Genome-Wide Identification and Characterization of the JAZ Gene Family in Malus sieversii

Background: Malus sieversii, the wild ancestor of cultivated apples, possesses high stress tolerance and rich nutritional value but suffers from low fruit firmness. Jasmonate-ZIM (JAZ) domain proteins are key repressors of jasmonic acid (JA) signaling, yet their roles in fruit softening remain largely unexplored, especially in M. sieversii. Methods and results: In this study, we performed a genome-wide identification of the JAZ gene family in M. sieversii and characterized their structural features, phylogenetic relationships, chromosomal distribution, promoter cis-elements, expression patterns, and protein interactions. A total of 18 MsiJAZ genes were identified, which could be classified into six subfamilies. Most members are predicted to localize in the nucleus, while three are also potentially targeted to chloroplasts. The MsiJAZ genes are unevenly distributed across ten chromosomes and are enriched in light-, ABA-, and drought-responsive cis-elements. Expression analysis under storage and 1-MCP treatments revealed both shared and divergent responses among selected MsiJAZ genes. Notably, MsiJAZ1 was significantly repressed by storage but induced by 1-MCP and physically interacted with MsiPUB24 (PLANT U-BOX 24), an E3 ubiquitin ligase involved in ethylene-mediated softening. These results suggest that MsiJAZ1 may participate in a novel CORONATINE INSENSITIVE 1 (COI1)-independent degradation pathway and mediate ethylene–JA crosstalk during fruit softening. Conclusions: This study provides a comprehensive characterization of the JAZ family in M. sieversii and lays a foundation for further functional studies on JA signaling in apple fruit softening.