This filtered dataset was obtained from a set of 971K SNPs from 3691 genes in all 19 chromosomes, using a collection of 435 P. trichocarpa and 448 P. balsamifera genotypes and other Populus species (i.e. P. deltoides, P. fremontii, P. heterophylla, P. angustifolia) (Geraldes et al in preparation). This dataset was filtered based on minimun allele frequency (MAF >0.1) and missing data (GR 0.95), for 25 reference P. trichocarpa, 25 reference P. balsamifera and 68 admixed accessions.