Rapid sex identification of Atlantic salmon (
            <i>Salmo salar</i>
            L.) by real‐time
            <scp>PCR</scp>

Eysturskarð, Jonhard; Dam, Margreta; Kongsstovu, Sunnvør í; Jacobsen, Ása; Petersen, Petra Elisabeth

doi:10.1111/are.13003

Cited by 4 publications

(5 citation statements)

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“…Variable copy numbers for sdY within salmonid populations have not previously been reported despite the use of real-time qPCR assays for detecting the presence of this gene in chinook salmon 22 and Atlantic salmon 26 . However, variations in copy number for other Y-chromosome markers have been reported by several studies.…”

Section: Discussionmentioning

confidence: 92%

“…Therefore, the absence of phenotypic males with a female genotype in the present study is intriguing. sdY positive phenotypic females have been previously documented in Atlantic salmon from Tasmania 27 and the Faroe Islands 26 , as well as in populations of north www.nature.com/scientificreports www.nature.com/scientificreports/ American sockeye salmon 23 and chinook salmon 9,22 . In chinook salmon, similar findings to the present study were reported, whereby all phenotypic males investigated possessed the sdY gene as did a proportion (~2-22%) of phenotypic females.…”

Section: Discussionmentioning

confidence: 98%

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

Brown

Evans²,

Afonso

2020

Sci Rep

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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 ...

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Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 98%

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

Brown

Evans²,

Afonso

2020

Sci Rep

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are among the best studied fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome ( sdY ) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of recent transposition events in this species. We hypothesized the existence of an autosomal copy of sdY , causing apparent discordance between phenotypic and genetic sex, that is transmitted in accordance with autosomal inheritance. To test this, we developed a qPCR methodology to detect the total number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2,025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomal copies of sdY in addition to the Y-specific copy present in males. Patterns across families were highly consistent with autosomal inheritance. These autosomal sdY copies appear to have lost the ability to function as a sex determining gene and were only occasionally assigned to the actual sex chromosome in any of the affected families.

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“…Genetic approaches now provide means to accurately and noninvasively determine sex of Atlantic salmon using the male‐specific sdY (sexually dimorphic on the Y‐chromosome) gene (first published by Yano et al, 2013 and further examined by Eysturskarð et al, 2017; Gabián et al, 2019; Kijas et al, 2018; King et al, 2022; King & Stevens, 2020; Lubieniecki et al, 2015; Quéméré et al, 2014). This method is very accurate (>96%), although the sdY gene moved between different chromosomes (Ayllon et al, 2020; Besnier et al, 2020; Eisbrenner et al, 2014; Gabián et al, 2019), likely via transposition (Lubieniecki et al, 2015), so genetic and phenotypic sex have been inconsistent (Brown et al, 2020; King & Stevens, 2020).…”

Section: Introductionmentioning

confidence: 99%

Genetic sex determination improves Canadian Atlantic salmon (Salmo salar) population assessments

Robertson,

Lehnert,

Kelly

et al. 2023

Fisheries Management Eco

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Estimating egg deposition for Atlantic salmon population assessments is made difficult by their lack of sexual dimorphism prior to the autumn spawning season. We quantified the effect of sex misclassification from subjective examination of external morphology on egg deposition estimates in four Atlantic salmon populations across multiple years. Sex classification of Canadian salmon using the genetic sex marker (sdY) was accurate (>97%), whereas sex classification based on subjective examination of external morphology was inaccurate, with misclassification rates dependent on sea age, life history, and sampling season. Sex misclassification led to annual egg deposition estimates that ranged from −36% to +56%. We found that sex could not be discriminated based on measures of external morphology.

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Rapid sex identification of Atlantic salmon ( Salmo salar L.) by real‐time PCR

Cited by 4 publications

References 5 publications

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

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

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

Genetic sex determination improves Canadian Atlantic salmon (Salmo salar) population assessments

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