Identification of genetic loci and candidate genes for salt tolerance in barley (Hordeum vulgare L.) at the germination stage using a genome-wide association study and multi-omics analysis

• GWAS analysis identified 306 significant SNPs associated with salt tolerance traits during barley germination. • Multi-omics integration revealed 24 candidate genes linked to antioxidant activity, ion transport, and stress signaling. • Amino acid and phenylpropanoid biosynthesis pathways were significantly enriched under salt stress. • The study provides genetic targets and molecular resources for improving barley salt tolerance through breeding. Elucidating the genetic basis of salt tolerance during barley seed germination is crucial for developing resilient cultivars and enhancing crop productivity. As a polygenic trait, salt tolerance requires detailed genetic analysis to decode its complex regulatory networks. Over two consecutive years, we assessed five key morphological traits (relative germination rate, relative shoot/root length, relative shoot/root fresh weight) in 250 diverse barley accessions under 200 mM NaCl stress. Salt treatment caused significant inhibition across all assessed traits. A subsequent genome-wide association study (GWAS) uncovered 306 significant Single Nucleotide Polymorphisms (SNPs) linked to germination-stage salt tolerance. Additionally, salt stress induced 324 differentially accumulated metabolites (DAMs) and 2351 differentially expressed genes (DEGs), respectively. Integrated transcriptomic and metabolomic analyses revealed that the DEGs and DAMs involved in alleviating salt stress were predominantly associated with the regulation of biosynthesis of amino acids and phenylpropanoid biosynthesis. Furthermore, through an integrative analysis of GWAS and transcriptome data, a total of 24 candidate genes were identified, predominantly associated with antioxidant enzymes, membrane protein transport, transcription factors (TFs) and receptor proteins, including GST, TP184C, KT, WRKY and RLKs . In conclusion, these findings provide novel genetic resources to enhance barley's salt tolerance at germination through genomic-assisted selection. These results also enable further functional analysis of identified candidate genes.