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Background  Plant Na + /H +  antiporters (NHXs) are membrane-localized proteins that maintain cellular Na + /K +  and pH homeostasis. Considerable evidence highlighted the critical roles of NHX family in plant development and salt response; however, NHXs in cotton are rarely studied.    Results  The comprehensive and systematic comparative study of NHXs in three  Gossypium  species was performed. We identified 12, 12, and 23 putative NHX proteins from  G. arboreum ,  G. raimondii , and  G. hirsutum , respectively. Phylogenetic study revealed that repeated polyploidization of  Gossypium  spp. contributed to the expansion of NHX family. Gene structure analysis showed that cotton  NHXs  contain many introns, which will lead to alternative splicing and help plants to adapt to high salt concentrations in soil. The expression changes of  NHX s indicate the possible differences in the roles of distinct  NHX s in salt response.  GhNHX1  was proved to be located in the vacuolar system and intensively induced by salt stress in cotton. Silencing of  GhNHX1  resulted in enhanced sensitivity of cotton seedlings to high salt concentrations, which suggests that  GhNHX1  positively regulates cotton tolerance to salt stress.    Conclusion  We characterized the gene structure, phylogenetic relationship, chromosomal location, and expression pattern of  NHX  genes from  G. arboreum ,  G. raimondii , and  G. hirsutum . Our findings indicated that the cotton  NHX  genes are regulated meticulously and differently at the transcription level with possible alternative splicing. The tolerance of plants to salt stress may rely on the expression level of a particular  NHX , rather than the number of  NHXs  in the genome. This study could provide significant insights into the function of plant  NHX s, as well as propose promising candidate genes for breeding salt-resistant cotton cultivars.

Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance