Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty–ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high-throughput sequencing data in the form of read counts. We bridge the gap from data collection (using restriction enzyme based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's p...

尽管当前群体基因组分析的大规模数据集获取机会日益增多，但利用高通量测序技术研究多倍体群体的应用却极少。这在很大程度上源于多倍体个体基因型中等位基因拷贝数判定的难题——等位基因剂量不确定性（allelic dosage uncertainty, ADU），该问题会使等位基因频率等关键群体遗传学参数的计算变得复杂。为此，本研究提出一种统计模型，可基于读长计数形式的高通量测序数据，估算同源多倍体群体中的双等位基因单核苷酸多态性（biallelic SNP）频率。本研究采用分层贝叶斯模型构建统一的推断框架，通过整合基因型不确定性，打通了从数据采集（基于限制性酶切技术，例如GBS、RADseq）到等位基因频率估算的完整链路。本研究针对四倍体、六倍体及八倍体群体在多种条件下生成模拟数据集，以评估该模型的p...