Mapping Environment-Specific Quantitative Trait Loci
Mapping Environment-Specific Quantitative Trait Loci
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DOI：
10.1534/genetics.110.120311
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发表时间：
2010-11-01
期刊：
影响因子：
3.3
通讯作者：
Xu, Shizhong
中科院分区：
文献类型：
--
作者：
Chen, Xin;Zhao, Fuping;Xu, Shizhong
环境特异性数量性状基因座（QTL）是指在不同环境中表达不同的QTL，这种现象称为环境QTL互作（QXE）。Q × E互作是传统QTL定位延伸出来的一个难题。混合模型最大似然法是QTL区间定位的常用方法，但该方法在处理QTL与环境互作时并不理想。将QTL效应分为主效应和互作效应。主效应用QTL效应在所有环境中的平均值表示，互作效应用QTL效应在不同环境中的方差表示。我们使用马尔可夫链蒙特卡罗（MCMC）实现贝叶斯方法来估计主效应和交互效应。使用因子分析协方差结构对残差协方差矩阵进行建模。仿真研究表明，因子分析结构是强大的，可以处理其他结构的特殊情况。该方法也应用于大麦产量性状的Q × E互作作图。8个标记主效应显著，18个标记Q × E互作显著。这18个相互作用的标记分布在整个基因组的所有7条染色体上。只有1个标记同时具有主效应和Q × E互作效应。其他标记物中的每一个都具有主效应或Q X E互作效应，但不是两者都有。
Environment-specific quantitative trait loci (QTL) refer to QTL that express differently in different environments, a phenomenon called QTL-by-environment (Q X E) interaction. Q X E interaction is a difficult problem extended from traditional QTL mapping. The mixture model maximum-likelihood method is commonly adopted for interval mapping of QTL, but the method is not optimal in handling QTL interacting with environments. We partitioned QTL effects into main and interaction effects. The main effects are represented by the means of QTL effects in all environments and the interaction effects are represented by the variances of the QTL effects across environments. We used the Markov chain Monte Carlo (MCMC) implemented Bayesian method to estimate both the main and the interaction effects. The residual error covariance matrix was modeled using the factor analytic covariance structure. A simulation study showed that the factor analytic structure is robust and can handle other structures as special cases. The method was also applied to Q X E interaction mapping for the yield trait of barley. Eight markers showed significant main effects and 18 markers showed significant Q X E interaction. The 18 interacting markers were distributed across all seven chromosomes of the entire genome. Only 1 marker had both the main and the Q X E interaction effects. Each of the other markers had either a main effect or a Q X E interaction effect but not both.