A Novel 26-bp Insertion in the PpMYB10.1 Promoter Is Associated with Anthocyanin Deficiency in Peach (Prunus persica) Fruit Skin

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.