Jighly Abdulqader
AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, Victoria, Australia.
Mol Ecol. 2022 Feb;31(4):1021-1027. doi: 10.1111/mec.16313. Epub 2021 Dec 16.
The sequencing depth required to genotype autopolyploid populations is a very controversial topic. Different studies have adopted variable depth values without a clear guide on the optimal sequencing depth value. Many studies suggest high depth thresholds for different ploidies that may not be practical and substantially increase the overall genotyping cost for different projects. However, such conservative thresholds may not be required to achieve the most common research goals. In fact, some recent reports in the field of quantitative genetics found that much lower sequencing depth thresholds could achieve the same accuracy as high depth thresholds. In this manuscript, I discuss when researchers need to use stringent sequencing depth thresholds and when they can use more relaxed ones. I support my argument by calculating the probabilities of sampling different homologues at a given sequencing depth. I also discuss the uses and the uncertainty in calculating a continuous allelic dosage as the proportion of sequencing reads that hold the alternative allele, which is becoming a common method now in quantitative genetics to replace discrete dosage estimation.
对同源多倍体群体进行基因分型所需的测序深度是一个极具争议的话题。不同的研究采用了不同的深度值，却没有关于最佳测序深度值的明确指导。许多研究针对不同的倍性提出了较高的深度阈值，这些阈值可能并不实用，而且会大幅增加不同项目的总体基因分型成本。然而，实现最常见的研究目标可能并不需要如此保守的阈值。事实上，数量遗传学领域最近的一些报告发现，低得多的测序深度阈值能够达到与高深度阈值相同的准确性。在本手稿中，我讨论了研究人员何时需要使用严格的测序深度阈值，以及何时可以使用更为宽松的阈值。我通过计算在给定测序深度下对不同同源染色体进行采样的概率来支持我的观点。我还讨论了将连续等位基因剂量计算为携带替代等位基因的测序读数比例的用途和不确定性，这一方法目前在数量遗传学中正逐渐成为取代离散剂量估计的常用方法。
