Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multi-allelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and non-additive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with 3 tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.

中文翻译：

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远交四倍体（和二倍体）二等位群中的 QTL 定位

在过去的十年中，多亲群体已成为二倍体物种遗传学研究的支柱。我们的目标是通过开发用于在来自一组共享亲本的连接 F1 种群中进行数量性状基因座 (QTL) 作图的软件，将这种范式扩展到同源四倍体。对于 QTL 发现，表型根据亲本单倍型的剂量进行回归，以估计加性效应。通过模拟具有不同种群大小和亲本数量的半二等体二倍体和四倍体种群来探索模型的统计特性。在各种情况下，每个亲本单倍型 (pph) 的后代数量在很大程度上决定了 QTL 检测的统计功效和估计单倍型效应的准确性。遗传力为 0 的多等位基因 QTL。在 25 pph 和全基因组显着性水平 0.05 下以 90% 的概率检测到 2，并且以超过 90% 的准确度估计了加性单倍型效应。在发现 QTL 之后，该软件可以比较具有多个 QTL 和非加性效应的模型。为了说明这一点，我们分析了具有 3 个四倍体亲本的半双列群体中的马铃薯块茎形状。在 10 号染色体上检测到一个众所周知的 QTL，与加性模型相比，包含双基因优势使偏差信息标准 (DIC) 降低了 17 个点。最终模型在 1 号染色体上还包含一个次要 QTL，但基于 DIC 排除了更高阶的优势和上位效应。在实际影响方面，