Discordance for genotypic sex in phenotypic female Atlantic salmon (Salmo salar) is related to a reduced sdY copy number

Abstract

the master sex determinant in rainbow trout (oncorhynchus mykiss), sexually dimorphic on the Y chromosome (sdY), is strongly but not perfectly associated with male phenotype in several other species from the family Salmonidae. currently, the cause and implications of discordance for sdYpredicted genotypic sex and phenotypic sex in these species is unclear. Using an established multiplex PCR test for exons 2 and 3 of sdY, we demonstrated that sdY-predicted genotypic sex was discordant with histologically evidenced phenotypic sex in 4% of 176 Tasmanian Atlantic salmon. All discordant individuals were phenotypic females presenting a male genotype. Using real-time qpcR assays that we developed and validated for exons 2, 3 and 4 of sdY, all genotype-phenotype discordant females were confirmed to possess sdY, albeit at a reduced number of copies when compared to phenotypic males. the real-time qpcR assays also demonstrated reduced levels of sdY in 30% of phenotypic females that the established multiplex pcR-based test indicated to be devoid of sdY. These findings suggest sdY may be reduced in copy number or mosaicked in the genomic DnA of sdY-positive phenotypic female Atlantic salmon and highlight the importance of understanding the effects of reduced sdY copies on the development of phenotypic sex. Many members of the family Salmonidae (comprised of three sub-families: Coregoninae, Thymalline and Salmoninae) are of high societal and economic importance for their value in aquaculture, wild stock fisheries and recreational sports fisheries 1,2. With particular reference to Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), they also present as important scientific models in the fields of toxicology, immunology, physiology, nutrition and genetics 3-5. The development of a reliable DNA-based method for identifying genotypic sex in salmonids has been of high interest to facilitate management of native populations and production of farmed stocks 6-9. Initial efforts resulted in the discovery of several markers tightly linked to the sex determining locus on the Y chromosome within the Oncorhynchus genera of the Salmonidae. These include OtY1 in chinook salmon (Oncorhynchus tshawytscha) 10 , GH-Y in chinook 11 , coho (Oncorhynchus kisutch), masu (Oncorhynchus masou) 12 , chum (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha) 13 , and OmyY1 in rainbow trout 14. However, variable rates of genotype-phenotype discordance using these sex markers have been reported 14-20. This is likely attributed to the fact that these markers are non-functional sequences residing close to the sex determination locus, and thus are not directly selected for 20. Recently the master sex determining gene sexually dimorphic on the Y chromosome (sdY) was discovered in rainbow trout, and its presence in genomic DNA (gDNA) was demonstrated to align 100% with male phenotype in this species (425 individuals studied) 21. sdY is also strongly associated with male phenotype in several other species from all three subfamilies of ...

Autosomal sdY Pseudogenes Explain Discordances Between Phenotypic Sex and DNA Marker for Sex Identification in Atlantic Salmon

“…These fish originated from three dams and five sires among the 88 parents. The number of discordant females observed here is higher than the 1% frequency observed in a domesticated Tasmanian Atlantic salmon strain ( Eisbrenner et al, 2014 ; Kijas et al, 2018 ) but similar to the 7% recently reported for the same Tasmanian strain ( Brown et al, 2020 ). Given the inheritance model presented here, it is likely that this difference is merely the result of the number of affected parents and the cross design, although strain specific differences in the frequency of the pseudocopy of sdY cannot be ruled out.…”

“…Since the sdY gene was discovered ( Yano et al, 2013 ), different mechanisms have been invoked to explain the existence of discordant phenotypes such as phenotyping or sampling errors, environment mediated sex reversal, female-specific gene inactivation, sequence variability, the existence of minor sex determining (SD) genes and recombination ( Yano et al, 2013 ; Cavileer et al, 2015 ; Larson et al, 2016 ; Eysturskarð et al, 2017 ; King and Stevens, 2020 ). Recently, a dosage-dependent mechanism has been suggested to explain these discrepancies in Atlantic salmon ( Brown et al, 2020 ), suggesting that sdY is present in a single copy in the male genome and might be also present as partial copies in the female genome. However, our results strongly point to the existence of non-functional autosomal copies as previously suggested for two coregoninae species ( Yano et al, 2013 ) and sockeye salmon ( Larson et al, 2016 ).…”

“…Discordance between DNA markers for sex and phenotypic sex is not uncommon in fishes, and it is typical in a species displaying a combination of genetic and environmental sex determination ( Hattori et al, 2019 ). However, environmental sex determination has not been reported in the family Salmonidae, and several alternative theories for this discordance have been put forward including phenotyping errors ( Yano et al, 2013 ; Eysturskarð et al, 2017 ), sex reversal ( Nagler et al, 2001 ; Williamson and May, 2002 ; Metcalf and Gemmell, 2006 ), loss of gene function ( Podlesnykh et al, 2017 ), or dose effects ( Brown et al, 2020 ) among others ( Guyomard et al, 2014 ; Larson et al, 2016 ; King and Stevens, 2020 ). Nevertheless, the mechanisms underpinning this discordance are still unclear.…”

The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome

“…It is also congruous with a previous study finding a high percentage of sdY-negative sockeye salmon males (~30%) in an upper Columbia River hatchery [ 27 ], and another study with similar findings in samples collected from Asian populations [ 147 ]. Atlantic salmon females have been identified with sdY, but likely have autosomal pseudocopies rather than a bonafide function sex-determining copy (bioRχiv [ 148 ]) [ 33 ]. This has been noted in other salmonid species as well [ 147 ].…”

“…Not all populations of sockeye salmon appear to have a strong association of sdY to sex [ 27 ] suggesting that an alternative sex-determination mechanism(s) may exist in certain populations. SdY-positive females in Atlantic salmon have been identified previously and explained as possible mosaicism, but sdY-negative males are less common and require another explanation [ 33 ].…”