Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traitsin Hordeum vulgare in Mediterranean environments

An association panel consisting of 185 accessionsrepresentative of the barley germplasm cultivated inthe Mediterranean basin was used to localise quantitativetrait loci (QTL) controlling grain yield and yield relatedtraits. The germplasm set was genotyped with 1,536 SNPmarkers and tested for associations with phenotypic datagathered over 2 years for a total of 24 year 9 locationcombinations under a broad range of environmental conditions.Analysis of multi-environmental trial (MET) databy fitting a mixed model with kinship estimates detectedfrom two to seven QTL for the major components of yieldincluding 1000 kernel weight, grains per spike and spikesper m2, as well as heading date, harvest index and plantheight. Several of the associations involved SNPs tightlylinked to known major genes determining spike morphologyin barley (vrs1 and int-c). Similarly, the largest QTLfor heading date co-locates with SNPs linked with eam6, amajor locus for heading date in barley for autumn sownconditions. Co-localization of several QTL related to yieldcomponents traits suggest that major developmental locimay be linked to most of the associations. This studyhighlights the potential of association genetics to identifygenetic variants controlling complex traits.