Metabolomics changes in ‘Honeycrisp’ apple during cold storage in association with soft scald disorder development and delayed cooling treatment

• Metabolomic analysis showed significant changes in metabolites in soft scald disorder apples. • Metabolomic analysis revealed the phenolic compounds responding to delayed cooling treatment. • Delay cooling treatment reduces the disorder and improves the nutritional benefits of HC apples. Soft scald is a common physiological disorder in ‘Honeycrisp’ apples that develops during cold storage and reduces fruit quality and marketability. Delayed cooling prior to cold storage and dynamic management of fruit storage temperature have been used to mitigate the development of soft scald with variable success. To explore biochemical changes associated with the development of soft scald and to identify mechanisms by which delayed cooling reduces its development, we conducted an untargeted metabolomics with data independent acquisition (DIA) on a liquid chromatography-mass spectrometry. Changes in ‘Honeycrisp’ apple metabolites were investigated during storage and in response to delayed cooling for two seasons. In total, 1212 features were detected and quantified. An ANOVA revealed significant changes in 114 metabolites at the metabolomic level. An ANOVA and orthogonal PLS-DA combined approach further showed 8 and 20 features changed significantly in association with development of soft scald features and in relationship to the delayed cooling treatment, respectively. Fifteen of these features were putatively identified indicating their role in soft scald development and mitigation. A group of flavonol compounds including isoquercitrin and rutin that increased during delayed cooling treatment were identified providing evidence that they may contribute to alleviate the disorder development. This study provides new evidence that metabolites associated with phenolic metabolism are involved in relation to soft scald disorder development and respond to delayed cooling treatment.