Genome-wide identification and characterization of the MADS-box gene family in Rosa chinensis

MADS-box transcription factors are essential regulators of plant growth, development, and 6 stress responses. Here, we identified 75 RcMADS-box genes in Rose chinensis, including 35 7 M-type and 40 MIKC-type members. Most encoded proteins were basic, hydrophilic, and 8 nuclear-localized. Chromosomal mapping revealed a non-random distribution enriched on 9 chromosomes 1, 2, 6, and 7. Phylogenetic analysis clearly distinguished M-type and MIKC-type 10 subclasses, supported by distinct domain architectures and motif compositions, with K-box motifs 11 exclusively present in MIKC-type proteins. Promoter analysis identified diverse hormone-and 12 stress-responsive cis-elements. Intraspecific synteny analysis indicated that segmental duplications 13 drove family expansion, while interspecific synteny with Arabidopsis thaliana revealed 24 14 conserved gene pairs with uneven chromosomal distribution. Notably, chromosome 7 exhibited 15 both extensive intraspecific duplication and strong synteny with Arabidopsis, suggesting it harbors 16 evolutionarily ancient and functionally conserved core members. In contrast, chromosome 6 17 showed extensive duplication but lacked interspecific synteny, implying lineage-specific 18 expansion. Our findings provide a comprehensive genomic characterization of the RcMADS-box 19 gene family and establish a foundation for future functional studies in rose.