Genome-wide identification and expression analysis of the DA1-like gene family in melon (Cucumis melo)

The <i>DA1</i> (DA means "large" in Chinese) <i>-like</i> gene family represents a class of key regulators that control organ and seed size in plants, yet its characteristics and functions in melon (<i>Cucumis melo</i>) remain unexplored. In this study, we performed a genome-wide identification and characterization of the <i>CmDA1</i> gene family in melon. A total of four <i>CmDA1</i> genes were identified and found to be unevenly distributed across chromosomes 3, 8, 10, and 11. Phylogenetic analysis grouped the <i>CmDA1</i> genes into three distinct subgroups with their orthologs from <i>Arabidopsis thaliana</i> (<i>Arabidopsis</i>) and <i>Oryza sativa</i> (rice). Structural analysis revealed high conservation within subfamilies, particularly in the characteristic UIM and LIM domains. The presence of hormone-responsive <i>cis</i>-elements, combined with divergent gene structures, suggests complex transcriptional regulation of the <i>CmDA1</i> genes. Expression profiling based on RNA-seq data and qRT-PCR validation demonstrated that <i>CmDA1</i> genes exhibit tissue-specific and fruit development-stage-specific expression patterns. Notably, <i>CmDA1-3</i> showed broad and high expression across multiple vegetative tissues and maintained consistently high expression throughout fruit development from 2 to 50 days after pollination. These findings provide a foundational resource for the DA1 family in melon and position <i>CmDA1-3</i> as a priority candidate for functional validation of its role in fruit size regulation.