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Background  Although the  HKT  transporter genes ascertain some of the key determinants of crop salt tolerance mechanisms, the diversity and functional role of group II  HKT  genes are not clearly understood in bread wheat. The advanced knowledge on rice  HKT  and whole genome sequence was, therefore, used in comparative gene analysis to identify orthologous wheat group II  HKT  genes and their role in trait variation under different saline environments.    Results  The four group II  HKT s in rice identified two orthologous gene families from bread wheat, including the known  TaHKT2 ; 1  gene family and a new distinctly different gene family designated as  TaHKT2 ; 2 . A single copy of  TaHKT2 ; 2  was found on each homeologous chromosome arm 7AL, 7BL and 7DL and each gene was expressed in leaf blade, sheath and root tissues under non-stressed and at 200 mM salt stressed conditions. The proteins encoded by genes of the  TaHKT2 ; 2  family revealed more than 93 % amino acid sequence identity but ≤52 % amino acid identity compared to the proteins encoded by  TaHKT2 ; 1  family. Specifically, variations in known critical domains predicted functional differences between the two protein families. Similar to orthologous rice genes on chromosome 6L,  TaHKT2 ; 1  and  TaHKT2 ; 2  genes were located approximately 3 kb apart on wheat chromosomes 7AL, 7BL and 7DL, forming a static syntenic block in the two species. The chromosomal region on 7AL containing  TaHKT2 ; 1 7AL - 1  co-located with QTL for shoot Na +  concentration and yield in some saline environments.    Conclusion  The differences in copy number, genes sequences and encoded proteins between  TaHKT2 ; 2  homeologous genes and other group II  HKT  gene families within and across species likely reflect functional diversity for ion selectivity and transport in plants. Evidence indicated that neither  TaHKT2 ; 2  nor  TaHKT2 ; 1  were associated with primary root Na +  uptake but  TaHKT2 ; 1  may be associated with trait variation for Na +  exclusion and yield in some but not all saline environments.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0714-7) contains supplementary material, which is available to authorized users.

A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na+ concentration in bread wheat