Unstable Linkage of Molecular Markers with Sex Determination Gene in Pacific Salmon (Oncorhynchus spp.)

Podlesnykh, A. V.; Брыков, Вл. А.; Kukhlevsky, A. D.

doi:10.1093/jhered/esx001

Cited by 15 publications

(11 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Male kokanee from the upper Columbia River drainage were sdY-negative (personal communication DS and RHD), which is consistent with the resequencing data aligned to the sdY sequence. 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 ].…”

Section: Discussionsupporting

confidence: 82%

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

et al. 2020

View full text Add to dashboard Cite

Sockeye salmon ( Oncorhynchus nerka ) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes—the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.

show abstract

Section: Discussionsupporting

confidence: 82%

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

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Members of the Coregoninae subfamily lack sdY male specificity and the existence of sex specific inactive copies in females has been invoked to explain this phenomenon ( Yano et al, 2012 ). Together with the mobile nature of the sdY gene, the loss of function may also explain the existence of inactive sdY copies in other salmonid species ( Podlesnykh et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

“…For example, assays have been used to determine genetic sex in adults that were not phenotyped but subsequently used for sex-specific studies such as investigation into the genetic basis of age at maturity ( Ayllon et al, 2015 ; Barson et al, 2015 ; Kusche et al, 2017 ; Ayllon et al, 2019 ). However, several studies have reported a discordance between phenotypic and sdY sex within the Salmonidae family ( Eisbrenner et al, 2014 ; Cavileer et al, 2015 ; Larson et al, 2016 ; Podlesnykh et al, 2017 ). 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 ).…”

Section: Introductionmentioning

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%

See 1 more Smart Citation

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

et al. 2020

View full text Add to dashboard Cite

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.

show abstract

“…Several studies have reported a discordance between phenotypic and sdY sex within the Salmonidae family (Eisbrenner et al 2014;Cavileer et al 2015;Larson et al 2016;Podlesnykh, Brykov, and Kukhlevsky 2017). Discordance between genetic 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).…”

Section: Introductionmentioning

confidence: 99%

Sex determining gene transposition as an evolutionary platform for chromosome turnover

Ayllón

Solberg

Besnier

et al. 2020

Preprint

View full text Add to dashboard Cite

Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are the best studied family of 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 transposition, suggesting a recent and non-random sex chromosome turnover in this species.We hypothesized the existence of an autosomic pseudocopy of sdY that is transmitted in accordance with Mendelian inheritance. To test this we developed a qPCR methodology to detect the number of sdY copies present in the genome. Based on the observed 2 phenotype/genotype frequencies and linkage analysis among 2025 offspring from 64 pedigreecontrolled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomic copies in addition to the Y-specific copy present in males. Copy number frequencies were consistent with Mendelian inheritance. Pseudocopy loci were mapped to different chromosomes evidencing non-random transitions of the sex determining gene in Atlantic salmon and the existence of functional constraints for chromosome turnover.

show abstract

Unstable Linkage of Molecular Markers with Sex Determination Gene in Pacific Salmon (Oncorhynchus spp.)

Cited by 15 publications

References 33 publications

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

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

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

Sex determining gene transposition as an evolutionary platform for chromosome turnover

Contact Info

Product

Resources

About