Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.)

Genome wide association (GWA) analysis of yield, yield components, developmental, physiological and anatomical traits was conducted for a barley germplasm collection consisting of 185 cultivated (Hordeum vulgare L.) and 38 wild (Hordeum spontaneum L.) genotypes, originating from 30 countries of four continents. Phenotypic evaluations were performed at a dry (Breda) and wet (Tel Hadya) location in Syria. Genome wide association study was done with 816 markers comprised of 710 diversity array technology (DArT), 61 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers. Diversity analysis revealed 5 groups of germplasm, related to origin (Middle East, North Africa), structural information (two-rows), and domestication (wild versus domesticated). Linkage disequilibrium (LD) decayed after 3 cM with a few exceptions at 10 and 15 cM. Although a few QTLs were identified that differed between the dry and wet site, these QTLs explained low phenotypic variation and could not unequivocally be related to drought tolerance when compared to earlier linkage mapping based QTL analysis studies. Therefore, GWA analysis seems to be not very effective for identification of major QTLs for complex traits like drought tolerance in highly structured germplasm collections.

► Genome wide association (GWA) analysis of yield, yield components, developmental, physiological and anatomical traits in a barley germplasm collection consisting of 185 cultivated (Hordeum vulgare L.) and 38 wild (Hordeum spontaneum L.) genotypes, originating from 30 countries of four continents.
► Phenotypic evaluations at a dry (Breda) and wet (Tel Hadya) location in Syria.
► Genotyping of the germplasm collection with 816 markers comprised of 710 diversity array technology (DArT), 61 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers.
► Diversity analysis of the germplasm collection that showed 5 groups of germplasm, related to origin (Middle East, North Africa), structural information (two-rows), and domestication (wild versus domesticated).
► Estimate on linkage disequilibrium (LD) that was decayed after 3 cM with a few exceptions at 10 and 15 cM.
► Identification of a few QTLs that were differed between the dry and wet site and contributed low phenotypic variation.
► Suggestion to explore the possibility of using marker-assisted recurrent (MARS) or genomic selection (GS) approaches for accumulating drought tolerance alleles in the elite genetic background of barley.