Data from: Development of a Chinook salmon sex identification SNP assay based on the growth hormone pseudogene

Genotypic sex identification assays can provide valuable information about fish populations when phenotypic sex determination is difficult. Here we describe the development of a TaqMan® assay (Ots_SexID) designed to identify the genotypic sex by targeting a region previously examined in the growth hormone pseudogene for Winter-Run Chinook salmon (Oncorhynchus tshawytscha) collected from the Sacramento River and spawned at the Livingston Stone National Fish Hatchery. Accuracy of the marker was assessed by comparing genotypic sex assignments for Chinook salmon spawned at Livingston Stone National Fish hatchery in 2012 (n = 84) to phenotypic sex recorded during spawning. Genotypic sex was observed to be concordant with phenotypic sex identified using Ots_SexID in 83/84 individuals, suggesting that the assay could be used to predict phenotypic sex with ~99% accuracy. To evaluate the utility of the TaqMan® assay in other parts of the species’ range, we examined collections from 29 other populations ranging from Alaska to California. Genotypic sex assignments based on the assay were generally concordant with observed phenotypes, but there were some strong exceptions. These results suggest that the new assay will be very useful in Sacramento River Winter-Run Chinook salmon, but also highlight the importance of thoroughly testing any genotypic sex identification assay prior to application in a population of interest.

当表型性别鉴定难以开展时，基因型性别鉴定检测可为鱼类种群研究提供极具价值的信息。本研究描述了一款名为Ots_SexID的TaqMan®检测方法的开发过程，该方法通过靶向此前针对萨克拉门托河种群、并在利文斯顿·斯通国家鱼类孵化场繁育的冬洄游奇努克鲑（Oncorhynchus tshawytscha）生长激素假基因中检测过的区域，实现基因型性别鉴定。通过将2012年于利文斯顿·斯通国家鱼类孵化场繁育的84尾奇努克鲑的基因型性别判定结果，与繁育过程中记录的表型性别进行比对，评估了该标记的准确性。在84尾个体中，有83尾的基因型性别与Ots_SexID检测得到的表型性别一致，表明该检测方法可用于预测表型性别，准确率约为99%。为评估该TaqMan®检测方法在该物种分布区内其他区域的适用性，我们对从阿拉斯加到加利福尼亚州的29个其他种群的样本进行了检测。基于该检测方法的基因型性别判定结果与观测到的表型总体上一致，但也存在部分显著例外情况。上述结果表明，这款新型检测方法对萨克拉门托河冬洄游奇努克鲑种群极具应用价值，但同时也凸显出：在将任意基因型性别鉴定检测方法应用于目标种群前，开展全面验证的重要性。