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

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.

解析并鉴定调控性别决定的遗传机制，对于物种管理具有重要意义，尤其在受开发利用的鱼类类群中，性别偏向性捕捞可能对种群动态与物种长期存续产生负面影响，这一点尤为突出。太平洋庸鲽（Hippoglossus stenolepis）是北太平洋重要的渔业捕捞对象。当前科研人员通过生长曲线估算年度捕捞群体中雌雄个体的占比，但遗传技术有望提供更为精准的估算方法。本研究采用限制性酶切位点相关DNA（Restriction-site Associated DNA, RAD）测序技术，基于雌雄个体间的遗传分化系数（Fixation Index, FST）筛选得到与遗传性别相关的RAD标记。将筛选获得的RAD标记比对至大西洋庸鲽（Hippoglossus hippoglossus）连锁图谱、大菱鲆（Scophthalmus maximus）基因组以及半滑舌鳎（Cynoglossus semilaevis）基因组，以定位潜在参与性别决定的基因组区域。本研究共筛选得到56个与性别相关的RAD标记，涵盖70个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，其中3个RAD标记仅在雌性个体中被检测到。上述性别连锁位点可比对至大西洋庸鲽的3个连锁群（LG07：7个位点、LG15：1个位点、LG24：1个位点）、大菱鲆的3条染色体（LG12：13个位点、LG01：1个位点、LG05：1个位点）以及半滑舌鳎的1条染色体（ChrZ：9个位点）。本研究结果支持"太平洋庸鲽的遗传性别由ZW型性别决定系统调控"这一假说。研究团队进一步将2个性别连锁位点开发为性别鉴定检测体系，并通过已完成形态学性别鉴定的个体对其检测效能进行验证。相较于形态学性别鉴定结果，单个检测体系的鉴定准确率可达97.5%。