Genotyping by sequencing was performed on 314 of the 318 accessions of the WBDC. DNA from the accessions were pooled together at 48-plex to create pooled libraries, which were then sequenced on Illumina Hi-Sequation 2500. After rigorous filtering, 50,842 markers were available for various analyses. Population structure and genetic relatedness assessments were completed for this dataset, thereby facilitating genome-wide association studies (GWAS)(e.g. Sallam et al. 2017). These data are available at The Triticeae Toolbox (T3) database for use by other researchers interested in using GWAS to map genes controlling target traits.