New insights on the utilitarian balance between fruit flavor development and counteracting saline-alkali stress in ‘Yali’ pear

• In this study, we found that saline-alkali stress always affects some key metabolites and metabolic pathways through multi-omics analysis, that is, metabolome transcriptome and miRNA sequencing. Thus, the mechanism of action of key genes and miRNAs is changed to resist the influence of the external environment. • In this study, the effect of saline-alkali stress on the quality metabolism of Yali pear fruit was studied by callus, which avoided the complex external factors and the breeding cycle of up to several years in the field research. • In this study, the targeting relationship between miRNA and target gene was proved by double verification of tobacco and pear fruit callus. The verification results of native materials increased the credibility of the experimental results. 'Yali' pear (Pyrus bretschneideri) is a centuried cultivar in China known to be highly susceptible to saline-alkali conditions. This study sought to examine the effects of saline-alkali stress on the flavor quality of 'Yali' pears. Findings indicated that exposure to salt-alkaline stress prompts a transition in the fruit's metabolic processes, shifting from carbon to nitrogen metabolism and from primary to secondary metabolism. In this study, a sugar transporter coding gene, PbBST , and the PbADH which is related to aroma substance synthesis were silenced separately. The proportions of several main soluble sugars in pears fluctuated, and the content of hexyl acetate, butyl acetate, and ethyl acetate decreased to 0 ng/g, 21.86 ng/g, and 11.44 ng/g, respectively. This change in fruit flavor quality after saline-alkali treatment aligns with the down-regulation of PbBST and PbADH gene expression, indicating a strong impact on sugars and aroma. At the macro level, callus could be used to demonstrate the influence on carbohydrate metabolism under stress, with alkalinity being identified as the key factor. At the micro perspective, callus, as an ideal empirical material, was prone to transgene, thus allowing for the implementation of functional verification of the key transcript factor PbRAP2–4 and the key miRNA miR7700 under saline-alkali stress. Finally, this research demonstrated that miR7700 induces the cumulative expression of the critical transcript factor PbRAP2–4 . Compared with the wild type, both miR7700 and PbRAP2–4 overexpressed callus exhibit a stronger ability to improve survivability under saline-alkali stress treatment.