Increased salinity is one of the major consequences of climatic change affecting global
crop production. The early stages in the barley (Hordeum vulgare L.) life cycle are considered the
most critical phases due to their contributions to final crop yield. Particularly, the germination and
seedling development are sensitive to numerous environmental stresses, especially soil salinity. In
this study, we aimed to identify SNP markers linked with germination and seedling development
at 150 mM NaCl as a salinity treatment. We performed a genome-wide association study (GWAS)
using a panel of 208 intermedium-spike barley (H. vulgare convar. intermedium (Körn.) Mansf.)
accessions and their genotype data (i.e., 10,323 SNPs) using the genome reference sequence of
“Morex”. The phenotypic results showed that the 150 mM NaCl salinity treatment significantly
reduced all recorded germination and seedling-related traits compared to the control treatment.
Furthermore, six accessions (HOR 11747, HOR 11718, HOR 11640, HOR 11256, HOR 11275 and
HOR 11291) were identified as the most salinity tolerant from the intermedium-spike barley collection.
GWAS analysis indicated that a total of 38 highly significantly associated SNP markers under control
and/or salinity traits were identified. Of these, two SNP markers on chromosome (chr) 1H, two
on chr 3H, and one on chr 4H were significantly linked to seedling fresh and dry weight under
salinity stress treatment. In addition, two SNP markers on chr 7H were also significantly associated
with seedling fresh and dry weight but under control condition. Under salinity stress, one SNP
marker on chr 1H, 5H and 7H were detected for more than one phenotypic trait. We found that in
most of the accessions exhibiting the highest salinity tolerance, most of the salinity-related QTLs
were presented. These results form the basis for detailed studies, leading to improved salt tolerance
breeding programs in barley.