Anthocyanins are important pigments in peach fruit and are beneficial to human health. Sugars are both energy-storing and signaling molecules and their roles in inducing anthocyanin biosynthesis have received a great deal of research attention. However, the mechanism by which sugars induce anthocyanin biosynthesis in peach fruit is unknown. In order to understand this induction mechanism, comprehensive transcriptome and metabolome were performed in fruit flesh treated with four different sugars for 12 and 24 h, respectively. Here, we found that cyanidin-3-O-(6-O-p-coumaroyl) glucosides accumulated in fruit flesh treated with glucose, sucrose, sorbitol, and fructose in vitro. Two key structural genes of the anthocyanin biosynthesis pathway, namely, PpDFR and PpUFGT, were upregulated in the flesh of sugar-treated peach fruit. By contrast, the two main transcription factors (TFs) PpMYB10.1 and PpBL regulating anthocyanin biosynthetic genes in peach fruit were not upregulated accordingly. Interestingly, two MYB family genes (PpMYB6 and PpMYB44-like) and three bHLH family genes (PpbHLH35, PpbHLH51, and PpbHLH36-like) were upregulated. A dual luciferase assay revealed that PpMYB6 strongly activated the PpUFGT promoter when it was co-infiltrated with PpbHLH35, PpbHLH51, and PpbHLH36-like. When PpMYB44-like was co-infiltrated with PpbHLH35, it also potently activated the PpUFGT promoter. The results of this study help clarify the molecular mechanisms by which glucose, sucrose, sorbitol, and fructose regulate anthocyanin accumulation in peach fruit.

Peach (Prunus persica) landrace has typical regional characteristics, strong environmental adaptability, and contains many valuable genes that provide the foundation for breeding excellent varieties. Therefore, it is necessary to assemble the genomes of specific landraces to facilitate the localization and utilization of these genes. Here, we de novo assembled a high-quality genome from an ancient blood-fleshed Chinese landrace Tianjin ShuiMi (TJSM) that originated from the China North Plain. The assembled genome size was 243.5 Mb with a contig N50 of 23.7 Mb and a scaffold N50 of 28.6 Mb. Compared with the reported peach genomes, our assembled TJSM genome had the largest number of specific structural variants (SVs) and long terminal repeat-retrotransposons (LTR-RTs). Among the LTR-RTs with the potential to regulate their host genes, we identified a 6688 bp LTR-RT (named it blood TE) in the promoter of NAC transcription factor-encoding PpBL, a gene regulating peach blood-flesh formation. The blood TE was not only co-separated with the blood-flesh phenotype but also associated with fruit maturity date advancement and different intensities of blood-flesh color formation. Our findings provide new insights into the mechanism underlying the development of the blood-flesh color and determination of fruit maturity date and highlight the potential of the TJSM genome to mine more variations related to agronomic traits in peach fruit.

Peach is an economically important fruit tree crop worldwide. The external color of the fruit governs the peach price, especially in fruits with different degrees of blush. Molecular marker-assisted breeding has become a necessary part of modern breeding practices, increasing their efficiency. Although the key related genes responsible for peel coloration have been found in peach, corresponding molecular markers have not been widely used in peach breeding. The development of molecular markers for peach peel color needs to be advanced and implemented in practice. This study aimed to explore the variation related to peach skin color and to develop molecular markers linked to these variants that can be used in breeding. By analyzing the expression of anthocyanin synthesis-related and regulatory genes, we confirmed that MYB10.1 is a key gene controlling skin color. We further identified that 5243 bp insertion and 483 bp deletion in the MYB10.1 promoter was highly associated with peach skin color phenotypes. In addition, we identified one transposon insertion mutation at the −2706 bp position of the MYB10.1 promoter associated with the non-red fruit skin trait and developed a molecular marker for validation. The insertion size amplified from the ‘ShiYuBaiTao’ genome DNA was approximately 3.5 kb. However, it explained a lower percentage of the non-red skin phenotype variance in peach, at 36.1%, compared to MYB10.1-2/MYB10.1-2 in this study. Based on these results, we propose that MYB10.1-2/MYB10.1-2 should not only be the only non-red skin genotype assessed but should also be combined with other molecular makers to increase the prediction accuracy of peach skin color.