Genome-wide identification and functional characterization of MAPKK gene family in Zanthoxylum armatum DC. reveal its potential role in ecological adaptive evolution

Abstract Background Zanthoxylum armatum is a vital economic crop in China, but its cultivation is challenged by abiotic stresses like drought and cold. Mitogen-activated protein kinase kinases (MAPKKs) are central signaling components regulating plant stress responses. However, the MAPKK gene family in Z. armatum remained uncharacterized. This study aimed to identify ZaMAPKK genes and elucidate their roles in stress adaptation. Understanding ZaMAPKK functions provides critical genetic targets for molecular breeding programs aimed at developing stress-tolerant cultivars, ensuring sustainable Z. armatum production in marginal environments. Results This study identified 14 MAPKK family members in Z. armatum (ZaMAPKK1-14) via genome-wide analysis. Bioinformatics and experimental analyses revealed that ZaMAPKKs were unstable hydrophilic proteins, predominantly localized in the nucleus. Phylogenetic analysis divided them into four subfamilies (A, B, C, and D), showing high homology with dicotyledonous plants such as Arabidopsis thaliana and soybean. Gene structure analysis indicated significant differences in intron numbers among subfamily members, suggesting functional differentiation. Promoter cis-element analysis identified abundant elements related to light response, hormone regulation, and stress in all genes. Transcriptome and reverse transcription-quantitative PCR (RT-qPCR) analyses revealed that ZaMAPKK7 and ZaMAPKK11 exhibited significantly higher expression across samples from different latitudes, implicating them in regulating Z. armatum stress resistance via activation of stress response pathways. Gene co-expression network analysis indicated that ZaMAPKK genes cooperate with various transcription factors to regulate stress response, light signaling, growth, and metabolism in Z. armatum. Conclusions This study identifies ZaMAPKK7 and ZaMAPKK11 as key regulators of stress resistance in Z. armatum. Future work will integrate RT-qPCR and co-expression analyses to validate their functions within the MAPKK cascade and explore synergistic mechanisms with other gene families. Unraveling this regulatory network will accelerate the breeding of stress-tolerant cultivars, ultimately enhancing Zanthoxylum productivity and industrial sustainability.