A Genetic Linkage Map for Yellowstone Cutthroat Trout-Rainbow Trout F2 Hybrids: Setting the Genomic Foundation for Investigating Introgression in the Wild

Widespread introductions of non-indigenous rainbow trout have caused significant declines in cutthroat trout, in part through introgressive hybridization, which involves recombination between parental genomes.  Although introgressive hybridization is a central concern for cutthroat trout conservation, nothing is known about its effect on genomic organization. For example, rainbow and Yellowstone cutthroat trout are chromosomally divergent; published genetic linkage maps indicate that rainbow trout contain 29 – 30 linkage groups, while karyotype data suggest that Yellowstone cutthroat trout contain 32 linkage groups.  To understanding how these linkage groups recombine within a hybrid background, we have developed a genetic linkage map for Yellowstone cutthroat-rainbow trout F2 hybrids.  Our results indicate that the F2 hybrids contain 28 linkage groups, which is fewer than expected.  The reduction in linkage group number compared to rainbow trout is the result of a metacentric and acrocentric rainbow trout chromosome acting as a single linkage group within F2 hybrids.  This is likely the result of different chromosome fission and fusion events between the species.  Our results also indicate that segregation of alleles is more commonly distorted in males than females.  In addition, we plan to localize meristic and morphological quantitative trait loci onto the F2 map, as well as assign species-specific markers to linkage groups.  Our map will serve as a genomic foundation for investigating the biology and evolution of hybrids in the wild.