Transcriptional variation is associated with differences in shoot sodium accumulation in distinct barley varieties

•Differences in alleles of barley HKT1;5 may be associated to the differences in blade and sheath Na+ accumulation.•Barley NHXs (e.g. HvNHX4) may play a role in differences in sheath accumulation of Na+.•High sheath Na+ accumulating barley varieties may retain knowledge of a stress experience through Epigenetic modifications.•Gene expression patterns varied among genotypes for terpenoid, phenylpropanoid and flavonoid metabolism related genes. Soil salinity causes large productivity losses for agriculture worldwide. Barley has been identified as one of the more salt tolerant staple crops compared to wheat and rice. Identification of genes and allelic variations underlying various salt tolerance mechanisms in barley will be a practical contribution towards the development of cereal lines with greater salinity tolerance. Here, RNA from six barley varieties with varying leaf blade and sheath Na+ accumulation following salt (NaCl) treatment were sequenced. Differential gene expression analysis, variant calling and gene co-regulatory network analysis was conducted to identify potential molecular components underlying the shoot Na+ phenotypes. We identified novel alleles of HKT1;5 that could be responsible for high Na+ accumulation in blade and sheath. Furthermore, through statistical modelling of gene expression, a Na+/H+ Exchanger (NHX) gene was identified as a candidate for high sheath Na+ accumulation. Through co-expression networks, we discovered expression pattern variation for genes related to terpenoid phenylpropanoid and flavonoid metabolism amongst the six varieties. The gene candidates identified in this study provide us with targets of interest for future characterisation of molecular mechanisms that may contribute to salt stress tolerance in barley.