Transmission ratio distortion (TRD) is the preferential transmission of one specific allele to offspring at the expense of the other. The existence of TRD is mostly explained by the segregation of genetic variants with deleterious effects on the developmental processes that go from the formation of gametes to fecundation and birth. A few years ago, a statistical methodology was implemented in order to detect TRD signals on a genome-wide scale as a first step toward uncovering the biological basis of TRD and reproductive success in domestic species. In the current work, we have analyzed the impact of SNP calling quality on the detection of TRD signals in a population of Murciano–Granadina goats. Seventeen bucks and their offspring (N = 288) were typed with the Goat SNP50 BeadChip, whereas the genotypes of the dams were lacking. Performance of a genome-wide scan revealed the existence of 36 SNPs showing significant evidence of TRD. When we calculated GenTrain scores for each of the SNPs, we observed that 25 SNPs showed scores below 0.8. The allele frequencies of these SNPs in the offspring were not correlated with the allele frequencies estimated in the dams with statistical methods, providing evidence that flawed SNP calling quality might lead to the detection of spurious TRD signals. We conclude that, when performing TRD scans, the GenTrain scores of markers should be taken into account to discriminate SNPs that are truly under TRD from those yielding spurious signals owing to technical problems.

中文翻译：

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具有低 GenTrain 分数的标记物会在全基因组扫描中产生虚假信号，导致传输率失真

传输比失真 (TRD) 是一种特定等位基因以牺牲另一种为代价优先传输给后代。TRD 的存在主要是通过遗传变异的分离来解释的，这些变异对从配子形成到受精和出生的发育过程具有有害影响。几年前，为了在全基因组范围内检测 TRD 信号，实施了一种统计方法，这是揭示 TRD 的生物学基础和国内物种繁殖成功的第一步。在当前的工作中，我们分析了 SNP 调用质量对 Murciano-Granadina 山羊种群中 TRD 信号检测的影响。十七块钱和他们的后代（N = 288) 使用山羊 SNP50 BeadChip 进行分型，而缺乏水坝的基因型。全基因组扫描的性能揭示了 36 个 SNP 的存在，显示了明显的 TRD 证据。当我们计算每个 SNP 的 GenTrain 分数时，我们观察到 25 个 SNP 的分数低于 0.8。后代中这些 SNP 的等位基因频率与使用统计方法估计的母猪中的等位基因频率无关，这提供了有缺陷的 SNP 调用质量可能导致检测到虚假 TRD 信号的证据。我们得出的结论是，在执行 TRD 扫描时，应考虑标记的 GenTrain 分数，以将真正处于 TRD 之下的 SNP 与由于技术问题产生虚假信号的 SNP 区分开来。