We developed a single-nucleotide polymorphism (SNP) - based linkage genetic map for American beech. Single locus Mendelian segregation was first tested using X 2 goodness-of-fit to 1:2:1 and 1:1 ratio at 5% and 1% significance levels. Linkage analysis produced 12 linkage groups (Fig. 2) using JoinMap 2.0 . Out of 3236 SNPs apparently segregating, 16 SNPs failed to be linked so the final number of linked SNPs was 3220 (Additional file 5).Fig. 2Genetic linkage map of F. grandifolia. Genetic linkage map of F. grandifolia constructed using 115 progeny individuals derived from the cross controlled experiment 1505 (R) × 1504 (R). Totally 3220 single nucleotide polymorphism markers are linked in twelve groups and presented on the right side of each linkage group. Map distances in centi-morgans are presented on the left side