*3.1. Genes within Anthocyanin Regulation Pathway Were Differentially Expressed*

Numerous molecular studies have revealed the processes controlling the genetics of plant organ coloration, which include differences in expressions of structural and transcription factor genes. For example, Han et al. [54] have reported that the downregulation of *CHI* and *DFR* by *anthocyanidin reductase* (*ANR*) results in yellow-skinned apple fruits. In bicolored flowers of *Petunia hybrida*, the enhancement of *CHS* expression induces blue or red coloration, respectively, in blue–white or red–white sectors of variegated flowers [5,23]. RNA-Seq technology has revealed that the significant upregulation of annotated anthocyanin biosynthetic genes *CHS*, *F3H*, *F3H*, *DFR*, *leucoanthocyanidin dioxygenase* (*LDOX*), *ANS*, and/or *UF3GT* is responsible for purple flesh coloration in a *Dioscoreaalata* cultivar, bicolored tepals in lily, and variegated petals in *P. mume* "Fuban Tiaozhi" [7,20,53]. In our study, we found that the anthocyanin biosynthetic gene homologs *Pm020453* (*YUCCA8*), *Pm004176* (*ANGLT*), and *Pm031359* (*UGT79B6*) were upregulated in red petal tissues, but other critical genes, such as *Pm013782* (*DFRA*), *Pm018402* (*DFRA*), *Pm023202* (*DFRA*), *Pm017146* (*FLRT*), and *Pm008680* (*UGFGT*) were downregulated. These differences between *P. mume* "Danban Tiaozhi" and "Fuban Tiaozhi" may be due to the temporal and tissue-specific nature of transcriptome expression [7], which has different development stages, and its genotypes show a variety of gene expression [8]. We also discovered that *GST* genes, which encode proteins transporting cyanidins and/or anthocyanins to the tonoplast [55], were upregulated in red tissues. This result is similar to the finding of a previous study that the *Riant* gene encoding a GST protein induces red flower coloration in peach [24].

The identification and functional characterization of flavonoid-related R2R3-MYB transcription factors, which show active or repressive effects on anthocyanin biosynthetic genes, is important for revealing plant pigmentation [56]. A study of blood-fleshed *P. persica* uncovered a mechanism whereby *BLOOD* (*BL*) was the key gene for the blood-fleshed trait via its activation of *PpMYB10.1*, and the silencing of *BL* reduced anthocyanin pigmentation in maturing fruits [6]. The MYB10 promoter is more variable in *Malus* × *domestica* "Honeycrisp" than in "Royal Gala", which results in a more variable color pattern in the peel of the first cultivar [36]. A transcriptomic comparison of red and green-colored leaves of *P. persica* has identified a MYB transcription regulator, *PpMYB10.4*, whose transient expression induces anthocyanin accumulation [57].

In "Lollypop" Asiatic lilies, the transcriptional profiling of *LhMYB12* has revealed that the presence of bicolored tepals is controlled by the transcriptional regulation of anthocyanin biosynthetic genes [53]. Differential expression of *Peace* (*peach anthocyanin colour enhancement*, a *R2R3 MYB-like* gene) determines the pattern of flower coloration in variegated petals within individual trees of flowering *P. persica* "Genpei" [25]. In addition, jasmonate has been reported to regulate WD-repeat/bHLH/MYB complex-mediated anthocyanin accumulation in *Arabidopsis thaliana* [58]. Using iTAK software, we detected 189 differentially expressed transcription factor genes, including *MYB*, *bHLH*, and *WD*, suggesting that transcription factors may play important roles in the formation of chimeras in *P. mume* "Danban Tiaozhi".
