Identification, characterization, and expression profiling of rice MADS-box transcription factor genes associated...

The MADS-box transcription factor (TF) superfamily, one of the largest gene groups in plants, is essential for regulating stress responses. However, its function in rice under pesticide stress remains unknown. To address this gap, we investigated the traits and roles of the rice MADS-box gene family under pesticide exposure. Transcriptome analysis of rice (Oryza sativa) treated with fluroxypyr-meptyl (FLUME) and oxyfluorfen (OFF) revealed 30 OsMADS-box genes and 3 MADS-box differentially expressed genes (DEGs). Phylogenetic analysis classified these genes into 12 subfamilies: Mα, Mβ, Mγ, SOC1, E, A, AGL12, SVP, ANR1, Bs, B, and MIKC*. Chromosomal mapping revealed uneven distribution of OsMADS-box genes across all 12 chromosomes, with segmental duplication contributing to gene family expansion. Collinearity analysis identified 14 orthologous gene pairs within rice and additional orthologous gene pairs shared with other plant species: 4 with Arabidopsis (Arabidopsis thaliana), 17 with soybean (Glycine max), 45 with maize (Zea mays), and 36 with wild sugarcane (Saccharum spontaneum). Structural analysis showed that OsMADS-box genes possess diverse gene architectures, cis-acting elements, motif compositions, and conserved domains, enabling responses to biotic and abiotic stress. Docking studies of OFF, FLUME, and the three MADS-box DEGs identified key amino acid residues implicated in pesticide binding. qRT-PCR confirmed preferential expression of several MADS-box DEGs under OFF- and FLUME-induced stress. Protein-protein interaction network analysis further supported the involvement of OsMADS-box proteins in FLUME and OFF metabolism. These findings provide insights into the OsMADS-box superfamily and offer valuable resources for functional studies on their roles in pesticide metabolism.