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较大难度时，基因型性别鉴定检测可为鱼类种群研究提供极具价值的研究信息。本文详述了一款TaqMan®检测试剂盒（Ots_SexID）的开发过程，该试剂盒用于鉴定从萨克拉门托河采集、于利文斯顿斯通国家鱼类孵化场繁育的冬洄游奇努克鲑（Winter-Run Chinook salmon）的基因型性别。该TaqMan®检测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年于利文斯顿斯通国家鱼类孵化场繁育的84尾冬洄游奇努克鲑（样本量n=84）的基因型性别分型结果，与繁育过程中记录的表型性别进行比对，评估了该分子标记的鉴定准确性。在84尾受试个体中，有83尾的基因型性别与通过Ots_SexID鉴定得到的表型性别完全吻合，这表明该检测试剂盒可用于预测表型性别，准确率约为99%。为评估该TaqMan®检测在该物种分布范围其他区域的应用效能，我们对从阿拉斯加到加利福尼亚的29个其他种群的采集样本开展了检测分析。基于该检测得到的性别分型结果通常与观测到的表型相符，但也存在部分显著例外情况。上述研究结果表明，这款新型检测试剂盒对萨克拉门托河冬洄游奇努克鲑种群具备极高的应用价值，但同时也凸显了在目标应用种群中，对任意一款性别鉴定检测开展全面验证的重要性。