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Background  Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored.    Results  Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton  G. hirsutum , which has 73 ARF genes, and its putative extent parental diploids  G. arboreum  and  G. raimondii , which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in  G. hirsutum ARF  genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that  GhARF2b , a homolog of the Arabidopsis  AtARF2 , was preferentially expressed in developing ovules and fibers. Overexpression of  GhARF2b  by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes.    Conclusion  Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07504-6.

Characterization of cotton ARF factors and the role of GhARF2b in fiber development