Fig 1. QTL mapping of the polymorphism in Daphnia magna resistance to Pasteuria ramosa genotype P21.

Overview of the workflow used in this study to narrow in on candidate genes underlying a resistance polymorphism. Using QTL mapping and recombination breakpoint mapping with additional markers, we associated the polymorphism in resistance phenotype (attachment of Pasteuria ramosa genotype P21 to the hindgut of Daphnia magna hosts) to a 28.8-kb region at the end of linkage group 3 (Daphnia magna genome version 2.4) which we call the F-locus region. A) Results of the single-QTL genome scan (i.e., interval mapping), showing LOD score (log₁₀ likelihood ratio) plotted at each SNP marker position in the D. magna genetic map. A strong peak with LOD score 63 explains 57% of the phenotypic variance in resistance to P21. The horizontal dashed line indicates the calculated threshold (LOD = 3.74) used to identify significant (α = 0.05) QTL. Effect plot (inset) of the SNP marker with the highest LOD score, showing proportion of F2 clones in each genotype group (ii = homozygous for Iinb1 parent clone; xi = heterozygous; xx = homozygous for Xinb3 parent clone) that are susceptible to hindgut attachment by P21. Error bars indicate ± 1 standard error. B) Enlarged schematic view of the 426-kb QTL containing the resistance locus (D. magna genome version 3.0). The fine-mapped location of the F locus, delimited by SNP markers U0_55 and D16, is shown in green. This F-locus region slightly overlaps with the previously described ABC region (black), which is delimited by SNP marker g311b. The ABC region includes the 50-kb ABC supergene (red), which contains the A, B, and C loci. C) Enlarged schematic of the F-locus region, which lies between positions 2,329,948 and 2,358,729 on contig 000011F and contains 13 putative genes (colored by functional annotation), plus two splice variants, in the reference genome (version 3.0) of clone Xinb3. The region colored in dark green indicates the overlap with the ABC region. D) Sequence comparisons and differential gene expression analysis between the two QTL parent clones identified eight biological candidate genes in the F-locus region.