New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain
yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and
phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We
used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National
Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or
cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component
analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and
spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across
the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The
genotype data were used to define ‘mini-core’ sets of accessions capturing the majority of the allelic diversity present in the
core collection. These ‘mini-core’ sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide
association studies (GWAS) of ‘hull cover’, ‘spike row number’, and ‘heading date’ demonstrate the utility of the core
collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new
barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are
effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections
