CircRNAs, are a class of covalently closed non-coding RNAs; they have been identified in many plants and play an important role in the response to abiotic stresses. However, little is known about the response of the circRNAs of salt-tolerant apple rootstock resources in response to salt stress. In this study, the leaves and roots of the salt-tolerant Malus resource, ZM-4, and the salt-sensitive rootstock M9T337, were used as test materials and were exposed to 75 mmol/L NaCl stress for 0 h and 24 h. A total of 2502 circRNAs were identified, and 218 and 242 circRNAs were uniquely expressed in M9T337 and ZM-4, respectively. Furthermore, it was shown that the up-regulated parental genes of the differentially expressed circRNAs were enriched in the metabolic pathways and the biosynthesis of secondary metabolites pathway in the leaves and roots of ZM-4 under salt stress, respectively. There were potential regulatory networks of ceRNA among 150 circRNAs, 139 miRNAs, and 397 mRNAs. Novel_circ_000845 and novel_circ_000266 could target and inhibit the expression of mdm-miR156 and up-regulate the expression of the salt-responsive gene SPL6. Six circRNAs, including novel_circ_000898 and novel_circ_001519, could target and inhibit the expression of mdm-miR10995 and up-regulate the expression of the salt-responsive gene COBL7. In conclusion, this study laid the foundation for the post-transcriptional molecular regulation mechanism of salt tolerance in apple rootstock resources.
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