Genome-wide studies and expression profiling of GhWRKY41 family genes in different tissues and stress conditions in upland cotton (Gossypium hirsutum)

The WRKY transcription factor (WRKY) gene family primarily functions as a defense mechanism against various stresses throughout the plant's life cycle. Prior studies have thoroughly examined specific WRKY gene groups across different plants. Nevertheless, there has not been a thorough investigation on the roles of GhWRKY41 family genes with their expression profiles after stress treatment to understand their mechanisms in regulating the various stresses in Gossypium hirsutum. In this study, an examination of the cotton genome identified 11 potential WRKY41 family genes, which were categorized into nine sub-families (I-XI) based on a phylogenetic analysis. The gene structure and motifs within each sub-family were relatively consistent with three exons and two introns, except Gohir.A12G184600, which has 20 exons and 19 introns indicating strongly they belong to the same family with minimal sequence difference. The GhWRKY41 genes exhibited an uneven distribution, spanning eight of the 26 chromosomes in upland cotton. Expression profile analysis revealed differential expression levels of all 11 GhWRKY41 family genes in different tissues at nine in ovule and four days post-anther (DPA) in the fiber developmental stage, respectively. The majority of GhWRKY41 genes demonstrated tissue-specific expression patterns, affirming their vital contributions to cotton growth and development, and stress regulation. Additionally, GhWRKY41 family genes duplicated in eight chromosomes (A07, A08, A11, A12, D07, D08, D11, D12). However, several duplications were identified in all the chromosomes, they are in a gene duplication analysis indicating that WRKY homologs are duplicated in some chromosomes, with many others observed in the redundant stage, suggesting their existence with undiscovered functions. The gene ontology (GO) analysis we conducted indicated that all members of the GhWRKY gene family were linked to the regulation of transcription, transcription factor activity, and sequence-specific DNA binding in both molecular function and biological process categories. Finally, we chronologically and graphically present the key roles of GhWRKY41 family genes in salt, drought, heat, and cold stress signaling the mechanisms involved in regulating the stresses until the plants attain tolerance level. Overall, this research enhances our understanding of the genetic mechanisms underlying cotton growth and development, with implications for stress response and the evolution of the GhWRKY gene family.