Lessons learned and remaining uncertainties
The lack of XY-gametologous loci in DArT SNPs in either perch species
and other fish with homomorphic sex chromosomes (Nguyen et al., 2021)
suggests that approaches other than reduced-representation sequencing
may be required to identify sex-linked loci in systems with young sex
chromosomes. Methylation-sensitive approaches, such as DArTseq, will
also have low power in detecting cis-regulatory regions that play a role
of sex-determining loci, because these regions might be methylated in
adults. Successful detection of a short XY-gametologous locus in
Macquarie perch using WGS data also implies that lack of sex-linked
markers in reduced-representation data cannot be used as evidence for
lack of sex chromosomes in a species. Acquiring WGS data for known-sex
samples from other populations will be crucial for improving our
understanding of sex determination in this and other percichthyid
species. The set of 22 Macquarie perch loci with male-specific alleles
(including eight XY-gametologous loci; Fig. 1) may not have the power to
predict the genotypic or phenotypic sex in some populations of Macquarie
perch, due to fast sex chromosome turnover and/or presence of
environmental sex-reversal. At least some of these loci appear to be
autosomally-inherited in golden perch, and in more distant relatives
from the family Percichthyidae (Murray cod and trout cod), suggesting
independent evolution of the Macquarie perch sex-determining locus.
However, these properties make these markers a great resource for
studying sex chromosome turnover across populations and species.
Whilst SOX1b appears to be a promising novel candidate
sex-determining gene, it is possible that we missed other important
sex-linked regions due to the highly repetitive nature of the fish
genomes precluding efficient short-read mapping, or due to our draft
genome missing relevant loci. Alternatively, polygenic sex-determination
in Macquarie perch is possible, given the many sex-linked loci detected
and some clustering of sex-specific alleles in scaffolds other than 633.
In sea bass Dicentrarchus labrax at least four loci are
associated with sex determination (Palaiokostas et al., 2015). Also,
both XY and ZW sex-determining systems are present on different
chromosomes in some Metriaclima cichlids, with epistasis between
genotypes at two loci controlling sex (Ser, Roberts, & Kocher, 2010).
Three alleles (X, Y, and W) segregate at the sex-determination locus and
interact in platyfish Xiphophorus maculatus (Schultheis et al.,
2009). Structural genomic variation can also play a major role in
adaptation, speciation and sex determination (Mérot, Oomen, Tigano, &
Wellenreuther, 2020; Natri et al., 2019), and the role of sex-linked
deletions and other structural variants in sex determination of
Macquarie perch and other percichthyids remains to be clarified
(Appendix H).