Modeling Population Genetic Data in Autotetraploid Species
Modeling Population Genetic Data in Autotetraploid Species
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DOI：
10.1534/genetics.105.044974
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发表时间：
2006-01
期刊：
影响因子：
3.3
通讯作者：
Z. Luo;Ze Zhang;R. M. Zhang;Madhav Pandey;O. Gailing;H. Hattemer;R. Finkeldey
中科院分区：
文献类型：
--
作者：
Z. Luo;Ze Zhang;R. M. Zhang;Madhav Pandey;O. Gailing;H. Hattemer;R. Finkeldey
等位酶和基于PCR的分子标记已被广泛用于研究同源四倍体物种的遗传多样性和群体遗传结构。然而，一种经验性但不准确的方法经常被用来根据凝胶条带的模式和强度来推断标记基因。显然，这给标记基因类型的预测带来了严重的错误，并严重影响了数据分析。本文提出了一个描述同源四倍体群体遗传标记基因座上等位基因分离的理论模型，并提出了一种新的基于似然估计模型参数的方法。该模型较好地考虑了自然群体中由于多个等位基因和同源四体基因座双重还原造成的分离复杂性，并适当考虑了四倍体群体中由于多剂量等位基因分离而产生的不完全的标记表型信息。利用计算机模拟研究对理论分析进行了验证，并通过对经济上重要的同源四倍体树种--梧桐枫的两个种群的微卫星标记数据的分析，验证了理论分析的实用性。基于仿真数据的数值分析表明，使用合理的样本量，可以充分估计模型参数，并以较好的功率检测到二次还原。
Allozyme and PCR-based molecular markers have been widely used to investigate genetic diversity and population genetic structure in autotetraploid species. However, an empirical but inaccurate approach was often used to infer marker genotype from the pattern and intensity of gel bands. Obviously, this introduces serious errors in prediction of the marker genotypes and severely biases the data analysis. This article developed a theoretical model to characterize genetic segregation of alleles at genetic marker loci in autotetraploid populations and a novel likelihood-based method to estimate the model parameters. The model properly accounts for segregation complexities due to multiple alleles and double reduction at autotetrasomic loci in natural populations, and the method takes appropriate account of incomplete marker phenotype information with respect to genotype due to multiple-dosage allele segregation at marker loci in tetraploids. The theoretical analyses were validated by making use of a computer simulation study and their utility is demonstrated by analyzing microsatellite marker data collected from two populations of sycamore maple (Acer pseudoplatanus L.), an economically important autotetraploid tree species. Numerical analyses based on simulation data indicate that the model parameters can be adequately estimated and double reduction is detected with good power using reasonable sample size.