To clarify the molecular characteristics of the WRKY gene family in highly cold-resistant Pennisetum alopecuroides and their functions in cold stress response， in this study we conducted systematic identification， phylogenetic analysis and cold stress-related expression pattern analysis of the WRKY gene family via combined genome-wide and transcriptome analyses. The results showed that a total of 104 PaWRKY genes with complete WRKY domains were identified， which were unevenly distributed on nine chromosomes. All the encoded proteins were hydrophilic， and most of them had poor in vitro stability and were susceptible to degradation. Based on phylogenetic analysis， the taxa were divided into seven subtribes， and Subtribe IIc comprises the most members， and ten core conserved motifs were predicted in total. Extensive homologous collinearity was found between this gene family and Oryza sativa subsp. japonica. The promoter regions of PaWRKY genes were enriched with numerous cis-acting elements responsive to abiotic stresses and phytohormones. Transcriptome data revealed that eight PaWRKY genes were differentially expressed under cold stress， including four upregulated and four downregulated genes， all of which harbored MeJA-responsive elements. This study clarified the molecular and evolutionary characteristics of the WRKY gene family in Pennisetum alopecuroides and screened out key cold stress-responsive genes， which laid a theoretical foundation for cold-tolerant molecular breeding of Pennisetum alopecuroides and evolutionary research of the WRKY gene family in Panicoideae.

Pennisetum alopecuroides  /  WRKY gene family  /  Cold stress  /  Differential expression