Polyphenols represent a significant class of nutrients in apples, contributing to human health and well-being. Among these, procyanidins stand out as the most prevalent polyphenolic compounds in apple fruits. These compounds are abundant in wild apples and generally low in modern apple cultivars. Therefore, it is crucial to identify and recover genetically lost genes that regulate polyphenol accumulation in order to improve the apple quality. To achieve this, we conducted a genome-wide association study (GWAS) on 15 traits related to polyphenol content, utilizing 134