Genome-wide identification of WRKY transcription factors in Giant Juncao (Cenchrus fungigraminus) and their transcriptional responses to salinity and drought stresses

Giant Juncao (Cenchrus fungigraminus) is a perennial C4 forage and bioenergy grass with high biomass productivity and strong tolerance to adverse environments. However, the transcriptional regulatory mechanisms underlying its stress adaptation remain poorly understood. WRKY transcription factors are key regulators of plant stress responses, but their genomic features and functional potential in this species have not been systematically investigated. Here, we identified 182 CfWRKY genes and classified them into three major groups based on phylogenetic relationships. Comprehensive analyses of their chromosomal distribution, gene structures, conserved motifs, cis-regulatory elements, and duplication patterns revealed that segmental duplication, alongside whole-genome duplication, was the primary force driving WRKY family expansion. Transcriptome analysis under salt treatments showed diverse and dynamic expression responses, with several CfWRKY genes exhibiting strong induction and early responsiveness. Weighted gene co-expression network analysis under drought and rehydration conditions further identified 31 stress-related modules and 27 CfWRKY candidates potentially involved in water-deficit adaptation. This study presents the first genome-wide characterization of the WRKY family in Giant Juncao and provides integrative insights into their evolutionary patterns and stress-responsive regulatory roles. Our findings offer valuable candidate genes and a molecular basis for functional genomics and breeding of stress-resilient forage and energy grasses.