Methods for identifying and interpreting sex‐linked SNP markers and carrying out sex assignment: application to thornback ray (Raja clavata)

Trenkel, Verena M.; Boudry, Pierre; Verrez‐Bagnis, Véronique; Lorance, Pascal

doi:10.1111/1755-0998.13225

Cited by 18 publications

(21 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Section: Discussionmentioning

confidence: 99%

“…This suggests that the genomic regions that are identified using a GWAS or similar method are not enough to assign sex to individuals. However, the number of SNPs controlling sex and specific genetic architecture of sex determination most likely have a large influence on this finding (Trenkel et al 2020), but nonetheless these results have implications for conservation and field work. Studies may use the results from investigations of sex determination for the assignment of sex for unknown individuals (Galindo et al 2011, Trenkel et al 2020, Mussmann et al 2021; we recommend that the predictive power of sex associated markers be explicitly evaluated before those markers are used to determine sex of un-sexed individuals, especially when this information may be used for conservation decisions.…”

Section: Linking Genomics To Sex Assignmentsmentioning

confidence: 98%

See 1 more Smart Citation

Identification of sex-determining loci in hybridizing Catostomus fish species

Pyne

McFarlane

Mandeville

2022

Preprint

View full text Add to dashboard Cite

Despite the near-universality of gonochorism (separate sexes) in eukaryotic organisms, the underlying mechanisms of sex determination are poorly understood and highly variable in some taxa. In hybridizing species, sex determination mechanisms may promote or impede reproductive isolation depending on whether mechanisms are similar between species. In Catostomus fishes, contemporary hybridization is variable and extensive. In the present study, we aim to describe the genetic basis of sex determination in bluehead (Catostomus discobolus) and white suckers (Catostomus commersonii) to understand the impact of sex determination on reproductive isolation. We used genotyping-by-sequencing genomic data from Catostomus species and their hybrids to identify regions of the genome associated with sex using a genome-wide association study and the identification of sex-specific loci. We found a genetic basis of sex determination in Catostomus fishes, with a region of the genome significantly associating with sex in bluehead suckers. This region is suggestive of a master sex-determining region in bluehead suckers but is not significant in white suckers, implying that either the sex-determining region of the genome differs in these two species that hybridize, or that sample size was insufficient to identify this genomic region in white suckers. By describing and comparing sex-determination systems across Catostomus fish species, we highlight the relationship between sex determining systems and hybridization in closely related fish species.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Linking Genomics To Sex Assignmentsmentioning

confidence: 98%

Identification of sex-determining loci in hybridizing Catostomus fish species

Pyne

McFarlane

Mandeville

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…BayeScan; Foll and Gaggiotti 2008) where the data is partitioned by sex (e.g. Benestan et al 2017;Trenkel et al 2020).…”

Section: Main Textmentioning

confidence: 99%

“…BayeScan; Foll and Gaggiotti 2008) where the data is partitioned by sex (e.g. Benestan et al 2017;Trenkel et al 2020).Many elasmobranchs (sharks and rays) are threatened with extinction (Dulvy et al 2014;Dulvy et al 2021). Their slow life history, low tness and low connectivity between populations, which is often male…”

mentioning

confidence: 99%

An R-based tool for identifying sex-linked markers from Restriction site-Associated DNA sequencing with applications to elasmobranch conservation

Devloo‐Delva

Gosselin

Butcher

et al. 2022

Preprint

View full text Add to dashboard Cite

Identifying sex-linked markers from genomic data has both theoretical and applied importance, especially in conservation. Yet, few methods and tools exist to detect such markers from Restriction-site-Associated DNA sequencing reads and even fewer tools can identify sex-linked markers from existing genotyped data. Here, we describe a new R function that can identify sex-linked markers in species with morphologically distinct sex chromosomes. We test the accuracy and speed of our function with an example dataset from a species of conservation concern, the White Shark, Carcharodon carcharias. We further compare our method against other approaches and find that our method detects more sex-linked markers that can be reliably mapped to reference genomes. Overall, we provide a conservation and fisheries-relevant tool that can reliably and efficiently assign sex from genetic data in species with a heterogametic sex and we demonstrate its utility by developing a sex-identification PCR test for White Sharks.

show abstract

“…See references for further details on how these approaches and techniques have been used. 1,Trenkel et al [2020]; 2,Dissanayake et al [2020]; 3, Rovatsos et al [2015]; 4, Deakin et al [2019]; 5, Hill et al [2018]; 6, 7, Antonio-Rubio et al [2015]; 8, Harlow [1996]; 9, Quinn et al [2007].…”

mentioning

confidence: 99%

Temperature-Induced Sex Reversal in Reptiles: Prevalence, Discovery, and Evolutionary Implications

Whiteley

Castelli

Dissanayake

et al. 2021

Sex Dev

View full text Add to dashboard Cite

Sex reversal is the process by which an individual develops a phenotypic sex that is discordant with its chromosomal or genotypic sex. It occurs in many lineages of ectothermic vertebrates, such as fish, amphibians, and at least one agamid and one scincid reptile species. Sex reversal is usually triggered by an environmental cue that alters the genetically determined process of sexual differentiation, but it can also be caused by exposure to exogenous chemicals, hormones, or pollutants. Despite the occurrence of both temperature-dependent sex determination (TSD) and genetic sex determination (GSD) broadly among reptiles, only 2 species of squamates have thus far been demonstrated to possess sex reversal in nature (GSD with overriding thermal influence). The lack of species with unambiguously identified sex reversal is not necessarily a reflection of a low incidence of this trait among reptiles. Indeed, sex reversal may be relatively common in reptiles, but little is known of its prevalence, the mechanisms by which it occurs, or the consequences of sex reversal for species in the wild under a changing climate. In this review, we present a roadmap to the discovery of sex reversal in reptiles, outlining the various techniques that allow new occurrences of sex reversal to be identified, the molecular mechanisms that may be involved in sex reversal and how to identify them, and approaches for assessing the impacts of sex reversal in wild populations. We discuss the evolutionary implications of sex reversal and use the central bearded dragon (Pogona vitticeps) and the eastern three-lined skink (Bassiana duperreyi) as examples of how species with opposing patterns of sex reversal may be impacted differently by our rapidly changing climate. Ultimately, this review serves to highlight the importance of understanding sex reversal both in the laboratory and in wild populations and proposes practical solutions to foster future research.

show abstract

Methods for identifying and interpreting sex‐linked SNP markers and carrying out sex assignment: application to thornback ray (Raja clavata)

Abstract: Sex-determination systems greatly vary between taxa and are generally classified as genetic, including monogenic or polygenic, or environmental. Genetic-based sex-determination systems have been characterized for a wide range of taxa, including plants

Cited by 18 publications

References 49 publications

Identification of sex-determining loci in hybridizing Catostomus fish species

Identification of sex-determining loci in hybridizing Catostomus fish species

An R-based tool for identifying sex-linked markers from Restriction site-Associated DNA sequencing with applications to elasmobranch conservation

Temperature-Induced Sex Reversal in Reptiles: Prevalence, Discovery, and Evolutionary Implications

Contact Info

Product

Resources

About