In this study, we used Affymetrix Axiom™ Genome-Wide 1.5 K – 50 K array (Santa Clara, CA) to genotype 327 individuals used for association mapping. Although SNP discovery was performed specifically for BBD, a very small proportion of the SNPs deemed informative in downstream analysis. The conversion rate, provided by Affymetrix genotypng facility, corresponded to 34.04% and was quite high compared to Pinus taeda (Loblolly pine) at only 5–10%. Overall, the number of informative SNPs was sufficiently high to provide us with association power on the genome scale for the disease resistance.