Association genetics of pitch canker resistance in loblolly pine (Pinus taeda L.)

Quantitative disease resistance usually involves many genes with small effects, whereas major gene resistance is simple and involves single genes with large effects. In this study, I aimed to quantify the genetic diversity of disease resistance in loblolly pine and provide a better understanding of the basis of quantitative disease resistance using association analyses.;Pitch canker is a disease that affects pine species and is incited by the necrotrophic fungus Fusarium circinatum Nirenberg et O'Donnell causing resinous lesions, seedling mortality, and crown dieback. Resistance to the disease is heritable and quantitative. In this study, I performed association studies on 498 unrelated loblolly pine genotypes using 3,938 SNP markers where 10 candidate genes with small effects were found that could be involved in pitch canker resistance. I then validated the results of association analysis on a population with a known pedigree and on a combined data set of both populations, where three of the 10 significant SNPs previously detected showed significant associations. Finally, I show that transcript abundance of these three genes changed significantly after pathogen challenge, and may possibly provide information on the mechanisms underlying pathogen recognition and response.;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.