Re-sequencing and physiological analysis reveals the differences in genetic variation and sugar metabolism between ‘Cuihong’ plum (Prunus salicina) and its early-ripening mutant ‘Hongyun’ plum

• A large number of polymorphisms were identified between CP and HP. • HP was an early ripening and high-sugar bud sport of CP. • Glucose was the predominant form of sugar in CP ripe fruits, whereas it was sucrose in HP. • Bud mutation altered the expression levels of sugar metabolism genes to regulate enzyme activity, thereby affecting soluble sugars in CP and HP. Soluble sugar is a key element influencing fruit flavor. Bud sports provide valuable resources for fruit tree breeding. ‘Hongyun’ plum (HP) is a new cultivar derived from a bud mutation of ‘Cuihong’ plum (CP). In this study, whole genome re-sequencing and physiological analysis were used to explore the differences between CP and HP. We identified 2,638,517 polymorphism variable sites, including 2,134,872 single nucleotide polymorphisms (SNPs) and 503,645 insertions/deletions (InDels) between CP and HP. Notable variations in fruit characteristics were observed between CP and HP fruits. Mature HP fruits exhibited an average weight of 32.14 g, compared to 27.48 g for CP fruits. The soluble sugar content in HP fruits reached 103.43 mg·g −1 , markedly exceeding the 75.29 mg·g −1 found in CP fruits. Glucose was the predominant form of sugar in CP ripe fruits, whereas it was sucrose in HP. HP displayed higher sucrose phosphatase (SPS) and sucrose synthase synthesis direction (SS-s) activities, as well as transcription levels of the corresponding genes to promote sucrose synthesis. Invertase (INV), hexokinase (HK), fructokinase (FK), and sorbitol dehydrogenase (SDH) were involved in sucrose catabolism and glucose and fructose synthesis. Overall, bud mutation altered the expression levels of sugar metabolism genes to regulate enzyme activity, thereby affecting soluble sugars in CP and HP. Our findings shed light on biochemical, enzymatic, and genetic studies of plums that will help develop new commercial varieties.