Transcriptomic and metabolomic analysis uncover core salt-responsive elements in Hordeum marinum

Sea barley (Hordeum marinum), a wild barley relative, exhibits superior salt tolerance. Although we previously assembled the de novo genome of sea barley accession H559, salt-tolerant mechanisms across marinum accessions remain poorly characterized. Here, we compared transcriptomic and metabolomic responses to salt stress between two sea barley accessions: salt-tolerant H512 and salt-sensitive H111. After 14 d of 300 mM NaCl treatment, H512 showed strong salt tolerance, reflected by larger biomass accumulation and shoot K⁺/Na⁺ ratio than H111. RNA-seq analysis identified 3298 and 3770 differentially expressed genes (DEGs) in roots of H512 and H111, respectively, as well as 372 and 341 differentially expressed metabolites (DEMs) by LC-MS technique. Notably, gene expressions related to ion transporters (e.g. NHX1 and GORK1), Ca²⁺ signaling (e.g. GLR1 and CML40) and transcription factors (e.g. WRKY22, bZIP1, ARF5, DREB1A, GT2 and bZIP2) were differentially expressed in H512 than those in H111. Multi-omics analysis revealed that H512 was more energy-saving by down-regulating expression of ATP synthesis-related genes and up-regulating ATP hydrolysis-related genes. H512 also enhanced antioxidant activity by elevating levels of dehydrin, caffeic acid, cinnamaldehyde, taraxacoside and rhamnazin. Our findings illustrated key candidate genes and metabolites governing ion homeostasis, oxidative defense, and energy metabolism in sea barley, which may provide novel insights for improving salt tolerance in crops.