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

Abstract

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.

Keywords: Atlantic salmon; SNP; autosome; evolution; pseudo-gene; sdY; sex; sex chromosome.

FIGURE 1

Phenotypic sex frequencies distribution across the 64 studied families showing PCR-based sdY genetic sex concordances. Concordant males and females are displayed in blue and orange, respectively. Discordant females (sdY positive phenotypic females) are shown in dark gray.

FIGURE 2

Real time PCR based fold change (FC) values for sdY exon2 and exon4 amplicons. (A) Validation RT PCR using XY males and YY super-males; round and square dots, respectively. (B) Parental individuals for the F1-K2012 families showing 1–2× sdY sires individuals, in blue, and the 1× sdY discordant dam in orange. Reference 1× sdY males are displayed in gray. (C) Example plate showing 1–3× sdY males and 1–2× sdY females in blue and orange, respectively, among the offspring. Reference males not displayed.

FIGURE 3

Conceptual diagram showing the inheritance model and the observed frequencies for the offspring of crosses with one parental individual carrying an sdY pseudocopy. (A) Cross between a 1× sdY phenotypic male and a 1× sdY discordant female denoted with ^∗. (B) conceptual diagram showing the inheritance model at a chromosome level. Sex chromosomes and autosomes are represented in dark blue and dark orange, respectively. Normal 1× sdY male (left) carrying a copy of the sex determining sdY gene (yellow) in the Y chromosome. Discrepant 1× sdY phenotypic female (right) carrying an sdY autosomic pseudocopy (dark gray) in heterozygosis. (C) Males and females expected proportions for the different sdY genotypes (1–2×). (D) Offspring observed proportions for the affected families of 1× and 2× sdY males and 0× and 1× sdY females: light blue, blue, light orange and orange, respectively. Dotted lines represent the sdY genotype expected frequencies.

FIGURE 4

Conceptual diagram showing the inheritance model and the observed frequencies for the offspring of crosses with both parental individuals carrying an sdY pseudocopy. (A) Cross between a 2× sdY phenotypic male and a 1× sdY discordant female: Both affected parental individuals are denoted with an asterisk. (B) Conceptual diagram showing the inheritance model at a chromosome level. Sex chromosomes and autosomes are represented in dark blue and dark orange, respectively. (B) 2× sdY male (left) carrying a copy of the sex determining sdY gene (yellow) in the Y chromosome and the extra autosomic copy (dark gray) in heterozygosis. Discrepant 1× sdY phenotypic female (right) carrying an sdY autosomic pseudocopy (dark gray) in heterozygosis. (C) Males and females expected proportions for the different sdY genotypes (1–3×). (D) Offspring observed proportions for the affected families of 1–3× sdY males and 0–2× sdY females: light blue, blue, dark blue, light orange, orange, and dark orange, respectively. Dotted lines represent the sdY genotype expected frequencies.