Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT.
Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT.
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基于SAT的杂合多倍体中未基于的SNP数据的单倍型推断。
DOI：
10.1186/1471-2164-9-356
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发表时间：
2008-07-30
期刊：
影响因子：
4.4
通讯作者：
Kersten, Birgit
中科院分区：
文献类型：
--
作者：
Neigenfind, Jost;Gyetvai, Gabor;Basekow, Rico;Diehl, Svenja;Achenbach, Ute;Gebhardt, Christiane;Selbig, Joachim;Kersten, Birgit
基于非定相SNP标记的单倍型推断是群体遗传学研究的重要内容。虽然有不同的方法来推断二倍体物种的单倍型，现有的软件是不适合推断单倍型从非定相的SNP数据在多倍体物种，如栽培马铃薯（马铃薯）。马铃薯物种是四倍体和高度杂合的。在这里，我们提出了软件SATlotyper，它能够处理多倍体和多等位基因数据。SATlo-typer使用布尔可满足性问题通过纯简约来公式化单体型推断。该软件排除了现有的单倍型推断，从而允许计算替代推断。由于它是不知道的多个单倍型推断是最好的支持，由给定的非定相数据集，我们使用一个自举程序，允许评分的替代推断。最后，通过自举得分，可以优化属于给定单倍型推断的定相基因型。该计划进行了评估与模拟和实验SNP数据产生的杂合四倍体群体的马铃薯。我们表明，而不是采取的程序报告的第一个单倍型推断，我们可以显着提高最终结果的质量，通过应用额外的方法，包括评分的替代单倍型推断和基因型优化。对于19个个体的亚群，通过SATlotyper计算的预测结果直接与通过克隆扩增子测序的实验单倍型推断获得的结果进行比较。预测和实验得到了相似的结果，关于推断的单倍型和分相的基因型。我们的研究结果表明，单倍型推断纯简约可以有效地解决SAT的方法，即使是从杂合多倍体的非定相SNP的数据集。SATlotyper是免费软件，并作为Java JAR文件分发。该软件可从GABI主要数据库的网页下载，网址为。利用SATlotyper可以为多倍体植物的单倍型关联分析提供单倍型信息。
Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potato species are tetraploid and highly heterozygous. Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes. Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at . The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.
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影响因子：
2.9
作者：
Ching A;Caldwell KS;Jung M;Dolan M;Smith OS;Tingey S;Morgante M;Rafalski AJ
通讯作者：
Rafalski AJ
影响因子：
14.9
作者：
Meyer S;Nagel A;Gebhardt C
通讯作者：
Gebhardt C
影响因子：
3.1
作者：
Sattarzadeh, Amirali;Achenbach, Ute;Gebhardt, Christiane
通讯作者：
Gebhardt, Christiane
影响因子：
4.4
作者：
Ballvora A;Jöcker A;Viehöver P;Ishihara H;Paal J;Meksem K;Bruggmann R;Schoof H;Weisshaar B;Gebhardt C
通讯作者：
Gebhardt C
影响因子：
4.2
作者：
Vaughan DA;Balázs E;Heslop-Harrison JS
通讯作者：
Heslop-Harrison JS