A Transcriptomics Approach to the Development of Predictive Molecular Markers for Tolerance to Tree Diseases: Ash Dieback

Elucidating mechanisms and exploiting genetic tolerance to pests and diseases are major challenges in tree species.  Ash dieback disease, caused by the fungal pathogen Hymenoscyphus fraxineus, is killing Fraxinus excelsior throughout Europe. To identify the molecular basis of the tolerance shown by a very small proportion of trees, with the aim of developing predictive molecular markers to assist breeding, we deployed for the first time in a tree species the technology of Associative Transcriptomics.  This method, first developed in the annual crop species Brassica napus (Harper et al. Nature Biotechnology 30:798-802, 2012), combines rapid marker discovery for both gene sequence and gene expression variation with association genetic and systems biology approaches.  We established functional genotypes for a training diversity panel of 186 trees with varying levels of disease susceptibility, comprising 174,470 Single Nucleotide Polymorphism (SNP) markers and 32,441 Gene Expression Markers (GEMs). We were able to find highly significant (P < 10^-8) associations between the extent of canopy damage and both SNP markers and GEM markers.  Predictive capability within the training panel was confirmed using a “take one out” assessment, so the top 3 markers were used to successfully predict canopy damage (R² = 0.24) in a test dataset of 58 additional, unrelated accessions based on differential gene expression levels in freshly flushed leaves, with prediction of low damage (highly tolerant) individuals being remarkably successful.