Fig. 5: Mediation effects of gene expression on variation in seven organism-level phenotypes of C. elegans.

GWA mapping and mediation analysis results of natural variation in C. elegans telomere length (a), responses to arsenic (b), zinc (c), etoposide (d), propionate (e), abamectin (f), and lifetime fecundity (g). Top panel: a Manhattan plot indicating the GWA mapping result for each phenotype is shown. Each point represents an SNV that is plotted with its genomic position (x-axis) against its −log₁₀(p) value (y-axis) in mapping. SNVs that pass the genome-wide EIGEN threshold (the dotted gray horizontal line) and the genome-wide Bonferroni threshold (the solid gray horizontal line) are colored pink and red, respectively. QTL were identified by the EIGEN (c–f) or Bonferroni (a, b, g) threshold. Only chromosomes with identified QTL were shown. Bottom panel: mediation estimates (y-axis) calculated as the indirect effect that differences in expression of each gene play in the overall phenotype are plotted against the genomic position (x-axis) of the eQTL. The horizontal gray line represents the 99th percentile of the distribution of mediation estimates. The mediator genes with adjusted p < 0.05 and interpretable mediation estimate >the 99th percentile estimates threshold are colored other than gray and labeled in a–e or below f, g. Tick marks on x-axes denote every 5 Mb. We used the GWAS() function in the R package rrBLUP⁸⁷ to perform the genome-wide mapping with the EMMA algorithm³² (see “Methods”).