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Background  Wild diploid wheat,  Triticum urartu  ( T. urartu ) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat.    Results  In this study, we investigated the morphological and genetic diversity and population structure of 238  T. urartu  accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and  Nei’s  gene diversity (GD) of high-molecular-weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238  T. urartu  accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL).    Conclusions  Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in  T. urartu , and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-017-1058-7) contains supplementary material, which is available to authorized users.

Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu