Genome-Wide Association Study Identifies a Major Gene for Beech Bark Disease Resistance in American Beech Tree (Fagus grandifolia Ehrh.)

The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is currently susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees. In this case-control genome-wide association study (GWAS), we tested 16K high quality SNPs using the Affymetrix Axiom 1.5K-50K assay to genotype an association population of 514 individuals. We also conducted linkage analysis in a full-sib family of 115 individuals. Fisher’s exact test and logistic regression tests were performed to test associations between SNPs and phenotypes. Association tests revealed four highly significant SNPs on chromosome (Chr) 5 for a single gene (Mt), which encodes an mRNA for metallothionein-like protein (metal ion binding) in Fagus sylvatica. The GWAS study revealed the genetic architecture of beech bark disease as a trait possibly controlled by as little as one major gene. A genetic marker diagnostic could rapidly be developed and applied to screen for resistant trees in breeding or natural populations.