Sex‐determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) F_ST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays (Raja clavata). Using method (a), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).

中文翻译：

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鉴定和解释性连锁 SNP 标记和进行性别分配的方法：对刺背鳅（Raja clavata）的应用。

许多物种的性别决定模式仍然未知，特别是在鱼类中，其中已经报道了多种模式。此外，对于没有外部性别属性的物种或生命早期阶段，非侵入性个体性别鉴定是有问题的，当性染色体或性相关标记已被表征时，需要进行细胞遗传学或分子分析。基因组学现在提供了实现这一目标的方法。在这里，我们回顾了常见的性别决定系统和相应的统计方法，用于识别性连锁遗传标记及其在性别分配中的用途，重点关注源自简化表示测序方法的单核苷酸多态性 (SNP) 标记。我们证明了预期性别分配误差对性连锁 SNP 数量和次要等位基因频率的依赖性。两种性别之间的F _ST异常值分析和 (c) 神经元网络建模。这些方法被应用于 1680 条刺背鳐（Raja clavata）的大型 SNP 数据集（4604 个 SNP ）。使用方法 (a)，鉴定了 19 个假定的性相关 SNP。与相关物种 ( Amblyraja radiata )的参考基因组进行比较表明，所有 19 个 SNP 可能位于同一条染色体上。这些结果表明 thornback ray 具有 XX/XY 性别决定系统。方法 (b) 鉴定了可能位于不同染色体上的八个 SNP。方法 (a) 导致三种方法中的性别分配错误最低（女性错误率为 4.2%，男性错误率为 3.7%）。