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Background  Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm.  WAK  genes are highly conserved and have been identified in plants, such as rice, but there is little research on the  WAK  gene family in cotton.    Results  In the present study, we identified 29  GhWAK  genes in  Gossypium hirsutum . Phylogenetic analysis showed that cotton WAK proteins can be divided into five clades. The results of synteny and Ka/Ks analysis showed that the  GhWAK  genes mainly originated from whole genome duplication (WGD) and were then mainly under purifying selection. Transcriptome data and real-time PCR showed that 97% of  GhWAK  genes highly expressed in cotton fibers and ovules. β-glucuronidase (GUS) staining assays showed that  GhWAK5  and  GhWAK16  expressed in Arabidopsis leaf trichomes. Fourteen  GhWAK  genes were found to possess putative gibberellin (GA) response elements in the promoter regions, 13 of which were significantly induced by GA treatment. Ten  GhWAK  genes contained auxin (IAA) response elements and the expression level of nine  GhWAKs  significantly increased under auxin treatment.    Conclusions  We provide a preliminary analysis of the  WAK  gene family in  G. hirsutum , which sheds light on the potantial roles of  GhWAK  genes in cotton fiber cell development. Our data also provides a useful resource for future studies on the functional roles of  GhWAK  genes.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07378-8.

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton