Genome-Wide Characterization and Expression Profiling of MADS-Box Family Genes Under Abiotic Stress in Arundo donax

MADS-box transcription factors play crucial roles in plant growth, development, and response to abiotic stresses. However, their functions in abiotic stress resistance remain largely unexplored in the bioenergy crop Arundo donax (A. donax). In this study, we identified and comprehensively analyzed 97 MADS-box genes (AdMADS) in the A. donax genome. Phylogenetic analysis classified these genes into type I (44 members) and type II (53 members) subfamilies, which were further subdivided into 12 subgroups. Comparative analysis revealed clear distinctions between type I and type II genes in terms of the physicochemical properties of their encoded proteins and their exon-intron structures. Promoter analysis identified numerous cis-regulatory elements associated with light responsiveness, plant hormones, and stress signals. Gene duplication analysis suggested that whole-genome duplication/segmental duplication was the major detected contributor to the expansion of the AdMADS gene family, with type II genes contributing predominantly to these duplication events. Collinearity analysis demonstrated a high conservation of MADS-box genes among A. donax, rice, and foxtail millet, reflecting their evolutionary conservation within Gramineae. By analyzing public RNA-seq data, we identified 45 AdMADS genes as stress-responsive candidates under waterlogging, drought, and salt stress, and selected candidates were further validated by RT-qPCR. Moreover, AdMADS33 and AdMADS53 were found to bind to and activate the promoter of the ABA synthesis gene AdNCED in tobacco, suggesting that they may contribute to salt tolerance by promoting AdNCED transcription. This study provides a valuable resource for future functional gene mining and offers a solid foundation for the molecular breeding of A. donax.