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 s...可用于鲑鱼性别筛查的基因座，可为野生与养殖种群的研究提供重要参考信息。本研究基于测序分型（genotyping-by-sequencing，GBS）数据集所包含的数千个基因座，开展性别与基因型的关联分析，以发掘红大麻哈鱼（Oncorhynchus nerka）的性别关联基因座。本研究共鉴定出7个性别关联基因座，针对其中2个开发了高通量检测方法，并在北美全域采样的8个红大麻哈鱼种群中验证了这两种检测方法的应用效能。此外，本研究还利用基于鲑鱼主性别决定基因sdY的现有检测方法，对上述种群进行了筛查。基于GBS得到的基因座进行表型性别判定的准确率在不同种群间存在显著差异，这表明本研究发掘的基因座与性别决定基因之间已发生重组。采用sdY检测方法进行性别判定的准确率显著更高，但仍未达到100%。对……的序列比对