Fig. 4

Gene networks comprised of SNPs and their associated wood-related gene expression and metabolite level phenotypes. The blue dot nodes represent SNPs. Details of the SNPs and the genes containing them are presented in Table 2. The large blue dot node 33 represents a SNP that resides in a GAMYB transcription factor (TF) gene. The yellow dot nodes represent genes, for which expression level was used as a phenotype trait in the SNP association analysis. The pink dot nodes represent metabolites, for which concentration level was used as a phenotype trait in the SNP association analysis. The grey and red edges represent SNP-gene-expression and SNP-metabolite-level associations, respectively. The purple edges represent SNP-SNP interactions that significantly impact the phenotypes. Expressed genes in the network include arabinogalactan-protein and cell wall protein genes (AGP1–6), cell expansion genes (COB and KORRI), cell wall related (resistance related) genes (CslA1), cellulose and callose synthase genes (CesA3, CslA2, and CS-1343), lignin biosynthesis enzyme genes (4CL1, C3H, CAD1, CCoAMT, COMT, Lac1–8, PAL1, and TC4H), α-tubulin gene (αtub2), wood development enzyme genes (BKACPS, BQR, Cellulase, EndChi, Importin, LP6, PCBER, PLR, prxC2, SAH7, SPL, and XET1), wood development protein genes (1CAB-3A, NH-10, NH-9, and RP-L2), wood development TF genes (SND1, AIP, APL, eIF-4A, FRA2, KNAT4, KNAT7, LZP, MYB1, MYB4, and MYB85)