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Background  Clarifying genetic diversity in a large germplasm resource plays important roles in experimental designs that provides flexible utility in fundamental research and breeding in crops. However, the work is limited due to small collections of barley that are insufficient representatives.    Results  In the present study, we collected 562 hulless barley ( Hordeum vulgare  L.) accessions with worldwide geographic origins and evaluated their genetic variability and relatedness based on 93 simple sequence repeat (SSR) markers. In an integrated analysis of the population structure, analysis of molecular variance (AMOVA) and pairwise  F   ST , the 562 barley accessions exhibited a strong stratification that allowed for them to be divided into two major subpopulations (p1 and p2) and an admixture subpopulation, with 93, 408 and 61 accessions, respectively. In a neutral test, considerable proportions of SSR alleles expressed the strong non-neutrality in specific subpopulations (44 and 37), which are probably responsible for population differentiation. To reduce the diversity redundancy in large barley collections, we delicately selected a core set of 200 barley accessions as a tradeoff between diversity and representativeness in an easily handled population. In comparing the 562 barley accessions, the core barley set accounted for 96.2% of allelic diversity and 93% to 95% of phenotypic variability, whereas it exhibited a significant enhancement in minor allelic frequencies, which probably benefit association mapping in the barley core set.    Conclusions  The results provided additional insight into the genetic structure in a large barley germplasm resource, from which an easily manageable barley core set was identified, demonstrating the great potential for discovering key QTLs and ultimately facilitating barley breeding progress.    Electronic supplementary material  The online version of this article (10.1186/s12863-017-0563-x) contains supplementary material, which is available to authorized users.

A microsatellite diversity analysis and the development of core-set germplasm in a large hulless barley (Hordeum vulgare L.) collection