High-resolution genetic maps for rainbow trout reveal striking sex-specific differences in recombination patterns

Construction of high resolution genetic maps for organisms is an important tool in assembling genomes, mapping genes, and, increasingly, for managing threatened populations. Rainbow trout (Oncorhynchus mykiss) is an important species that would benefit from an improved genetic map. Genetic maps can be created by hybridizing inbred or clonal lines and mapping loci in the resulting F1 generation. Here we developed much improved genetic maps for O. mykiss using recombination events generated via both male and female meiosis. The new genetic maps contain about three times the number of mapped loci than our previous map. Strikingly, we find that male recombination events predominantly take place at chromosomal telomeres whereas female recombination events largely occur in chromosome interiors. Our results have produced much improved genetic maps for O. mykiss that will enable higher resolution mapping of loci in a variety of salmonids and better whole genome assemblies.