Characterization analyses of MADS-box genes highlighting their functions with seed development in Ricinus communis

The <i>MADS-box</i> gene family plays a pivotal role in regulating floral organ development and various aspects of plant growth. Despite its well-established importance in many species, the function and evolution of <i>MADS-box</i> genes in <i>Ricinus communis</i> (castor) remain unexplored. This study presents an extensive genome-wide analysis of the <i>MADS-box</i> gene family in castor, covering their physicochemical characteristics, phylogenetics, gene architecture, chromosomal distribution, evolutionary dynamics, expression profiles, and co-expression networks. In total, 56 <i>MADS-box</i> genes were categorized into two main phylogenetic groups: type-I and type-II, which were further subdivided into three and two subgroups, respectively. Segmental duplication was found to be the primary driver of <i>MADS-box</i> gene expansion in castor, while purifying selection was evident across the entire gene family, as indicated by the <i>Ka</i>/<i>Ks</i> ratio. In-depth analyses of gene expression, promoter motifs, co-expression networks, and experimental validation (Y1H assays and qRT-PCR) revealed that <i>RcMADS16</i> and <i>RcMADS4</i>1 are key regulators of castor seed development, with <i>RcMADS16</i> may involve in seed coat formation and <i>RcMADS41</i> in oil accumulation. This study not only provides the first detailed insight into the evolutionary and functional landscape of <i>MADS-box</i> genes in castor, but also establishes a foundation for future investigations into the role of these genes in seed and organ development, both in castor and other plant species.