A model selection-based interval-mapping method for autopolyploids
A model selection-based interval-mapping method for autopolyploids
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DOI：
10.1534/genetics.104.035410
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发表时间：
2005-04-01
期刊：
影响因子：
3.3
通讯作者：
Doerge, RW
中科院分区：
文献类型：
--
作者：
Cao, DC;Craig, BA;Doerge, RW
虽然在二倍体物种的QTL定位方面取得了广泛的进展，但由于多倍体的遗传结构复杂，在多倍体物种的QTL定位方面进展有限。迄今为止，多倍体的QTL定位主要集中在具有显性和/或共显性标记的四倍体上。在这里，我们将这一观点扩展到显性标记系统下的任何偶数倍性水平。我们的方法首先使用贝叶斯选择标准选择最可能的染色体标记配置，然后对每个候选序列拟合区间映射模型。通过EM算法获得了包括QTL效应在内的参数的似然比检验统计量和最大似然估计（MLEs）。然后使用基于重采样的显著性阈值检测假定的QTL，并将相应的亲本配置确定为观察数据的基础亲本配置。虽然是通过伪双回交实验提出的，但这种方法可以很容易地推广到其他育种系统。将该方法应用于单剂量限制性片段自体四倍体紫花苜蓿数据，并通过仿真研究对其性能进行了研究。
While extensive progress has been made in quantitative trait locus (QTL) mapping for diploid species, similar progress in QTL mapping for polyploids has been limited due to the complex genetic architecture of polyploids. To date, QTL mapping in polyploids has focused mainly on tetraploids with dominant and/or codominant markers. Here, we extend this view to include any even ploidy level under a dominant marker system. Our approach first selects the most likely chromosomal marker configurations using a Bayesian selection criterion and then fits an interval-mapping model to each candidate. Profiles of the likelihood-ratio test statistic and the maximum-likelihood estimates (MLEs) of parameters including QTL effects are obtained via the EM algorithm. Putative QTL are then detected using a resampling-based significance threshold, and the corresponding parental configuration is identified to be the underlying parental configuration from which the data are observed. Although presented via pseudo-doubled backcross experiments, this approach can be readily extended to other breeding systems. Our method is applied to single-dose restriction fragment autotetraploid alfalfa data, and the performance is investigated through simulation studies.