The use of an association platform that uses genotypic information of SNPs distributed across the loblolly pine genome rather than a candidate gene approach allowed the detection of significant SNPs with unknown function. This allowed the detection of SNPs that may be taxonomically unique or that have no previously described function which would have otherwise been overlooked using a candidate gene approach. Although the functional effects of the candidate genes found need to be assessed, in the long term, this work may be useful as these candidate genes could be used to assess the implications of these discoveries for durable disease resistance breeding. This would provide a better understanding of the mechanisms of quantitative disease resistance in loblolly pine as well as host-pathogen coevolution.