Analysis of phenomics, metabolomics and transcriptomics reveals the differences in fruit quality between on-tree...

This study systematically elucidated the differences in fruit quality between bagged and non-bagged apples by integrating phenomics, transcriptomics, and metabolomics. Significant variations were observed between the two groups in peel color, single fruit weight, epidermal cells, collenchyma, cuticular wax, peel hardness, peel toughness, flesh hardness, and flavor. The content of volatile compounds, represented by 26 key aroma metabolites, was significantly higher in non-bagged fruits than in bagged ones. Compared to bagged fruits, non-bagged fruits exhibited elevated soluble sugar levels (e.g., sorbitol), accompanied by a minor increase in organic acids. In contrast, bagged fruits accumulated higher levels of free amino acids (e.g., asparagine) and their metabolites. Spatial distribution maps for L-asparagine, L-aspartate, L-glutamine, L-glutamate, sorbitol, sucrose, fructose, glucose, and malic acid in fruits were generated via mass spectrometry imaging. Furthermore, key candidate genes potentially responsible for the differential accumulation of amino acids, sugars, volatile compounds, wax, and cellulose were screened.