Identification and Expression Analysis of the WOX Transcription Factor Family in Foxtail Millet ( Setaria italica L.)

WUSCHEL-related homeobox (WOX) transcription factors are unique to plants and play pivotal roles in plant development and stress responses. In this investigation, we acquired protein sequences of foxtail millet gene family members through homologous sequence alignment and a hidden Markov model (HMM) search. Utilizing conserved domain prediction, we identified 13 foxtail millet genes, which were classified into ancient, intermediate, and modern clades. Multiple sequence alignment results revealed that all WOX proteins possess a homeodomain (HD). The genes, clustered together in the phylogenetic tree, exhibited analogous protein spatial structures, gene structures, and conserved motifs. The foxtail millet genes are distributed across 7 chromosomes, featuring 3 pairs of tandem repeats: and , and , and and . Collinearity analysis demonstrated that genes in foxtail millet exhibit the highest collinearity with green foxtail, followed by maize. The genes primarily harbor two categories of -acting regulatory elements: Stress response and plant hormone response. Notably, prominent hormones triggering responses include methyl jasmonate, abscisic acid, gibberellin, auxin, and salicylic acid. Analysis of expression patterns and hormone responses unveiled potential functional diversity among different genes in foxtail millet. These findings lay a solid foundation for further elucidating the functions and evolution of genes.