Phenotypes of sessile organisms, such as plants, rely not only on their own genotype but also on the genotypes of neighboring individuals. Previously, we incorporated such neighbor effects into a single-marker regression using the Ising model of ferromagnetism. However, little is known about how to incorporate neighbor effects in quantitative trait locus (QTL) mapping. In this study, we propose a new method for interval QTL mapping of neighbor effects, named "Neighbor QTL". The algorithm of neighbor QTL involves the following: (i) obtaining conditional self-genotype probabilities with recombination fraction between flanking markers, (ii) calculating neighbor genotypic identity using the self-genotype probabilities, and (iii) estimating additive and dominance deviation for neighbor effects. Our simulation using F2 and backcross lines showed that the power to detect neighbor effects increased as the effective range became smaller. The neighbor QTL was applied to insect herbivory on Col x Kas recombinant inbred lines of Arabidopsis thaliana. Consistent with previous evidence, the pilot experiment detected a self QTL effect on the herbivory at GLABRA1 locus. We also observed a weak QTL on chromosome 4 regarding neighbor effects on the herbivory. The neighbor QTL method is available as an R package (https://cran.r-project.org/package=rNeighborQTL), providing a novel tool to investigate neighbor effects in QTL studies.

中文翻译：

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邻域QTL：一种用于植物邻域效应潜在数量性状基因座的区间作图方法

固着生物（例如植物）的表型不仅依赖于其自身的基因型，还依赖于邻近个体的基因型。以前，我们使用铁磁性的伊辛模型将此类邻近效应纳入单标记回归中。但是，关于如何在定量性状基因座（QTL）映射中纳入邻居效应知之甚少。在这项研究中，我们提出了一种用于邻居效应的间隔QTL映射的新方法，称为“邻居QT​​L”。邻居QTL的算法涉及以下内容：（i）获得带有侧翼标记之间重组分数的条件性自我基因型概率，（ii）使用自我基因型概率计算邻居基因型同一性，以及（iii）估计邻居的加性和优势偏差效果。我们使用F2和回交线进行的仿真表明，随着有效范围变小，检测邻居效应的能力也随之提高。邻居QTL应用于Col x Kas重组自交系的昆虫食草。拟南芥。与先前的证据一致，该初步实验在GLABRA1位点检测到对草食动物的自我QTL效应。我们还观察到了第4号染色体上的弱QTL，这与食草动物的邻居效应有关。邻居QTL方法以R包（https://cran.r-project.org/package=rNeighborQTL）的形式提供，为研究QTL研究中的邻居效应提供了一种新颖的工具。