Association mapping is becoming an important tool for identifying alleles and loci responsible for dissecting highly complex traits in barley. This study describes the population structure and marker-trait association using general linear model (GLM) analysis on a site of 60 barley genotypes, evaluated in six salinity environments. Ninety-eight SSR and SNP alleles were employed for the construction of a framework genetic map. The genetic structure analysis of the collection turned out to consist of two major sub-populations, mainly comprising hulled and naked types. LD significantly varied among the barley chromosomes, suggesting that this factor may affect the resolution of association mapping for QTL located on different chromosomes. Numerous significant marker traits were associated in different regions of the barley genome controlling salt tolerance and related traits; among them, 46 QTLs were detected on 14 associated traits over the two years, with a major QTL controlling salt tolerance on 1H, 2H, 4H and 7H, which are important factors in improving barley's salt tolerance.

The success of salt tolerance breeding programs employing traditional screening and selection has been limited in the past decades. This study was designed to characterize the genetic diversity within a subset of barley germplasm using microsatellite markers under different adaptations to salt conditions. Twenty-five microsatellites (SSR) representative of the barley genome, were used in 30 barley accessions and cultivars. A total of 59 alleles were generated, the mean number of alleles per locus was 2.4 and the PIC was 0.22. The four genomic Locus Bmac0030, Bmag0125, EBmac0701 and EBmac0871 were sufficient to differentiate the diversity of all genotypes since they generated a high number of allele with high PIC values. Cluster analysis UPGMA based on SSRs data clearly the most differentiate genotypes according to their Salinity tolerance and the PCA recorded 58.8 % of the total variance. Five markers pairs were found to be associated with salinity and showed linkage disequilibrium with r 2 values higher than 0.05. Association analysis along with specific significant alleles of grain yield showed a significant association of the marker Bmag749 (2H, 176 bp) with salinity. Our results shown a small sample and limited markers were used in this study and the results need to be confirmed using linkage mapping with a large association population. However, the results are credible because many of the loci that were identified were associated with traits that were common with previous reports of linkage or association mapping. These will be useful for molecular marker assist selection and molecular design breeding.