Fusarium head blight (FHB) disease is one of the most challenging crop diseases; it reduces kernel weight, cause significant yield losses and quality reductions that may occur if fungal mycotoxins, especially deoxynivalenol (DON) are produced in infected seed. DON contamination has raised serious food safety concerns. Furthermore, straw of barley or wheat may be consumed by livestock could contain significant amounts of DON in chaff. Association mapping of a trait is to identify chromosomal regions that contain genes affecting the trait. The discovery of dense polymorphic markers covering the entire genome provides us an opportunity to localize these regions by trying to find the markers closest to the genes of interest.

Association mapping was conducted in a structured barley population consists of (103 accessions of wild barley (H. vulgare ssp. spontaneum) core collection and 21 spring barley cultivars (H. vulgare ssp. vulgare)) in this study for identification of promising tolerance QTLs in barley against FHB. These experiments were carried out in the green-house during years 2009, 2010 and 2011 and under field-potted conditions in 2011, arranged in a completely randomized design with five replications, by using two different ways of scoring for disease infection leaves disease scoring (LDS) and spikes disease scoring (SDS) and two different fungus isolates. Heading date (HD) also had been recorded as a related trait for FHB in 2011. The accessions were genotyped by using 895 Diversity Arrays Technology (DArT) markers. Structure analysis was carried out for the all accessions using principal component analysis (PCA) the accessions were divided into 3 clusters and the relative kinship coefficients (K matrix) among all pairs of accessions were calculated by “SPAGeDi-1.3d” Software. The association analysis was performed in mixed linear model (MLM) including PCA values and K matrix. All studied traits LDS, SDS and HD were exhibited highly significantly differences in three years. Results from combined means in two years and two isolates showed that; 18 accessions had lower than 20 infection percentage for LDS and 48 accessions had lower than 20 infection percentage, 9 accessions from this group were lower than 10 infection percentage for SDS. Positive and significant phenotypic correlation has been recorded between LDS and SDS and negative correlation also have been recorded between SDS and HD in 2011. Seventy three markers were correlated significantly with all studied traits and covered the whole genome of the studied population. Different QTLs have been identified for LDS, leaves disease scoring isolates in 2011 (LDSI), SDS, spikes disease scoring isolates in 2011 (SDSI), visual leaves disease scoring (VS), HD, marker isolate interaction within leaves disease scoring (MILDS) and marker isolate interaction within spikes disease scoring (MISDS). Some of these QTLs were identified in two traits; marker bPb-0522 detected to SDSI and MISDS and also marker bPb-6466 detected to LDS and MILDS. Few of this QTLs were identified for two traits in the same/nearly position on the chromosome; in the position 122.08 cM on chromosome 6H two markers (bPb-4379 and bPb-3375) were identified to be associated with SDS and HD. Also in chromosome 2H on 70.8 cM two markers detected to LDS and SDS. In the study a mixed model was tested for the epistatic interaction between all DArT markers and studied traits. Interactions were detected between 11 pairs of QTLs for FHB resistance/tolerance and one interaction for heading date, which involved 24 QTLs on 6 chromosomes. The results indicated that barley FHB resistance/tolerance is a complicated trait and may be controlled by a complicated gene network