Pangenome-wide analysis of the barley JAZ gene family reveals a core–accessory structure and divergent expression pattern

JAZ proteins are key repressors of jasmonate (JA) signaling, yet their pangenome-level evolution in barley remains unexplored. Here, we analyzed the JAZ family across 76 barley genomes. A total of 1188 JAZ proteins were clustered into 16 orthogroups (OGs), comprising 8 core and 8 accessory OGs. Phylogenetic analysis resolved these OGs into six groups, with Group 3 exhibiting the largest barley-specific expansion. The 16 representative JAZ OGs contained intact TIFY and Jas domains with conserved motifs, although gene structures varied in exon number and intron length. Most JAZ genes were single-copy core genes, whereas a few accessory genes (e.g., AC009 , AC010 ) showed dynamic copy number variations (CNVs) and presence/absence variations (PAVs). Only one segmental duplication pair, HvJAZ.CR007 – HvJAZ.AC013 , was retained, and its divergent expression pattern is consistent with functional divergence following duplication; it displayed divergent expression and a Ka/Ks of 0.308. Ka/Ks analysis indicated strong purifying selection, with internal heterogeneity detected in Group 3. Expression profiling revealed tissue- and stress-specific responses, and protein-protein interaction (PPI) and promoter analyses highlighted COI1-JAZ-MYC modules as well as hormone/stress-responsive elements. This study provides a foundational resource for JAZ-mediated JA signaling and for breeding stress-resilient barley.