Inference of individual ploidy level using codominant markers
Inference of individual ploidy level using codominant markers
复制标题
使用共显性标记推断个体倍性水平
DOI：
10.1111/1755-0998.13032
复制
发表时间：
2019-07-25
影响因子：
7.7
通讯作者：
Li, Baoguo
中科院分区：
文献类型：
--
作者：
Huang, Kang;Dunn, Derek W.;Li, Baoguo
很大一部分植物物种是多倍体，其中倍性水平有时在个体和/或群体之间变化。目前确定个体倍性的技术，例如，流式细胞术、染色体计数或测序基因分型通常很麻烦。基于双还原条件下多体遗传的基因型概率，我们建立了一个模型来估计等位基因频率，并从共显性遗传标记的等位基因表型推断个体的倍性状态。在存在无效等位基因、假等位基因、负扩增和自花受精的情况下，通过期望最大化算法估计等位基因频率，并使用后验概率将个体分配到不同的倍性水平。对不同条件下该方法的准确度进行了评价。我们的方法可以在一个新的软件包中免费获得，ploidyinferor，供其他研究人员使用，可以从下载。
A significant portion of plant species are polyploids, with ploidy levels sometimes varying among individuals and/or populations. Current techniques to determine the individual ploidy, e.g., flow cytometry, chromosome counting or genotyping-by-sequencing, are often cumbersome. Based on the genotypic probabilities for polysomic inheritance under double-reduction, we developed a model to estimate allele frequency and infer the ploidy status of individuals from the allelic phenotypes of codominant genetic markers. The allele frequencies are estimated by an expectation-maximization algorithm in the presence of null alleles, false alleles, negative amplifications and self-fertilization, and the posterior probabilities are used to assign individuals into different levels of ploidy. The accuracy of this method under different conditions is evaluated. Our methods are freely available in a new software package, ploidyinfer, for use by other researchers which can be downloaded from .