Sweet cherry (Prunus avium L.), with attractive appearance, desirable taste, dietary properties and various biological activities, which not only directly influence consumer choice, but also are important directions of new fruit varieties selection and breeding today (Nawirska-Olszańska et al., 2017). The color of the sweet cherry fruit ranges from dark red to yellow is determined by the pigments present (e.g. anthocyanins, carotenoids, etc.). Most sweet cherry species in red color are particularly rich in anthocyanins, and are predominantly cyanidin glycosides (Gonçalves et al., 2007; González-Gómez et al., 2010; Liu et al., 2013).
Anthocyanin is a class of water-soluble natural pigment in plants that widely presents in the nature belongs to a subgroup of flavonoids. To date, there have been more than 635 anthocyanins identified, and approximately 95% of which are derived from 6 anthocyanins: pelargonidin, cyanidin, delphinidin, peonidin, petunidin, and malvidin (He and Giusti, 2010; Eder, 2000; Kong et al., 2003). Various enzymes have been reported to be involved in the anthocyanin biosynthesis process, including chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3′H), dihydroflavonol-reductase (DFR), and anthocyanidin synthase (ANS) (Koes and Verweij, 2005). The mechanisms of anthocyanin biosynthesis have been elucidated in a variety of plant species, such as apple, peach, sweet cherry, eggplant, tomato, etc (Meng et al., 2015; Ye et al., 2019; Wei et al., 2015; Li et al., 2021; Sun et al., 2019). UFGT family showed differences between red and non-red apple fruits in previous study. Among them, UFGT2 was up-regulated only in non-red cultivar, while UFGT4 was up-regulated only in red cultivar, indicating that UFGT play an important role in anthocyanin accumulation in apple skin of different colors (Meng et al., 2015). In the epidermis of purple eggplant (Solanum melongena), MYB86 could directly bind to the promoters of CHS, F3H, and ANS and suppress their activities, resulting to the reduction of the anthocyanin (Li et al., 2021). In sweet cherry, the anthocyanin content increased gradually during the development, especially from the young fruits to the breaker fruits stage. Some unigenes have been reported to be up-regulated in red-colored fruit, including 4CL, CHS, CHI, F3H, DFR, etc. Among them, UFGT was suggested to play a key role in red and bicolored (red and yellow) fruits, and the expession of which are maintained at high levels in red cultivars in the late ripening stage. Some transcription factor families, such as MYB, bHLH and WD40, may involved in anthocyanin biosynthesis control (Wei et al., 2015; Liu et al., 2013).
Carotenoids are a class of widespread secondary metabolites that are crucial to humans and plants, mainly divided into α-carotene, β-carotene, lycopene, lutein, astaxanthin and zeaxanthin. Carotenoids are not synthesized by humans but are essential for several functions, so they must be obtained through the diet, especially fresh fruits (Luo et al., 2021; Kopec and Failla, 2017). To date, many data have been available related to the molecular characterization of genes involved in carotenoid biosynthesis. Hu et al. (2021) elucidated that one LCYE gene (LOC113688784) expressed 2.21 times higher in matured seeds of red coffee (Coffea arabica) than that in yellow coffee seeds. Li et al. (2021) found that the imbalanced regulation of HYE and HYB resulted in an increase of zeaxanthin and a decrease of lutein in Chinese raspberry (Rubus chingii). Likewise, Wu et al. (2020) reported that down-regulation of transcription factor SlMYB72 of R2R3-MYB promoted β-carotene production and decreased lycopene content in tomato (Solanum lycopersicum). Despite these findings, the molecular regulation mechanism of carotenoid biosynthesis between different color sweet cherry fruits remained unclear.
RNA-seq analysis is commonly used to identify the differential genes and understand their mechanism underlying gene expression regulation in the biosynthetic pathway of different species from a transcriptomic perspective. Based on the transcriptome analysis, scientists have found that the reduction of key anthocyanin gene expression at the late stage of in white bayberry (Morella rubra) compared with red bayberry fruits, resulting in the failure to turning red (Lin, Zhong and Zhang, 2019). Wei et al.(2015) obtained the transcriptome and DGE profiling data to compare the transcripts involved in the anthocyanin biosynthesis. However, for carotenoid biosynthesis, reports on the transcriptional regulation at specific ripening stages and finally determines the quality in red and yellow sweet cherry are still limited. Herein, in order to identify the major disparity of pigmental substance and the molecular mechanisms in anthocyanin and carotenoid biosynthesis of sweet cherry, we have explored the anthocyanin and carotenoid compounds and transcriptome profiling of a red cultivar (JNH) and a yellow cultivar (CY) in four ripening stages.