Sex identification by male-specific growth hormone pseudogene (GH-psi) in Oncorhynchus masou complex and a related hybrid

Identification and Genomic Localization of Autosomal sdY Locus in a Population of Atlantic Salmon (Salmo salar)

The determination of sex in salmonid fishes is controlled by genetic mechanisms, with males being the heterogametic sex. The master sex-determining gene, the sexually dimorphic gene on the Y chromosome (sdY), is a conserved gene across various salmonid species. Nevertheless, variations in the genomic location of sdY have been observed both within and between species. Furthermore, different studies have reported discordances in the association between the sdY and the phenotypic gender. While some males seem to lack this locus, there have been reports of females carrying sdY. Although the exact reasons behind this discordance remain under investigation, some recent studies have proposed the existence of an autosomal, non-functional copy of sdY as a potential cause. In this study, we confirmed the presence of this autosomal sdY in the SalmoBreed strain of Atlantic salmon using a genotyping platform through a novel approach that allows for high-throughput screening of a large number of individuals. We further characterized the segregation profile of this locus across families and found the ratio of genetically assigned female-to-male progeny to be in accordance with the expected profile of a single autosomal sdY locus. Additionally, our mapping efforts localized this locus to chromosome 3 and suggested a putative copy on chromosome 6.

Lessons from an unusual vertebrate sex-determining gene

So far, very few sex-determining genes have been identified in vertebrates and most of them, the so-called 'usual suspects', evolved from genes which fulfil essential functions during sexual development and are thus already tightly linked to the process that they now govern. The single exception to this 'usual suspects' rule in vertebrates so far is the conserved salmonid sex-determining gene, sdY (sexually dimorphic on the Y chromosome), that evolved from a gene known to be involved in regulation of the immune response. It is contained in a jumping sex locus that has been transposed or translocated into different ancestral autosomes during the evolution of salmonids. This special feature of sdY, i.e. being inserted in a 'jumping sex locus', could explain how salmonid sex chromosomes remain young and undifferentiated to escape degeneration. Recent knowledge on the mechanism of action of sdY demonstrates that it triggers its sex-determining action by deregulating oestrogen synthesis that is a conserved and crucial pathway for ovarian differentiation in vertebrates. This result suggests that sdY has evolved to cope with a pre-existing sex differentiation regulatory network. Therefore, 'limited options' for the emergence of new master sex-determining genes could be more constrained by their need to tightly interact with a conserved sex differentiation regulatory network rather than by being themselves 'usual suspects', already inside this sex regulatory network. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.

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

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 sdY-predicted 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.

A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus)

Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to confirm whether intersex fish in the wild arise from genetic males or females, or whether sex reversal occurs in the wild, as this condition can be induced experimentally in controlled exposures to WwTW effluents and a steroidal oestrogen. Using restriction site-associated DNA sequencing (RAD-seq), we identified a candidate for a genetic sex marker and validated this marker as a sex probe through PCR analyses of samples from wild roach populations from nonpolluted rivers. We also applied the sex marker to samples from roach exposed experimentally to oestrogen and oestrogenic effluents to confirm suspected phenotypic sex reversal from males to females in some treatments, and also that sex-reversed males are able to breed as females. We then show, unequivocally, that intersex in wild roach populations results from feminisation of males, but find no strong evidence for complete sex reversal in wild roach at river sites contaminated with oestrogens. The discovered marker has utility for studies in roach on chemical effects, wild stock assessments, and reducing the number of fish used where only one sex is required for experimentation. Furthermore, we show that the marker can be applied nondestructively using a fin clip or skin swab, with animal welfare benefits.

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

In the present study, we tested the congruence between the sdY sex-specific marker and other commonly used male markers, located on the Y-chromosome, with the sex phenotypes in 5 species of Pacific salmon in Asian waters, including Chinook, chum, sockeye, masu, and pink salmon. We found that the localization of the sex-specific marker of both males and females of these species is not consistent with the phenotypic sex. Also, no linkage was found between noncoding markers and the sdY gene in the same species samples. Possible genetic and physiological mechanisms underlying this discrepancy are discussed.

Comparison of the frequency of the growth hormone pseudogene between juvenile and adult female masu salmon Oncorhynchus masou

The proportions of individual masu salmon Oncorhynchus masou whose genotypic and phenotypic sex differed were compared among juvenile and adult fish in three rivers, and genotypically male but phenotypically female individuals were observed 6-16% more often among adults than among juveniles. This suggests that during the transition from juvenile to adult, survival rates of genotypically male but phenotypically female individuals are higher than those of normal females. In contrast, genotypically female but phenotypically male individuals were only found in the juvenile period, which suggests that they exhibit a decreased survival rate in comparison with normal males.

Reduced oceanic growth of growth hormone pseudogene-positive female masu salmon Oncorhynchus masou

This study compared the growth rates of female masu salmon Oncorhynchus masou, who possessed a male-specific gene marker, the growth hormone pseudogene (GHp), and normal females, as estimated from their scale growth. There was a difference between the growth rates of GHp-positive females and those of normal females of the same age during the ocean period, although their growth rates during the river period were similar. These results suggest that GHp-positive salmonid females exhibit male-like characteristics such as reduced feeding activity during the ocean period, which depresses their growth.

Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (Salmo salar)

Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.

Chromosome painting of Z and W sex chromosomes in Characidium (Characiformes, Crenuchidae)

Some species of the genus Characidium have heteromorphic ZZ/ZW sex chromosomes with a totally heterochromatic W chromosome. Methods for chromosome microdissection associated with chromosome painting have become important tools for cytogenetic studies in Neotropical fish. In Characidium cf. fasciatum, the Z chromosome contains a pericentromeric heterochromatin block, whereas the W chromosome is completely heterochromatic. Therefore, a probe was produced from the W chromosome through microdissection and degenerate oligonucleotide-primed polymerase chain reaction amplification. FISH was performed using the W probe on the chromosomes of specimens of this species. This revealed expressive marks in the pericentromeric region of the Z chromosome as well as a completely painted W chromosome. When applying the same probe on chromosome preparations of C. cf. gomesi and Characidium sp., a pattern similar to C. cf. fasciatum was found, while C. cf. zebra, C. cf. lagosantense and Crenuchus spilurus species showed no hybridization signals. Structural changes in the chromosomes of an ancestral sexual system in the group that includes the species C. cf. gomesi, C. cf. fasciatum and Characidium sp., could have contributed to the process of speciation and could represent a causal mechanism of chromosomal diversification in this group. The heterochromatinization process possibly began in homomorphic and homologous chromosomes of an ancestral form, and this process could have given rise to the current patterns found in the species with sex chromosome heteromorphism.

Variable incidences and morphological characteristics of female masu salmon Oncorhynchus masou with growth hormone pseudogene

The genetic sex of mature masu salmon Oncorhynchus masou (212 males and 243 females) collected from three rivers located in the mid-western part of Hokkaido was determined using the male-specific genetic marker growth hormone pseudogene (GHp). A total of 72 phenotypic females were found to have GHp, whereas none of the phenotypic males lacked GHp. The occurrence of females with incongruence between genotypic and phenotypic sex varied with the river and reached the highest rate of 67%. In contrast, none of the phenotypic males were found to have a female genotype. Comparison of adult body size showed that females with GHp were significantly smaller than those without GHp. Moreover, comparison of secondary characteristics revealed that both upper jaw length and head length were greater in females with GHp than in those without GHp. These results suggest that genetic changes (e.g. transposition and mutation) may also affect morphological characteristics.

Oncogenic Ras increases sensitivity of colon cancer cells to 5-FU-induced apoptosis

Despite the fact that objective response rates to 5-FU are as low as 20%, 5-FU remains the most commonly used drug for the treatment of colorectal cancer. The lack of understanding of resistance to 5-FU, therefore, remains a significant impediment in maximizing its efficacy. We used intestinal epithelial cells with an inducible K-RasV12 to demonstrate that expression of oncogenic Ras promotes cell death upon 5-FU treatment. Accordingly, transient expression of the mutant RasV12, but not the WT Ras, enhanced 5-FU-induced apoptosis in 293T cells. Consistent with these data, we showed that targeted deletion of the mutant Ras allele in the HCT116 colon cancer cell line protected cells from 5-FU-induced apoptosis. Using isogenic colon cancer cell lines that differ only by the presence of the mutant Ras allele, HCT116 and Hke-3 cells, we demonstrated that signaling by oncogenic Ras promotes both accumulation of p53 and its phosphorylation on serine15 in response to 5-FU, a situation that favors apoptosis over growth arrest. However, despite the differential induction of p53 in HCT116 and Hke-3 cells, the expression of Puma, a gene with an important role in p53-dependent apoptosis, was not affected by Ras signaling. In contrast, we showed that Ras interferes with 5-FU-induced expression of gelsolin, a protein with known antiapoptotic activity. We ascertained the role of gelsolin in 5-FU-induced apoptosis by demonstrating that silencing of gelsolin expression through RNAi sensitized cells to 5-FU-induced apoptosis and that re-expression of gelsolin in cells harboring mutant Ras protected cells from 5-FU-induced apoptosis. These data therefore demonstrate that Ras mutations increase sensitivity to 5-FU-induced apoptosis at least in part through the negative regulation of gelsolin expression. Our data indicate that Ras mutations promote apoptosis in response to 5-FU treatment and imply that tumors with Ras mutations and/or reduced expression of gelsolin may show enhanced apoptosis in response to 5-FU also in vivo.

Tobacco smoke-induced lung tumorigenesis in mutant A/J mice with alterations in K-ras, p53, or Ink4a/Arf

A/J mice with genetic alterations in K-ras, p53, or Ink4a/Arf were employed to investigate whether mice carrying these germline mutations would be susceptible to tobacco smoke-induced lung tumorigenesis. Transgenic mice of both genders and their wild-type littermates were exposed to environmental cigarette smoke for 6 months, followed by recovery in air for 5 months. A significant increase of lung tumor multiplicity was observed in K-ras, p53, or Ink4a/Arf mutant mice when compared with wild-type mice. Furthermore, an additive effect was observed between the mice with a mutant p53 transgene and an Ink4A/Arf deletion during tobacco smoke-induced lung tumorigenesis. Sequence analysis of the K-ras gene indicated that the mutations had occurred at either codon 12/13 or 61 in both spontaneously occurring (air control) and tobacco smoke-induced lung tumors. K-ras mutations were found in 62% of the tumors from air-control animals and 83% in those exposed to tobacco smoke. The mutation spectrum found in tumors from mice exposed to tobacco smoke is somewhat similar to that in tumors from air-control mice. In addition, we identified three novel mutations at codon 12: GGT (Gly) --> TTT (Phe), ATT (Ile), and CTT (Leu). These findings provide evidence that K-ras, p53, and Ink4a/Arf mutations play a role in tobacco smoke-related lung carcinogenesis. The similarity of the mutation spectra in the K-ras oncogene observed in tobacco smoke-induced tumors, as compared to spontaneous tumors, suggests that tobacco smoke enhances lung tumorigenesis primarily through promoting spontaneously occurring K-ras mutations.

Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes

A defining character of the piscine family Salmonidae is autotetraploidy resulting from a genome-doubling event some 25-100 million years ago. Initially, duplicated genes may have undergone concerted evolution and tetrasomic inheritance. Homeologous chromosomes eventually diverged and the resulting reduction in recombination and gene conversion between paralogous genes allowed the re-establishment of disomic inheritance. Among extant salmonine fishes (e.g. salmon, trout, char) the growth hormone (GH) gene is generally represented by two functional paralogs, GH1 and GH2. Sequence analyses of salmonid GH genes from species of subfamilies Coregoninae (whitefish, ciscos) and Salmoninae were used to examine the evolutionary history of the duplicated GH genes. Two divergent GH gene paralogs were also identified in Coregoninae, but they were not assignable to the GH1 and GH2 categories. The average sequence divergence between the coregonine GH genes was more than twofold lower than the corresponding divergence between the salmonine GH1 and GH2. Phylogenetic analysis of the coregonine GH paralogs did not resolve their relationship to the salmonine paralogs. These findings suggest that disomic inheritance of two GH genes was established by different mechanisms in these two subfamilies.

GFP reporter gene confirms paternity in the androgenote Buenos Aires tetra,Hemigrammus caudovittatus

A protocol for successful induction of androgenetic cloning of the Buenos Aires tetra (BT), Hemigrammus caudovittatus, with contrasting gray and golden strains is described. At the intensity of 4.2 W/m(2), UV irradiation for 2.75 min totally inactivated the maternal genome in eggs of gray BT. Following activation by sperm of golden BT, the 25-min-old embryos were shocked at 41 degrees C for 2 min to restore diploidy. Interestingly, the hatching success of the haploid fry was always higher than that of the diploid fry, indicating that the enhanced homozygosity (Y(2)Y(2)) is more deleterious than haploidy. Maternal genomic inactivation was confirmed by (i) expression of green fluorescent protein (GFP) gene in the 6-16 hr old live haploid and aneuploid embryos, (ii) golden body color in the diploid fry and adult and (iii) progeny testing. Survival of androgenotes was 10% at hatching and 6% at sexual maturity. Reproductive performance of F(0) and F(1) males (Y(2)Y(2)) was superior to that of normal ones (X(1)Y(2)), but that of the F(0) and F(1) females (X(2)X(2)) was inferior to the control (X(1)X(2)). Of 21 crosses involving homozygous androgenetic (Y(2)Y(2)) males and heterozygous (X(1)X(2)) females, 7 of them (33%) produced 3-9% unexpected female progenies. But only a single cross (14%) generated 3-4% unexpected female progenies, when 7 pairs of homozygous androgenetic (Y(2)Y(2)) males and (X(2)X(2)) females were crossed. Hence, the paternal autosomes, inherited by the homozygous androgenetic female (X(2)X(2)), produced female progenies in significantly less number of crosses, also at lower frequencies than the crosses with heterozygous females (X(1)X(2)), which carried an equal number of paternal and maternal autosomes. However, progenies resulting from the cross between gray female (X(1)X(2)) and golden male (Y(2)Y(2)), after undergoing androgenesis, were males, with paternal chromosomes alone, indicating that the presence of Y(2)Y(2) appears to override the modifying effect of autosomes, but the paternal or maternal autosomes seemed to override the single Y(2) present with X(1) or X(2), and induced the production of unexpected female progenies. Using Double sex Mab3 related transcription factor (DMRT 1)-specific primers, PCR analyses of the genomic DNA of the normal (X(1)Y(2)) and androgenetic males (X(1)Y(2)) produced two amplicons of 237 and 300 bp length. However, they were not detectable in the female (X(1)X(2)) genomic DNA, which amplified only one amplicon of 100 bp. Genomic DNA extracted from the 18 unexpected female progenies expressed the (X(1)Y(2)) genotype-specific banding pattern with two amplicons of 237 and 300 bp length and thereby confirmed that they were genotypic males. A partial sequencing of the male-specific sequence indicated that DMRT 1-specific primer was bound to the fragment of the genomic DNA of the male tetra, although the male-specific sequence of DMRT 1 was not completely detectable.

Polymorphism and differentiation of rainbow trout Y chromosomes

Most fish species show little morphological differentiation in the sex chromosomes. We have coupled molecular and cytogenetic analyses to characterize the male-determining region of the rainbow trout (Oncorhynchus mykiss) Y chromosome. Four genetically diverse male clonal lines of this species were used for genetic and physical mapping of regions in the vicinity of the sex locus. Five markers were genetically mapped to the Y chromosome in these male lines, indicating that the sex locus was located on the same linkage group in each of the lines. We also confirmed the presence of a Y chromosome morphological polymorphism among these lines, with the Y chromosomes from two of the lines having the more common heteromorphic Y chromosome and two of the lines having Y chromosomes morphologically similar to the X chromosome. The fluorescence in situ hybridization (FISH) pattern of two probes linked to sex suggested that the sex locus is physically located on the long arm of the Y chromosome. Fishes appear to be an excellent group of organisms for studying sex chromosome evolution and differentiation in vertebrates because they show considerable variability in the mechanisms and (or) patterns involved in sex determination.Key words: sex chromosomes, sex markers, cytogenetics, rainbow trout, fish.

Linkage disequilibrium between the pseudoautosomal PEPB-1 locus and the sex-determining region of chinook salmon

Allele frequency differences between sexes and an excess of heterozygotes in males had suggested that the PEPB-1 locus is sex-linked in chinook salmon (Oncorhynchus tshawytscha). We here estimate less than 1% recombination between PEPB-1 and a growth hormone pseudogene known to be in the sex-determining region (SEX) in 374 progeny from eight experimental matings. We present modified maximum likelihood methods for estimating haplotype frequencies from population samples at a sex-linked locus in which functional alleles occur on both the X and Y chromosomes (pseudoautosomal loci). We find nearly complete linkage disequilibrium between PEPB-1 and SEX in 20 population samples from the Puget Sound region of Washington and southern British Columbia. However, allele frequencies at PEPB-1 were similar in males and females in 35 population samples from the coast of Washington and the Columbia River basin. Pseudoautosomal regions have been described in a broad taxonomic array of vertebrates and invertebrates, and they are likely candidate regions to find genes associated with differences in life history, morphology, or behavior between males and females.

Hormonal induction of supermale golden rosy barb and isolation of Y-chromosome specific markers

Viable supermales of the golden rosy barb Puntius conchonius are generated through hormonal sex reversal and progeny testing. Discrete immersion (3 h/day on the second, fourth, and sixth day after hatching) of the fry in Estradiol-17beta (E2) at doses of 400-600 microg/L ensures greater than 40% survival and production of more than 98% F1 females; of these 50% are heterogametic females, that when crossed with normal males, sire 25% YY supermales. Supermales sire female progenies at the frequencies between 0 and 8%. Reproductive performance of hormonally sex-reversed females and androgenetic females is inferior to the normal ones. Conversely, the performance of androgenetic males is superior but suffers from low fertilizability. The relative performance of supermale produced by breeding sex-reversed parents is superior to those produced by androgenesis. Using the SRY-specific primers, the PCR analysis of the genomic DNA of the male golden rosy barb produces three products of 588, 333, and 200 bp length. However only the 200 bp product is amplified in the female genome. Hence it is possible to use the first two products as molecular markers to rapidly identify fish possessing a Y chromosome. The presence of 333 and 588 bp fragments in normal (X1Y2), hormonally induced (Y1Y2) and androgenetic (Y2Y2) males and the absence of relation between the 200 bp fragment and the X-chromosome indicates that the male specific markers are specific to Y-chromosome. For the first time, a Y-chromosome specific molecular marker for a cyprinid has been identified, isolated, and characterized.

Comparative genome analysis of the primary sex-determining locus in salmonid fishes

We compared the Y-chromosome linkage maps for four salmonid species (Arctic charr, Salvelinus alpinus; Atlantic salmon, Salmo salar; brown trout, Salmo trutta; and rainbow trout, Oncorhynchus mykiss) and a putative Y-linked marker from lake trout (Salvelinus namaycush). These species represent the three major genera within the subfamily Salmoninae of the Salmonidae. The data clearly demonstrate that different Y-chromosomes have evolved in each of the species. Arrangements of markers proximal to the sex-determining locus are preserved on homologous, but different, autosomal linkage groups across the four species studied in detail. This indicates that a small region of DNA has been involved in the rearrangement of the sex-determining region. Placement of the sex-determining region appears telomeric in brown trout, Atlantic salmon, and Arctic charr, whereas an intercalary location for SEX may exist in rainbow trout. Three hypotheses are proposed to account for the relocation: translocation of a small chromosome arm; transposition of the sex-determining gene; or differential activation of a primary sex-determining gene region among the species.

Genetic mapping of Y-chromosomal DNA markers in Pacific salmon

Sex chromosomes in fish provide an intriguing view of how sex-determination mechanisms evolve in vertebrates. Many fish species with single-factor sex-determination systems do not have cytogenetically-distinguishable sex chromosomes, suggesting that few sex-specific sequences or chromosomal rearrangements are present and that sex-chromosome evolution is thus at an early stage. We describe experiments examining the linkage arrangement of a Y-chromosomal GH pseudogene (GH-Y) sequence in four species of salmon (chum, Oncorhynchus keta; pink, O. gorbuscha; coho, O. kisutch; chinook, O. tshawytscha). Phylogenetic analysis indicates that GH-Y arose early in Oncorhynchus evolution, after this genus had diverged from Salmo and Salvelinus. However, GH-Y has not been detected in some Oncorhynchus species (O. nerka, O. mykiss and O. clarki), consistent with this locus being deleted in some lineages. GH-Y is tightly linked genetically to the sex-determination locus on the Y chromosome and, in chinook salmon, to another Y-linked DNA marker OtY1. GH-Y is derived from an ancestral GH2 gene, but this latter functional GH locus is autosomal or pseudoautosomal. YY chinook salmon are viable and fertile, indicating the Y chromosome is not deficient of vital genetic functions present on the X chromosome, consistent with sex chromosomes that are in an early stage of divergence.