Figure 3.

Whole-genome synteny between Astyanax and Danio and a proof-of-concept analysis of albinism. Syntenic links between our GBS map and the Danio genome were visualized using Circos (A). Each line represents a connection between the position of a particular marker in our linkage map (black; scale in cM) and a homologous sequence in Danio (various colors; scale in Mb). We scored albinism, a Mendelian trait associated with the Oca2 gene in cave-dwelling Astyanax (C), and performed QTL analysis using R/qtl. Each of three mapping methods (MR in red; EM in blue; HK in black) revealed peak LOD scores of ∼20 (LOD at 0.001α threshold = 6.75) at, or adjacent to, GBS marker TP71406 on Astyanax linkage group 13 (B). Homologous sequences to TP71406 and several of its neighbors on Astyanax linkage group 13 are clustered together on Danio chromosome 6 near the Oca2 gene. A phenotypic effect plot for marker TP71406 revealed the predicted association between the homozygous “cave” condition (genotype CC) and albinism in F₂ individuals (D).