Data from: Identification and characterization of sex-associated loci in sockeye salmon using genotyping-by-sequencing and comparison with a sex-determining assay based on the sdY gene

Loci that can be used to screen for sex in salmon can provide important information for study of both wild and cultured populations. Here, we tested for associations between sex and genotypes at thousands of loci available from a genotyping-by-sequencing (GBS) dataset to discover sex-associated loci in sockeye salmon (Oncorhynchus nerka). We discovered seven sex-associated loci, developed high-throughput assays for two loci, and tested the utility of these two assays in eight collections of sockeye salmon sampled throughout North America. We also screened an existing assay based on the master sex-determining gene in salmon (sdY) in these collections. The ability of GBS-derived loci to assign fish to their phenotypic sex varied substantially among collections suggesting that recombination between the loci that we discovered and the sex-determining gene has occurred. Assignment accuracy to phenotypic sex was much higher with the sdY assay but was still less than 100%. Alignment of sequences from GBS-derived loci to draft genomes for two salmonids provided strong evidence that many of these loci are found on the chromosome orthologous to the known sex chromosome in sockeye salmon. Our study is the first to describe the approximate location of the sex-determining region in sockeye salmon and indicates that sdY is also the master sex-determining gene in this species. However, discordances between sdY genotypes and phenotypic sex and the variable performance of GBS-derived loci warrant more research.

可用于鲑鱼性别鉴定的基因座，可为野生与养殖种群的相关研究提供关键信息。本研究基于测序分型（genotyping-by-sequencing, GBS）数据集的数千个基因座，开展性别与基因型的关联分析，以筛选红大马哈鱼（Oncorhynchus nerka）的性别相关基因座。本研究共筛选得到7个性别相关基因座，针对其中2个基因座开发了高通量检测方法，并在北美全域采样的8个红大马哈鱼种群中验证了这两种检测方法的实用性。此外，本研究还针对上述种群，开展了基于鲑鱼主性别决定基因sdY（master sex-determining gene）的现有检测体系的筛查实验。基于GBS得到的基因座对红大马哈鱼表型性别的鉴定准确率在不同种群间存在显著差异，提示本研究筛选得到的基因座与性别决定基因之间已发生重组。采用sdY检测体系得到的表型性别鉴定准确率显著更高，但仍未达到100%。将GBS得到的基因座序列比对至两种鲑科鱼类的基因组草图后，结果显示其中多数基因座位于与红大马哈鱼已知性染色体同源的染色体上，该结论具备较强证据支持。本研究首次明确了红大马哈鱼性别决定区域的大致位置，并证实sdY同样是该物种的主性别决定基因。但sdY基因型与表型性别之间存在的不一致现象，以及GBS得到的基因座检测性能的不稳定性，仍需开展更多研究。