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 of Winter-Run Chinook salmon collected from the Sacramento River and spawned at the Livingston Stone National Fish Hatchery. The TaqMan® assay targets a region previously examined in the growth hormone pseudogene. 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. 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 sex identification assay prior to application in a population of interest.

当表型性别鉴定存在困难时，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。本研究详述了一款名为Ots_SexID的TaqMan®检测体系的开发流程，该体系用于鉴定从萨克拉门托河采集、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鱼的基因型性别。该TaqMan®检测体系靶向此前在生长激素假基因中被研究过的基因组区域。通过将2012年在利文斯顿·斯通国家鱼类孵化场繁育的奇努克鲑鱼（样本量n=84）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，评估了该检测标记的准确性。结果显示，84尾受试个体中有83尾的基因型性别与通过Ots_SexID鉴定的表型性别完全吻合，表明该检测体系可用于预测表型性别，准确率约为99%。为评估该TaqMan®检测体系在该物种分布范围内其他区域的应用价值，我们对采自阿拉斯加州至加利福尼亚州的29个其他种群的样本进行了检测。基于该检测体系的性别判定结果与观测到的表型性别总体一致，但存在若干显著例外案例。上述结果表明，该新型检测体系在萨克拉门托河冬洄游奇努克鲑鱼种群中具备极高的应用潜力，但同时也强调，在将任一性别鉴定检测体系应用于目标种群前，开展全面验证的重要性。