Identification of Genomic Regions Associated With Sex in Pacific Halibut

Abstract

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 3 RAD-tags were identified in only females. Sex-linked loci aligned to 3 linkage groups in the Atlantic halibut (LG07: 7 loci, LG15: 1 locus, and LG24: 1 locus), 3 chromosomes in the turbot (LG12: 13 loci, LG01: 1 locus, and LG05: 1 locus), and 1 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.

RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data

“…RAD-Seq generates short sequences for a small but consistent fraction of the genome and thus allows the sequencing and comparison of multiple individuals from several populations at relatively low cost (Davey et al, 2011) and without requiring additional genomic resources. RAD-Seq has been successfully used to identify sex-specific sequences in non-model species from diverse taxa, including fish (Drinan, Loher, & Hauser, 2018) , amphibians (Bewick et al, 2013) , non-avian reptilia (Gamble, 2016;Gamble et al, 2017Gamble et al, , 2015Gamble et al, , 2018Gamble & Zarkower, 2014;S. V. Nielsen, Banks, Diaz, Trainor, & Gamble, 2018;Stuart V. Nielsen, Daza, Pinto, & Gamble, 2019) , invertebrates (Carmichael et al, 2013;Mathers et al, 2015;Pratlong et al, 2017) , and plants (Kafkas, Khodaeiaminjan, Güney, & Kafkas, 2015) , and to identify the sex chromosomes and the sex locus in some of these species (Wilson et al, 2014) .…”

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

“…The F ST outlier analysis identified eight SNPs potentially under sex‐related selection, with one SNP having a deficit of homozygous individuals for the minor allele, which might indicate that it is deleterious for its carrier. Furthermore, even the largest F ST value (0.06) was much smaller than the threshold value 0.3 used by Drinan et al (2018) for identifying SNPs under selection. Comparison with the starry ray genome indicated the locations of six of these SNPs on different chromosomes.…”

“…The proportion of heterozygous individuals might differ between sexes for taxa with sex-determining genes spread throughout the genome (type 3 in Table 1). SNPs with significantly different allele frequencies between the two sexes have been detected using the fixation index F ST (Benestan et al, 2017;Drinan et al, 2018;Galindo et al, 2011). In this case, the F ST is defined as the relative difference between the average expected heterozygosity of the two sexes given their respective allele frequencies and the expected heterozygosity ignoring sex.…”

“…The type 1 pattern was found for salmon louse (Carmichael et al, 2013), while the type 2 pattern was identified for rockfishes (Fowler & Buonaccorsi, 2016), a lizard (Gamble & Zarkower, 2014) and fur seal (Stovall et al, 2018). Drinan, Loher, and Hauser (2018) found SNPs of type 1 and type 2 in Pacific halibut.…”

“…Validation of sex‐linked loci can be achieved in several ways: (a) cross‐validation using part of the data set used for identifying sex‐linked loci and/or (b) predicting sex for an independent sample with morphologically determined sex. Certain authors have also developed specific assays for DNA sequences including the putative sex‐linked identified SNPs and then used them to identify the sex for an independent sample to be compared with morphologically determined sex (Carmichael et al, 2013; Drinan et al, 2018; Shi et al, 2018; Suda et al, 2019; Utsunomia et al, 2017).…”