Multiparental populations (MPPs) are experimental populations in which the genome of every individual is a mosaic of known founder haplotypes. These populations are useful for detecting quantitative trait loci (QTL) because tests of association can leverage inferred founder haplotype descent. It is difficult, however, to determine how haplotypes at a locus group into distinct functional alleles, termed the allelic series. The allelic series is important because it provides information about the number of causal variants at a QTL and their combined effects. In this study, we introduce a fully-Bayesian model selection framework for inferring the allelic series. This framework accounts for sources of uncertainty found in typical MPPs, including the number and composition of functional alleles. Our prior distribution for the allelic series is based on the Chinese restaurant process, a relative of the Dirichlet process, and we leverage its connection to the coalescent to introduce additional prior information about haplotype relatedness via a phylogenetic tree. We evaluate our approach via simulation and apply it to QTL from two MPPs: the Collaborative Cross (CC) and the Drosophila Synthetic Population Resource (DSPR). We find that, although posterior inference of the exact allelic series is often uncertain, we are able to distinguish biallelic QTL from more complex multiallelic cases. Additionally, our allele-based approach improves haplotype effect estimation when the true number of functional alleles is small. Our method, Tree-Based Inference of Multiallelism via Bayesian Regression (TIMBR), provides new insight into the genetic architecture of QTL in MPPs.

中文翻译：

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推断多亲群体中 QTL 的等位基因系列。

多亲群体（MPP）是实验群体，其中每个个体的基因组都是已知创始人单倍型的镶嵌体。这些群体对于检测数量性状基因座 (QTL) 非常有用，因为关联测试可以利用推断的创始人单倍型血统。然而，很难确定基因座上的单倍型如何组合成不同的功能等位基因，称为等位基因系列。等位基因序列很重要，因为它提供了有关 QTL 因果变异数量及其综合效应的信息。在本研究中，我们引入了用于推断等位基因系列的完全贝叶斯模型选择框架。该框架解释了典型 MPP 中发现的不确定性来源，包括功能等位基因的数量和组成。我们对等位基因系列的先验分布是基于中餐馆过程（狄利克雷过程的亲戚），并且我们利用其与聚结的连接通过系统发育树引入有关单倍型相关性的额外先验信息。我们通过模拟评估我们的方法，并将其应用于两个 MPP 的 QTL：协作杂交 (CC) 和果蝇合成种群资源 (DSPR)。我们发现，尽管精确等位基因系列的后验推断通常是不确定的，但我们能够将双等位基因 QTL 与更复杂的多等位基因病例区分开来。此外，当功能等位基因的真实数量很小时，我们基于等位基因的方法可以改善单倍型效应估计。我们的方法，通过贝叶斯回归进行基于树的多等位性推断 (TIMBR)，为 MPP 中 QTL 的遗传结构提供了新的见解。