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Fig. 3 | Genome Biology

Fig. 3

From: A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

Fig. 3

Co-expression network and candidate eQTLs associated with lignin and cellulose structural genes of pear. a Genes in the lignin biosynthesis pathway in pear, adapted from Humphreys and Chapple (2002) [29]. b Genes in the cellulose biosynthesis pathway in pear, adapted from Balaji et al. (2017) [30]. Black arrows and blue shadows indicate key reaction steps. Genes in orange indicate enzymes in the pathways. Round boxes next to the enzymes contain the numbers of core pathway genes. c Co-expression network of the lignin and cellulose biosynthesis. The outer ring of the network represents structural genes implicated in lignin and cellulose synthesis (circles), while inside are TFs (rhombus). Nodes are labeled with gene names colored based on the edge number. TFs and pathway genes are connected via undirected edges. Internal connections among TFs and among pathway genes were not shown for clarity. Detailed IDs, names, and connection information for all genes in the network can be found in Additional files 12 and 13. d Combined Manhattan plots of eQTLs of genes associated with lignin and cellulose biosynthesis. The red horizontal line depicts the significance threshold (P = 1.99 × 10−12). All significant SNP signals in local and distant eQTLs were combined. Genes in black indicate those located in local eQTLs, while genes in red indicate those located in distant eQTLs. A full list of gene names is provided in Additional file 12. e Circle Manhattan plot for chromosome 6 from the eQTL results of Pbr4CL4, PbrLAC4, PbrLAC5, PbrCESA4a, PbrCESA7a, PbrCESA8b, and PbrMYB169. The plot was constructed using the “CMplot” package in R software. The red circular dotted line depicts the significance threshold (P = 1.99 × 10−12). The signal points highlighted in red indicated the locus of PbrNSC

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