A Genome Map for a Species with Male Tetrasomic Inheritance, Coho Salmon, and Location of Quantitative Trait Loci

Linkage maps are integral resources for dissecting complex traits in commercially important species. However, construction of linkage maps for some fish species is often challenging in cases where species are descended from a whole genome duplication event. The aims of this study were to use a combination of cross types to construct a dense linkage map for coho salmon (Oncorhynchus kisutch), a residual tetraploid, and to identify quantitative trait loci underlying weight, length, growth rate and age at sexual maturity. Because these traits are related to fitness in the wild, such information will not only inform future breeding strategies, but will also help understand the mechanisms of adaptive evolution in this species.

The map comprised 30 linkage groups with 8681 restriction site associated DNA (RAD) markers, with a map distance of 6597cM. The map positions of 1266 duplicated loci revealed 8 homeologous linkage groups.  Uneven distribution of these loci across chromosomes suggests that homeologous pairs have diverged at different rates following a whole genome duplication event. Interspecies comparisons between Chinook salmon O. tshawytscha and coho salmon successfully identified homologies and revealed chromosomal arrangements unique to each species since divergence from a common ancestor. High marker density enabled fine-scale QTL mapping in this species, and a number of QTLs associated with all traits were located on several linkage groups. The linkage map and QTLs depicted herein can be used in marker assisted selection, and will also facilitate discovery of the loci involved in driving adaptive evolution in wild.