Linear models for joint association and linkage QTL mapping
Linear models for joint association and linkage QTL mapping
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DOI：
10.1186/1297-9686-41-43
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发表时间：
2009-09-29
影响因子：
4.1
通讯作者：
Fernando, Rohan L.
中科院分区：
文献类型：
--
作者：
Legarra, Andres;Fernando, Rohan L.
背景：群体连锁不平衡和家系内连锁常用于QTL定位和标记辅助选择。两者的结合导致QTL的定位更加稳健和准确，但到目前为止提出的模型要么是单一标记，在实践中复杂，要么很好地适合特定的家庭结构。我们在此提出线性模型理论来提出QTL等位基因在一般系谱的任何成员中的加性效应，条件是观察到的标记和系谱，解释了QTL和标记之间可能存在的连锁不平衡。该模型是基于关联分析的创始人，进一步的QTL传递给后代的加性效应是一个加权（由传递概率）平均值的替代效应创始人的单倍型。该模型允许非完全连锁不平衡QTL标记的创始人。提供了两个子模型：半同胞家系的Haley-Knott型回归简单易行，一般家系的混合（方差分量）模型通用。该模型可以使用来自所有标记的信息。回归方法的性能进行了比较，通过模拟与一个更复杂的IBD方法Meuwissen和戈达德。结论：线性模型理论为利用密集标记图进行QTL定位提供了一个有用的框架。结果显示类似的精度，但IBD方法对该区域的中心的偏差。与IBD方法相比，线性回归模型的计算非常简单。将该模型扩展到基因组选择和多QTL定位是简单的。
Background: Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure.Results: We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission) average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component) model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided.Conclusion: The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.