Data from: Identification of genomic regions associated with sex in Pacific halibut

• Main Authors: Drinan, Daniel P., Loher, Timothy, Hauser, Lorenz
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2017
• Subjects: RAD; Conservation genetics and biodiversity; Pacific halibut; genomics and gene mapping; Comparative genomics; sex determination; Sex Identification; Scophthalmus maximus; Turbot
• Online Access: https://doi.org/10.5061/dryad.ff072

Understanding and identifying the genetic mechanisms responsible for sex-determination are important for species management, particularly in exploited fishes where sex biased harvest could have implications on population dynamics and long-term persistence. The Pacific halibut (Hippoglossus stenolepis) supports important fisheries in the North Pacific Ocean. The proportion of each sex in the annual harvest is currently estimated using growth curves, but genetic techniques may provide a more accurate method. We used restriction-site associated DNA (RAD) sequencing to identify RAD-tags that were linked to genetic sex, based on differentiation (FST) between the sexes. Identified RAD-tags were aligned to the Atlantic halibut (Hippoglossus hippoglossus) linkage map, the turbot (Scophthalmus maximus) genome, and the half-smooth tongue sole (Cynoglossus semilaevis) genome to identify genomic regions that may be involved in sex determination. In total, 56 RAD-tags (70 single nucleotide polymorphisms) were linked to sex, and three RAD-tags were identified in only females. Sex-linked loci aligned to three linkage groups in the Atlantic halibut (LG07: 7 loci, LG15: 1 locus, and LG24: 1 locus), three chromosomes in the turbot (LG12: 13 loci, LG01: 1 locus, and LG05: 1 locus), and one chromosome in the half-smooth tongue sole (ChrZ: 9 loci). Results add support to the hypothesis that Pacific halibut genetic sex is determined in a ZW system. Two sex-linked loci were further developed into sex identification assays, and their efficacy was tested on individuals that had been morphologically sexed. The accuracy of each assay on its own was 97.5% compared to morphological sex. halibut_genepop File containing all genotypes. File in Genepop format. Locus names are formatted with an underscore between the RADtag name and SNP position. supplemental_material_199_sex_assays Results of two TaqMan assays linked to sex. supplemental_material_primers_and_probes Primer and probe sequences for TaqMan assays. ...