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)’.

Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosome

Autosomal origins of heterogametic sex chromosomes have been inferred frequently from suppressed recombination and gene degeneration manifested in incompletely differentiated sex chromosomes. However, the initial transition of an autosome region to a proto-sex locus has been not explored in depth. By assembling and analyzing a chromosome-level draft genome, we found a recent (evolved 0.26 million years ago), highly homologous, and dmrt1 containing sex-determination locus with slightly reduced recombination in large yellow croaker (Larimichthys crocea), a teleost species with genetic sex determination (GSD) and with undifferentiated sex chromosomes. We observed genomic homology and polymorphic segregation of the proto-sex locus between sexes. Expression of dmrt1 showed a stepwise increase in the development of testis, but not in the ovary. We infer that the inception of the proto-sex locus involves a few divergences in nucleotide sequences and slight suppression of recombination in an autosome region. In androgen-induced sex reversal of genetic females, in addition to dmrt1, genes in the conserved dmrt1 cluster, and the rest of the sex determination network were activated. We provided evidence that broad functional links were shared by genetic sex determination and environmental sex reversal.

Sex chromosome and sex locus characterization in the goldfish, Carassius auratus

BackgroundGoldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. We used sequencing approaches to better characterize sex determination and sex-chromosomes in goldfish.ResultsOur results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18°C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (∼11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the goldfish amh gene or its 5 kb proximal promoter sequence.ConclusionsThese results show that goldfish have a relatively large sex locus on LG22, which is likely the goldfish Y chromosome. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers in goldfish, which will be important for future research on sex determination and aquaculture applications in this species.

The genetic basis of sex determination in grapevines (Vitis spp.)

Sex determination in grapevine evolved through a complex succession of switches in sexual systems. Phased genomes built with single molecule real-time sequencing reads were assembled for eleven accessions of cultivated hermaphrodite grapevines and dioecious males and females, including the ancestor of domesticated grapevine and other related wild species. By comparing the phased sex haplotypes, we defined the sex locus of the Vitis genus and identified polymorphisms spanning regulatory and coding sequences that are in perfect association with each sex-type throughout the genus. These findings identified a novel male-fertility candidate gene, INP1, and significantly refined the model of sex determination in Vitis and its evolution.

Genomic landscape of reproductive isolation in Lucania killifish: The role of sex chromosomes and salinity

ABSTRACTUnderstanding how speciation occurs and how reproductive barriers contribute to population structure at a genomic scale requires elucidating the genetic architecture of reproductive isolating barriers. In particular, it is crucial to determine if loci underlying reproductive isolation are genetically linked or if they are located on sex chromosomes, which have unique inheritance and population genetic properties. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are closely related species that have diverged across a salinity gradient and are reproductively isolated by assortative mating, hybrid male infertility, viability of hybrid offspring at high salinities, as well as reduced overall fitness of F2 offspring and backcrosses to L. goodei. We conducted QTL mapping in backcrosses between L. parva and L. goodei to determine the genetic architecture of sex determination, mate attractiveness, fertility, and salinity tolerance. We find that the sex locus appears to be male determining and located on a chromosome that has undergone a Robertsonian fusion in L. parva relative to L. goodei. We find that the sex locus on the fused chromosome is involved in several genomic incompatibilities, which affect the survival of backcrossed offspring. Among the backcrossed offspring that survived to adulthood, we find that one QTL for male attractiveness to L. goodei females is closely linked to this sex locus on chromosome 1. Males homozygous for L. goodei alleles at the sex locus laid more eggs with L. goodei females. QTL associated with salinity tolerance were spread across the genome but did not tend to co-localize with reproductive isolation. Thus, speciation in this system appears to be driven by reinforcement and indirect selection against hybrids rather than direct natural selection for salinity tolerance. Our work adds to growing evidence that sex chromosome evolution may contribute to speciation.

Development and Characterization of Molecular Markers Associated with Female Plants in Muscadine Grape

Muscadine (Vitis rotundifolia Michx.) vines may be male (M), female (F), or hermaphroditic (H). Male flowers have only filaments and anthers, whereas female and hermaphroditic flowers are morphologically perfect. Female flowers are distinguished from hermaphroditic flowers by their reflexed stamens (as opposed to upright) and nonfunctional pollen. Primers derived from previously identified candidate genes located at the sex locus of Vitis vinifera L. were used to generate amplicons from M, F, and H muscadine cultivars. Sequence analysis of the amplicons revealed insertion/deletion (indel) polymorphisms in a trehalose-6-phosphate phosphatase (TPP) gene (VR006) and a WRKY transcription factor 21 gene (VR009). Primers were designed to create diagnostic markers for each indel polymorphism. Associations between the marker alleles and the plant sex trait were examined in a wide range of muscadine germplasm and in segregating populations derived from F × H, F × M, and H × H crosses. VR006 produced a codominant marker that was able to differentiate the female-associated allele from the male- and hermaphroditic-associated alleles. The marker was able to detect female plants and will be suitable for screening breeding program progenies. VR009 was able to detect the presence of the female allele in most germplasm, but a crossover event appears to have separated the marker from the sex locus in some germplasm. As shown in previous muscadine genetic studies, H × H-derived populations produced male seedlings. Marker analysis of these populations indicates that male flowers only occur in seedlings which are heterozygous for F- and H-associated marker alleles and inheritance of flower type in muscadine remains unclear.