Deletion and Copy Number Variation of Y‐Chromosomal Regions in Coho Salmon, Chum Salmon, and Pink Salmon Populations

Abstract

AbstractThe linkage between the Y‐chromosomal DNA marker GH‐Y (growth hormone pseudogene) and the Y‐associated sex‐determining locus was examined in 31 populations of Coho Salmon Oncorhynchus kisutch, 29 populations of Chum Salmon O. keta, and 14 populations of Pink Salmon O. gorbuscha from North America (British Columbia [BC] and Yukon, Canada; Oregon and Washington, USA) and Japan to examine the stability of Y‐chromosome sequences in salmonids. This marker is used for genetic sexing of multiple salmon species both for population studies and for aquaculture strain development. We found a strong association between GH‐Y and sex in Coho Salmon (with rare exceptions seen in Washington and Oregon only), whereas the association of GH‐Y and sex was weak in Chum Salmon and Pink Salmon. Up to 100% of males lacking GH‐Y were found in some BC Chum Salmon populations, whereas there were no exceptional (GH‐Y‐negative) males in Japan, the Yukon, or Washington, indicating strong geographic clustering of GH‐Y marker deletion. For Pink Salmon, there was an average of 29% male exceptions in BC populations. For both Pink Salmon and Chum Salmon, many more GH‐Y‐negative males than GH‐Y‐positive females were observed. To investigate whether sex reversal, recombination, or differential mutation and selection mechanisms occur in Pink Salmon, we conducted reciprocal single‐pair crosses using regular males, regular females, and exceptional individuals (GH‐Y‐negative males and GH‐Y‐positive females). The results showed that the GH‐Y locus from GH‐Y‐positive males and females was stably inherited by the F1 progeny independently of the sex‐determining locus and that this chromosomal region was not necessary for male differentiation. The present data suggest that the genomic organization of the salmonid Y‐chromosome is highly dynamic and subject to multiple forms of sequence copy number variation at multiple loci. Whether this variation has fitness implications or is selectively neutral in populations remains to be examined.Received July 13, 2016; accepted October 19, 2016 Published online January 20, 2017