Additional file 1:The list of sampled trees and their phenotypes. (XLSX 146 kb) Additional file 2:RNA‐seq data quality assessment. (PDF 853 kb) Additional file 3:Examples of RNA vs. mRNA Agilent Bioanalyzer quality profiles. (PDF 288 kb) Additional file 4:The sequences and statistics for the high quality and most informative SNPs used in the GWAS. (XLSX 1080 kb) Additional file 5:The list of mapped SNPs in 12 linkage groups (LGs). (XLSX 91 kb) Additional file 6:(A) DAPC analysis revealed three main genetic clusters where the individuals shown as dots and the groups as inertia ellipses. Eigenvalues of the analyses are displayed inset. (B) Quantile-quantile (QQ) plot of GWA p-values where on x-axis, are expected –log10 P values and on y-axis observed –log10 P values. The plot is showing large deviation from the null distribution where the inflation factor was higher than the threshold of 1, indicating a high genomic inflation in Beech association data and an existence of the population stratification. (PDF 90 kb) Additional file 7:The statistics for Fisher exact test and Logistic regression test. (XLSX 4534 kb) Additional file 8:(A) Four highlighted markers with significance level higher than genome-wide threshold (P value >1.585 × 10–﻿﻿5﻿) located on the chromosome (Chr) 5. (B) Alignment of four nucleotide sequences to reference sequence Fagus sylvatica mRNA (Sequence ID: AJ130886.1). The FASTA sequence order corresponds as AX-156994126 (SEQ_1), AX-156989406 (SEQ_2), AX-156988334 (SEQ_3) and AX-157000652 (SEQ_4). Highlighted red nucleotides refer to polymorphism to reference sequence and green nucleotides present diagnostics SNPs, respectively. (DOCX 4155 kb) Additional file 9:RNA sequence reads from each cDNA library mapped to the full-length copy of the candidate gene transcript sequence from contig 03321, representing the expression of the candidate Mt gene after the challenge by the insect vector. (DOCX 161 kb) Additional file 10:Linkage disequilibrium (LD) structure across four SNPs associated to BBD. (Red) strong LD between markers; (white) no LD. The block-like pattern represents the regions of high LD. Pairwise LD among four SNPs listed as squared allelic correlation (r2)  and Lewontin’s D’ . (DOCX 162 kb)