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Background  Salinization is a primary abiotic stress constraining global plant growth and production. Weedy rice, though highly homologous to cultivated rice, is more salt tolerant during seed germination and seedling growth; we hypothesize that this is owing to ionic homeostasis and changes in the expression of genes encoding ion transport regulators.    Results  The four different genotypes of weedy ( JYGY-1  and  JYFN-4 ) and cultivated ( Nipponbare  and  9311 ) rice have different salt-tolerance during seed germination and seedling vegetative growth under salt stress. In this study, Na +  and Ca 2+ content increased in weedy and cultivated rice genotypes under salt stress while K +  and Mg 2+ decreased; however,  JYGY-1  had the lowest Na + /K +  ratio of assessed genotypes. Genes in the high-affinity K +  transporter ( HKT ) and tonoplast sodium-hydrogen exchanger ( NHX ) families, and salt overly sensitive 1 ( OsSOS1 ) have more than 98% homology in amino acid sequences between weedy and cultivated rice genotypes. Under salt stress, the  HKT  family members were differentially expressed in the roots and shoots of four different genotypes. However, the  NHX  family transcripts were markedly up-regulated in all genotypes, but there are significant differences between different genotypes.  OsSOS1  was significantly up-regulated in roots, especially in  JYGY-1 genotype.    Conclusions  The results showed that different genotypes had different germination and nutrient survival under salt stress, which was related to the difference of ion content and the difference of a series of ion transport gene expression. At the same time this study will provide new insight into the similarities and differences in ion homeostasis and gene regulatory mechanisms between weedy and cultivated rice under salt stress, which can aid in novel rice breeding and growth strategies.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1586-9) contains supplementary material, which is available to authorized users.

Na+/K+ Balance and Transport Regulatory Mechanisms in Weedy and Cultivated Rice (Oryza sativa L.) Under Salt Stress