Salinity limits crop production through osmotic and ionic stress in combination with oxidative strain and nutrient imbalance. Osmotic tolerance, ionic exclusion, and tissue tolerance are some of the adaptive mechanisms in plants when exposed to salinity stress. These physiological adaptive mechanisms are quantitative in nature and are manifested genetically by affecting ~ 8% of genes expression. Barley, the fourth most important cereal crop in the world, is relatively salinity tolerant. However, salinity causes a significant reduction in its growth and grain yield. Adaptation to salinity in barley is varied with growth stage where germination and early growth stages are the most sensitive. This is because excessive salt accumulation in the rhizosphere affects the germinating seed and the subsequent developmental processes including revitalization of plants development after exposure to salinity stress during the sprouting stage. Studies are yet to close the lack of information between the germination and/or seedling stage salinity tolerance, and the genotypic differences in developing young plants regeneration after exposure to salinity stress. The current study explored the genetics of salinity tolerance during the germination stage and the seedling survival in barley after germination under salinity stress (NaCl). To detect the genetic loci and candidate genes responsible for salinity tolerance in barley during germination and early growth stages, four barley populations comprising of a diversity panel of 350 accessions from across the globe, two doubled haploid (DH) populations (CM72/Gairdner and Skiff/CM72), and a back-cross population of CM72/Gairdner/*Spartacus CL were used for phenotyping and mapping. These germplasm sets were exposed to different levels of salinity stress (75, 90, 120 AND 150 mM NaCl) along with a control treatment (deionized water) and various phenotypic traits recorded at germination and early seedling stages. Genome-Wide Association (GWAS) analysis was conducted on a diversity panel of 350 accessions using ~24,000 genetic markers, where 19 Quantitative Traits Nucleotides (QTNs) were detected across all 7 barley chromosomes and 4 genes predicted for salinity tolerance at germination. A study with CM72/Gairdner DH population mapped six Quantitative Traits Loci (QTLs) on chromosomes 1H, 3H and 4H for traits associated with seedling survival under salinity stress. Three QTLs on 1H (1) and 3H (2) with closely linked significant markers that were detected in more than one salinity survival traits were proposed as the regions with highest probability of having candidate genes. To narrow down the location of genetic regions associated with salinity tolerance at germination on chromosome 2H, a major QTL was fine–mapped using CM72/Gairdner and Skiff/CM72 DH populations, F2 and F3 generations of CM72/Gairdner/*Spartacus CL to a region of ~ 0.341 Mb and designed 2 diagnostic markers. Further, this study reported two Receptor-like protein kinase 4 as the candidate genes for enhanced germination under salinity stress. The diversity of seven reported genes in barley was explored further in 40 different species where three of them; dehydration-responsive element-binding (DREB) protein, somatic embryogenesis receptor-like kinase and aquaporin genes, were found to be the most varied. While all three gene families show great diversity in most plant species, the DREB gene family was more diverse in barley than in wheat and rice. Sixty-five barley homolog genes were identified from salinity tolerance genes characterized in Arabidopsis, maize, rice, soybean, and wheat. Besides, the homologs have been reported to express themselves in first three barley’s developmental stages. The results of this study provide new genetic resources and information for further functional characterization of the identified candidate genes and to improve salinity tolerance at germination and early seedling stage via genomic and marker-assisted selection (MAS) in barley. The findings in this thesis together with other existing information will facilitate breeding and release of new high yielding barley varieties that can grow in extreme environment including saline soils of the world
