Abstract
Background: The Na+/H+ antiporter (NHX) gene subfamily is essential for plant adaptation to salt stress, contributing significantly to ion homeostasis. These antiporters play crucial function in various biological processes by regulating Na+ and H+ balance within plant cells. Yet their genomic features and roles of salicylic acid (SA) in regulating them, activating antioxidant defense mechanisms as well as nutrients acquisition under salt stress conditions remain largely unknown in many crop species. Results: In this study, we identified the NHX gene family members of three Brassicaceae species including Brassica napus, Brassica rapa and Brassica oleracea and analyzed the expression patterns of NHX genes in response to salt stress and phytohormonal application (SA). Comprehensive computational analyses, encompassing domain and motif prediction, cellular localization, cis-regulatory elements (CREs), and post-translational modification (PTM) sites revealed distinct group-specific characteristics within the NHX gene family. These characteristics included chromosomal distribution, motif composition, exon count and protein length (amino acids). qRT-PCR analysis depicted significantly induced expression of NHXs, specifically, BnNHX7, BraNHX6 and BoNHX6 (4 ~ 6 folds) using different concentrations of NaCl (100 mM and 200 mM) and SA (10 mg/L and 20 mg/L) at different periods of time. SA induced antioxidant enzymatic activity (SOD 3 ~ 4 folds, POD 2 ~ 3 folds, CAT 1 ~ 2 folds and APX 11 ~ 12 folds), upregulated antioxidant genes (SOD, POD, APX, CAT) by 3 ~ 5 folds under salt stress, and improved nutrient acquisition in all respective Brassicaceae species. Conclusions: We have conducted the first molecular characterization of NHX genes in three Brassica species, revealing their dual role in salt stress adaptation through ion homeostasis and salicylic acid induced antioxidant regulation, thus identifying promising targets for crop improvement. Clinical trial number: Not applicable. Supplementary Information: The online version contains supplementary material available at 10.1186/s12870-025-06759-5.