Interval mapping for loci affecting unordered categorical traits
Interval mapping for loci affecting unordered categorical traits
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DOI：
10.1038/sj.hdy.6800783
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发表时间：
2006-02-01
期刊：
影响因子：
3.8
通讯作者：
Awata, T
中科院分区：
文献类型：
--
作者：
Hayashi, T;Awata, T
许多性状，包括植物的花、果实和种子的形状和颜色，以及动物的毛色和一些行为特征，都被记录在离散的类别中。如果类别是有序的，分类性状的遗传分析通常使用阈值模型进行，该模型认为一个潜在的连续变量，称为负债，潜在的性状，并假设表型和负债之间的单调关系。然而，在某些分类性状中，表型的描述纯粹是名义上的，表型得分不能排序。阈值模型不适用于这类无序分类性状的分析。在这项研究中，我们开发了一种方法区间定位基因座影响无序分类性状的两个以上的类别。个体表型落入每个类别的概率由多分类逻辑模型表示，其中假设每个类别相对于参考类别的对数优势遵循线性模型，包括影响性状的基因座处的基因型作为协变量。在此基础上，设计了一种基于最大似然法的区间映射方法，用于分析用无序类别描述的复杂类别性状。我们仅限于两个自交系之间的杂交F2群体的情况下，虽然这种方法可以很容易地扩展到一般结构的其他群体的分析。模拟数据的分析结果表明，该方法在检测影响无序分类性状的基因座方面具有较高的效率。
Many traits including shapes and colors of flowers, fruits and seeds in plants, as well as coat colors and some behavioral properties in animals, are recorded in discrete categories. If categories are ordered, genetic analyses of the categorical traits are often performed using the threshold model, which considers a latent continuous variable, called the liability, underlying a trait and assumes the monotonic relationship between the phenotype and the liability. In some categorical traits, however, descriptions of phenotypes are purely nominal and the phenotypic scores cannot be ordered. The threshold model is unreasonable for the analyses of such unordered categorical traits. In this study, we developed a method for interval mapping of loci affecting unordered categorical traits with more than two categories. The probability of the phenotype of an individual falling in each of the categories was expressed by a polychotomous logistic model, in which the log-odds for each category relative to the reference category were assumed to follow a linear model including genotype at a locus affecting a trait as covariate. Based on the model, the interval mapping using a maximum likelihood method was devised for the analysis of complex categorical traits described with unordered categories. We confined ourselves to the case of F2 populations derived from a cross between two inbred lines, although this approach can easily be extended to the analyses for other populations of general structures. As results of analyses of simulated data show, the method showed high efficiency in detecting the loci affecting unordered categorical traits.