Abstract

Summary The genetic basis of linear growth rate in the red alga Gracilariopsis lemaneiformis remains poorly characterized. This study functionally characterized the gene LXC001294 , a prior genome-wide association studies (GWAS) candidate associated with growth variation, to elucidate its molecular role. We employed phylogenetic analysis, yeast assays, and subcellular localization to characterize LXC001294. Its genome-wide binding sites were identified by ChIP-seq, and transcriptomic profiles of fast- (YT13) and slow-growing (QHD9) strains were compared via RNA-seq. Direct regulation of key targets was validated using yeast one-hybrid and dual-luciferase assays. LXC001294 was confirmed as a nuclear-localized C 2 H 2 zinc finger transcription factor. Integrated multi-omics analysis revealed its direct targeting and upregulation of five minichromosome maintenance ( MCM ) genes, core components of the DNA replication machinery, in the fast-growing strain. We demonstrate that LXC001294 promotes algal growth by activating the MCM complex, thereby enhancing DNA replication. This study provides a mechanistic link from a GWAS signal to a growth phenotype in a macroalga and establishes the transcriptional regulation of replication licensing as a key node controlling growth rate in nonmodel species. Graphical This study integrated genome-wide association studies and multiomics to identify a C 2 H 2 zinc finger transcription factor linked to linear growth in Gracilariopsis lemaneiformis . Structural and functional analyses, plus binding site validation, revealed it regulates growth by activating minichromosome maintenance helicase genes, bridging genetic variation to phenotypic traits in macroalgae.