Resurrecting Information Hidden in Duplicated Salmonid Genomes

Many polyploid-origin plants and animals are currently enjoying a genomics revolution fueled by modern sequencing and genotyping technologies. Studies that rely upon genotyping by sequencing often filter duplicated loci in order to meet assumptions such as Hardy-Weinberg equilibrium, effectively trimming subtelomeric regions. As a result, filtering duplicate loci introduces an unacceptable bias given that subtelomeric regions are known to harbor adaptively important genes. Studies of polyploids, mostly in economically important crops, deal with the problem by distinguishing homeologs using doubled haploids. Until now very little attention has been given to sorting homeologs in vertebrates. Salmonids provide an ideal system for assessing this genotyping challenge in vertebrates because genomic studies are rapidly providing unprecedented amounts of data to inform conservation, management, and aquaculture. We review the issues and discuss how chromosome set manipulations can provide insight into genotyping and mapping confounded duplicated genes, especially for nonmodel organisms that lack genomic resources. We propose and demonstrate a strategy using haploid-assisted mapping to first identify and map duplicated genes - then we develop genotyping approaches that enable scoring of duplicated loci in natural populations. Inclusion of duplicated loci in future studies will reveal novel evolutionary insights and enhance the value of genomic tools in conservation and management of polyploid species.