Identification of sex-linked SNP markers in wild populations of monomorphic birds

Abstract

Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. SNPs could also be useful for sexing individuals in species with reduced sexual dimorphism, yet this possibility remains poorly explored. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they are heterozygotic for the Z-linked SNP and females when they are homozygote for the Z-linked SNP and have the W-linked SNP. We validated the method in the Jackdaw (Corvus monedula), a species whose reduced sexual dimorphism makes it difficult to sex individuals in the wild. We assessed the reliability of the method with 36 individuals of known sex, and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need of additional sexing techniques.

Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals

“…Identifying sex chromosomes can be achieved by looking for loci that are present on only one of the sex chromosomes (Gautier, 2014;Stovall et al, 2018;Feron et al, 2021;Garcia-Raventós et al, 2023), or by looking at heterozygosity and differentiation between sexes at homologous loci (e.g. Berset-Brändli et al, 2006;Brelsford et al, 2017;Käfer et al, 2021;Hearn et al, 2022; see also Pyne et al, 2022 for an association study).…”

Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals

“…These values should be interpreted as rough estimates because they depend on sample size (number of sexed individuals), methodology (conservative threshold set by our simulations to decide whether a locus is sex-linked), and XY polymorphism. Also, they do not consider the potential genome sequences present only on the X or only on the Y (not investigated in this study, see Gautier, 2014;Feron et al, 2021;Garcia-Raventós et al, 2023). Moreover, further analyses are needed to reveal i) if repeated elements are involved in the length of the Y chromosome, and ii) the position of sex-linked RAD-loci within each scaffold.…”

“…Identifying sex chromosomes can be achieved by looking for loci that are present on only one of the sex chromosomes (Gautier, 2014;Stovall et al, 2018;Feron et al, 2021;Garcia-Raventós et al, 2023), or by looking at heterozygosity and differentiation between sexes at homologous loci (e.g. Berset-Brändli et al, 2006;Brelsford et al, 2017;Käfer et al, 2021;Hearn et al, 2022; see also Pyne et al, 2022 for an association study).…”