Figure 1.
Variation in retinal thickness among Astyanax F2 hybrids.
(A) Diagram of the eye, retina, and retinal landmarks. Black box indicates an example region where we recorded retinal thickness. (B) Example retinal sections from the eyes of four F2 hybrids. Scale bar denotes 50 µm and brackets denote individual retinal layers. Cavefish-like retinas (first two panels) were generally thin and may be missing some layers entirely, including the photoreceptor cell layer. Surface fish-like retinas (last two panels) were generally thicker with layers that are well-differentiated and clearly laminated. In some individuals, the retinal pigment epithelium (RPE) was hypopigmented (first and third panels). (C) Retinal thickness among 115 Astyanax SFxCF F2 hybrids. Yellow bars denote RPEs that were hypopigmented. (D) Box-plots illustrate variance in the thickness of individual retinal layers. The retinal layers shown are: ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL), outer nuclear layer (ONL), photoreceptor cell layer (PCL), and retinal pigment epithelium (RPE).
Table 1.
Pearson's correlation coefficients for retinal thickness among 115 Astyanax F2 hybrids.
Figure 2.
Comparative mapping of the Astyanax and zebrafish genomes.
Colored boxes represent Astyanax linkage groups 1−25; grey boxes represent zebrafish (Danio rerio) chromosomes 1–25. Colored lines link genetic markers from Astyanax to their BLAST position in zebrafish. Circle plot created with Circos [37].
Figure 3.
QTL mapping of retinal thickness in F2 hybrids.
(A) LOD scores of association between genotypes on each linkage group and the thickness of seven retinal layers. Retinal layers include the ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL), outer nuclear layer (ONL), photoreceptor cell layer (PCL), and retinal pigment epithelium (RPE). Horizontal lines represent the genome-wide significant threshold at P = 0.05 (solid) and 0.15 (dotted). (B) Significant QTL include those for INL thickness on Astyanax LG 2, OPL thickness on LG 7, GCL thickness on LG 11, and ONL thickness on LG 24. Highlighted regions represent the 95% Baysian credible interval for each QTL position. (C) Markers within and around each QTL region map to four ∼35 Mb regions of the zebrafish (Danio rerio) genome on chromosomes 5, 21, 9, and 12. Within each region, we find several candidate genes that are either: (red) differentially expressed between Astyanax surface fish and cavefish; (green) implicated in vertebrate retinal degeneration; or (blue) important for eye development and function (see Discussion).
Figure 4.
Mean thickness of retinal layers among genotypic classes at each QTL.
Mean values of inner nuclear (INL), outer plexiform (OPL), ganglion cell (GCL), and outer nuclear (ONL) layer thickness are plotted for genotypic classes at the peak marker for each QTL (see Figure 3). The distributions of mean OPL, GCL, and ONL thickness indicate that cavefish alleles are inherited dominantly and contribute to a clear decrease in retinal thickness. The distribution of mean INL thickness indicates that cavefish alleles for this QTL may be inherited overdominantly. Error bars indicate standard deviation. SS: surface fish homozygote; CC: cavefish homozygote; SC: heterozygote.
Table 2.
Summary statistics of four QTL for Astyanax retinal degeneration.