Multilocus tetrasomic linkage analysis using hidden Markov chain model
Multilocus tetrasomic linkage analysis using hidden Markov chain model
复制标题
使用隐马尔可夫链模型进行多位点四体连锁分析
DOI：
10.1073/pnas.0908477107
复制
发表时间：
2010-03-02
影响因子：
11.1
通讯作者：
Luo, Zewei
中科院分区：
文献类型：
--
作者：
Leach, Lindsey J.;Wang, Lin;Luo, Zewei
可靠的遗传连锁图谱的可用性是至关重要的功能和进化的基因组分析。遗传连锁分析的理论和方法的建立使作图成为二倍体的常规工作。然而，许多在进化、生态和/或农学上重要的物种是同源多倍体，同源四倍体是一个典型的例子。这些物种在减数分裂中经历比二倍体复杂得多的染色体分离和重组。此外，有证据表明多倍体诱导的基因组结构高度动态变化。这些多体特征表明，在二倍体连锁分析的理论和方法，用于这些物种和四倍体作图的理论和方法的差距不适当。本文提出了一个同源四倍体多位点连锁分析的理论模型和统计框架，用于显性和/或共显性DNA分子标记。该理论和方法结合了四体遗传下等位基因分离和重组的基本特征以及统计建模和标记数据分析中的主要挑战。我们验证了该方法，并探讨了其统计特性，通过深入的模拟研究，并证明了其效用分析AFLP和SSR标记数据从远交同源四倍体马铃薯人口。
The availability of reliable genetic linkage maps is crucial for functional and evolutionary genomic analyses. Established theory and methods of genetic linkage analysis have made map construction a routine exercise in diploids. However, many evolutionarily, ecologically, and/or agronomically important species are autopolyploids, with autotetraploidy being a typical example. These species undergo much more complicated chromosomal segregation and recombination at meiosis than diploids. In addition, there is evidence of polyploidy-induced and highly dynamic changes in the structure of the genome. These polysomic characteristics indicate the inappropriateness of the theory and methods of linkage analysis in diploids for use in these species and a gap in the theory and methodology of tetraploid map construction. This paper presents a theoretical model and statistical framework for multilocus linkage analysis in autotetraploids for use with dominant and/or codominant DNA molecular markers. The theory and methods incorporate the essential features of allele segregation and recombination under tetrasomic inheritance and the major challenges in statistical modeling and marker data analysis. We validated the method and explored its statistical properties by intensive simulation study and demonstrated its utility by analysis of AFLP and SSR marker data from an outbred autotetraploid potato population.