As a proof of concept, we successfully mapped a strong QTL associated with albinism and demonstrated significant conserved genomic architecture in the regions surrounding the gene Oca2, between Astyanax and Danio. We successfully anchored emerging Astyanax genomic information to our GBS-based linkage map, identifying the putative location of thousands of anonymous GBS marker sequences within unplaced Astyanax genome scaffolds. Here, OCA2 is linked to albinism.