As a predominant phenolic compound in apple fruits, chlorogenic acid (CGA) benefits human health due to its various antioxidant properties. However, little has been known regarding the molecular mechanism underlying the CGA accumulation in apple fruits. In this study, we measured the CGA content and relative enzymes’ activities during fruit development in two different flesh-colored cultivars ‘Huashuo’ and ‘Red Love’. The CGA content in both cultivars decreased sharply from 30 days after full bloom (DAFB) to 60 DAFB. Notably, the CGA content in fruit flesh was relatively higher than that in the peel. Further, the activities of C3H and HCT enzymes downstream of the CGA biosynthesis showed the similar changing trend as CGA content. Based on the transcriptome data of ‘Huashuo’ fruit at 30 DAFB and 60 DAFB, 23 differentially expressed CGA synthesis-related genes were screened. Gene expression analyses further showed that MdHCT1/2/4/5/6 and MdC3H1/2/3 were positively correlated to the variation of CGA content in two cultivars. These findings establish a theoretical foundation for further mechanism study on CGA biosynthesis and provide guidance for nutrient improvement in apple breeding programs.

Fruit skin color is a decisive agronomic trait governing the commercial value of peaches; although PpMYB10.1 is known to regulate anthocyanin accumulation in peach, the specific promoter structural variant that silences PpMYB10.1 expression in non-red skin types has not been identified and functionally validated. Here, using a first backcross (BC1) population, we integrated bulked segregant analysis sequencing (BSA-seq), transcriptome profiling, and whole-genome resequencing to map the causal locus to a 453.083-kb interval on chromosome 3 harboring the R2R3-MYB transcription factor PpMYB10.1. Transient overexpression and virus-induced gene silencing (VIGS), together with stable tobacco transformation, confirmed that PpMYB10.1 regulates the non-red skin phenotype in this population. Sequence comparison revealed a 26-bp insertion in the PpMYB10.1 promoter of non-red fruit; reporter assays demonstrated that this insertion strongly reduces promoter activity and silences PpMYB10.1 expression. A co-dominant InDel marker co-segregated with the skin color phenotype in all tested accessions and populations. Our findings suggest a promoter structural variant is associated with the molecular switch controlling anthocyanin accumulation in peach skin and provide a practical tool for marker-assisted selection.