QTL mapping of VAB, SN number and size, and eye size. (A) LOD scores computed with single-QTL model genome-scan are plotted against the distance across each linkage group (LG). Red solid lines indicate LOD scores for VAB-level at 35 Hz vibration stimulus, yellow dotted lines for VAB at 50 Hz stimulus, and lime green dotted lines for VAB at 10 Hz stimulus. Significant VAB QTL were detected at LG2 and 17 only at 35 Hz stimulus. The horizontal line indicates the genome-wide significance thresholds at P < 0.05. (B, C) LOD scores computed following multiple QTL mapping. Nine QTL were found across five different LG (see also Table 1). Six overlapping Bayesian credible intervals of QTL for VAB, EO SN number and eye size were found on LG 2 and 17. The X-axis indicates genetic distance in centimorgans (cM), and colored bars denote Bayesian credible intervals with probability coverage as 0.95 for each significant QTL. Insets with gray background show effect plots of phenotypic values against each genotype (mean ± s.e.m.) at the peak locus denoted by the black triangle. Sf/Sf, surface fish homozygote, Sf/Cf, heterozygote, and Cf/Cf, cavefish homozygote. Horizontal dotted lines are genome-wide significant thresholds (P < 0.05) calculated from the single-QTL model (see Methods).