Transcriptome Analysis Reveals Association of E-Class AmMADS-Box Genes with Petal Malformation in Antirrhinum majus L

Snapdragon (Antirrhinum majus) serves as a model system for dissecting floral morphogenesis mechanisms. Petal malformation in A. majus impacts ornamental value, but its genetic basis remains poorly understood. We compared transcriptomes of the wild-type (Am11) and a petal-malformed mutant (AmDP2) to identify 2303 differentially expressed genes (DEGs), including E-class MIKC-type MADS-box genes SEP3 (AmMADS25/61/20/26) and SEP2 (AmMADS85). Weighted gene co-expression network (WGCNA), protein-protein interaction (PPI), qRT-PCR and virus-induced gene silencing (VIGS) analyses revealed interactions between SEP2/SEP3 and C/A/B-class MADS-box genes (AG, AP1, AP3), co-regulated MADS transcription factors (MTFs) AGL15 (AmMADS16), and auxin signaling genes (SAUR1, IAA13). qRT-PCR validated upregulation of SEP3 and downregulation of SEP2 in AmDP2. Our results suggest that E-class MADS-box genes are associated with petal malformation through coordinated interactions with hormonal pathways. These findings provide candidate targets for further functional studies in snapdragon.