High-density linkage maps detail sex-specific regions of suppressed recombination near fusions of polymorphic chromosomes in purebred and hybrid North American Atlantic salmon ( L.).

The North American (NA) Atlantic salmon typically has 27 pairs of chromosomes, whereas the European (EU) subspecies typically has 29. We investigated within-family recombination within three previously identified chromosome rearrangements (01p/23, 08/29, and 26/28) in NA Atlantic salmon by creating high-density linkage maps using a custom 50K SNP chip developed for the Saint John River aquaculture strain. Linkage maps created for individual purebred and EU hybrid parents in 10 full-sibling families averaged 14 337 SNPs per cross, covering 43 033 SNPs from the 50K SNP chip. Chromosomal translocation 01p/23 was fixed except in one hybrid female map. In contrast, fusion 08/29 was present in maps in 4 out of 10 females and 8 out of 10 males, whereas fusion 26/28 was present in maps in 6 out of 10 females and 8 out of 10 males. The orientation of 08/29 differed from the previous map; the short arm of the metacentric 08 was fused to the centromere of the acrocentric 29. We detected large regions of recombination suppression in female maps at the fusion of 08 to 29. This suppression may reduce the impacts of aneuploidy resulting from pairing of fused and unfused chromosomes, thereby allowing the persistence of chromosomal polymorphisms in this population.