Genome-wide identification of the MIKC<sup>C</sup>-type genes in <i>Vanilla planifolia</i> and expression studies in the development of the rostellum

Vanilla planifolia, a highly valued spice in the beverage, food, and cosmetics industries, is faced with a significant challenge. Its unique flower structure restricts natural pollination and impedes industrial progress. MADS-box transcription factors are essential in multiple biological processes, especially in the formation of flower organ structures. In response, we launched investigations to identify the MADS-box gene family in V. planifolia and explored their functions in the development of the gynostemium and rostellum. Through genome-wide screening, 47 VpMADS genes were identified, with 22 members classified into the MIKCC subgroup. Based on genomic data, we analyzed the locations, structures, and conserved motifs of the genes. All MIKCC-type genes were grouped into 10 phylogenetic clusters. Gene duplication analysis revealed that segmental duplications were the main driver of MADS-box gene expansion in V. planifolia. Samples were collected and underwent RNA-seq to identify differentially expressed genes. qRT-PCR was also used to validate differentially expressed genes. Weighted gene co-expression network analysis (WGCNA), and Gene Ontology (GO) enrichment analysis were conducted to study co-expressed genes related to MADS-box genes in the gynostemium. Overall, this study provides fundamental insights into the MADS-box gene family in V. planifolia, serving as a vital reference for future research on the development of the gynostemium and rostellum in this plant.