Genetic sex assignment in wild populations using genotyping-by-sequencing data: A statistical threshold approach

Area of Science:

• Genetics
• Wildlife Biology
• Bioinformatics

Background:

• Determining sex in wild populations is often difficult and requires genetic analysis.
• Reduced-representation DNA sequencing (RRS) methods like genotyping-by-sequencing (GBS) allow large-scale genetic data analysis.

Purpose of the Study:

• To develop and validate a novel computational pipeline for discovering and statistically validating sex-specific genetic loci from GBS data.
• To accurately assign sex to individuals of unknown sex in silico and develop a PCR-based method for independent sex ascertainment.

Main Methods:

• Genotyping-by-sequencing (GBS) was used to genotype 166 New Zealand fur seals of known sex.
• A sex-specific locus threshold (SSLT) and sex-assignment threshold (SSAT) were developed to identify and assign sex based on male-specific loci.
• A panel of three sex-specific PCR primers was designed from validated loci.

Main Results:

• The pipeline achieved high accuracy in sex assignment (98.9% for females, 95.8% for males) via cross-validation.
• Sex was assigned to 86 individuals of unknown sex.
• Developed PCR primers reliably amplified sex-specific loci in at least two other pinniped species.

Conclusions:

• Utilizing normally discarded monomorphic loci from SNP datasets is an effective strategy for identifying robust sex-linked markers in non-model species.
• The novel pipeline provides a robust method for identifying and validating sex-specific markers across various species and RRS datasets.