Comprehensive analysis of the morphological, physiological, and transcriptional reveals the nutritional properties and pigmentation mechanism of Malus crabapple

The fruits of Malus crabapple have gained significant attention due to their high nutritional value and vibrant colors. However, research on their bioactive compounds has primarily focused on their ornamental appeal. This study examined quality differences among three representative color development paths in nine newly bred crabapple varieties, analyzing their morphological, physiological, biochemical characteristics, as well as gene expression patterns. The findings revealed variability in composition and biological activities based on fruit color. Anthocyanin was the dominant pigment in both ‘Green to Red’ (G to R) and ‘Purple to Red’ (P to R) varieties, while chlorophylls also contributed to peel color in the P to R varieties. Additionally, jasmonic acid (JA) influenced anthocyanin synthesis through interactions with indole-3-acetic acid (IAA) and abscisic acid (ABA) during the color transition from green to red. DFR, ANS, and UFGT were identified as key regulators of anthocyanin, with DFR further contributing to the maintenance of red coloration in fruits. Promising varieties for functional food (JD, XH, and YPQS) and future ornamental breeding parents (QLYX, YZY, and ZXZ) were identified. These results provide a strong foundation for targeted improvement and future investigations into the mechanisms of fruit coloration in crabapple breeding efforts.