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

Snapdragon (<i>Antirrhinum majus</i>) serves as a model system for dissecting floral morphogenesis mechanisms. Petal malformation in <i>A. majus</i> 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 <i>SEP3</i> (<i>AmMADS25/61/20/26</i>) and <i>SEP2</i> (<i>AmMADS85</i>). 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 <i>MADS-box</i> genes (<i>AG</i>, <i>AP1</i>, <i>AP3</i>), co-regulated MADS transcription factors (MTFs) AGL15 (AmMADS16), and auxin signaling genes (<i>SAUR1</i>, <i>IAA13</i>). qRT-PCR validated upregulation of <i>SEP3</i> and downregulation of <i>SEP2</i> 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.