fruits (yellow “Bing Hu” and dark-red “Hong Deng” fruits). A total of 12 flavonoid differential metabolites, including hesperetin, rutin, and quercetin, and 18 differential structural genes, including PAL, CHS, FLS, and DFR, were identified. Possible key regulatory genes for the second stage of color change (from green to yellow) of “Bing Hu” sweet cherry fruits were identified as SBP, bHLH, WD40, and bZIP, which regulated the accumulation of flavonoids, including hesperetin and naringenin. In addition, the possible important roles of transcription factors, which were mainly MYB, bHLH, AP2, and WRKY, in the third stage of color change in both fruits were also identified. This study offers new insights into the changes in fruit coloration between yellow and dark-red sweet cherries, while the analysis of key metabolites and differential genes lays a molecular foundation for future color improvement and breeding programs.