Phasing and imputation of single nucleotide polymorphism data of missing parents of biparental plant populations.
Phasing and imputation of single nucleotide polymorphism data of missing parents of biparental plant populations.
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DOI：
10.1002/csc2.20409
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发表时间：
2021-07
期刊：
影响因子：
2.3
通讯作者：
Hickey JM
中科院分区：
文献类型：
--
作者：
Gonen S;Wimmer V;Gaynor RC;Byrne E;Gorjanc G;Hickey JM
本文提出了一种扩展的启发式方法，在双亲群体中的后代基因型的定相和插补，使它可以相位和插补的父母是未分型或部分基因型的基因型。使用亲本的插补基因型将低密度（Ld）基因分型后代插补至高密度（Hd）。该扩展是作为AlphaPlantImpute软件的一部分实现的，分为三个步骤。首先，它确定父母是否有没有或Ld基因型，并确定其亲属有Hd基因型。第二，使用亲属的Hd基因型，它确定亲本对于给定的基因座是纯合的还是杂合的。第三，它通过将单倍型与其亲属相匹配来对亲本的杂合位置进行定相。我们测量的准确性（真实和估算的基因型之间的相关性），估算父母的基因型在模拟的双亲人口从不同的情况。我们使用父母的真实基因型测试缺失父母后代的插补准确性，并将其与使用父母的插补基因型进行比较。在所有情况下，父母的插补准确度>0.98，并且没有低于0.96。当亲本是近交系时，其插补准确度总是高于远交系。包括在Hd处的亲本的祖先，增加杂交的数量和Hd后代的数量增加了插补精度。父代获得的高插补准确性对其后代的插补准确性影响很小或没有影响。植物育种群体中的Hd SNP数据对于基因组选择越来越有价值。HD基因分型成千上万的候选人是昂贵的，插补是一个具有成本效益的替代方案。本文提出了一种扩展的启发式方法的定相和基因型的插补。在所有情况下，父母的插补准确度>0.98，并且没有低于0.96。父代的高插补准确性转化为对后代插补无影响。
This paper presents an extension to a heuristic method for phasing and imputation of genotypes of descendants in biparental populations so that it can phase and impute genotypes of parents that are ungenotyped or partially genotyped. The imputed genotypes of the parent are used to impute low‐density (Ld) genotyped descendants to high density (Hd). The extension was implemented as part of the AlphaPlantImpute software and works in three steps. First, it identifies whether a parent has no or Ld genotypes and identifies its relatives that have Hd genotypes. Second, using the Hd genotypes of relatives, it determines whether the parent is homozygous or heterozygous for a given locus. Third, it phases heterozygous positions of the parent by matching haplotypes to its relatives. We measured the accuracy (correlation between true and imputed genotypes) of imputing parent genotypes in simulated biparental populations from different scenarios. We tested the imputation accuracy of the missing parent's descendants using the true genotype of the parent and compared this with using the imputed genotypes of the parent. Across all scenarios, the imputation accuracy of a parent was >0.98 and did not drop below ∼0.96. The imputation accuracy of a parent was always higher when it was inbred than outbred. Including ancestors of the parent at Hd, increasing the number of crosses and the number of Hd descendants increased the imputation accuracy. The high imputation accuracy achieved for the parent translated to little or no impact on the imputation accuracy of its descendants. Hd SNP data in plant breeding populations is increasingly valuable for genomic selection. Hd genotyping thousands of candidates is expensive, imputation is a cost‐effective alternative. This paper presents an extension to a heuristic method for phasing and imputation of genotypes. Across all scenarios, imputation accuracy of a parent was >0.98 and did not drop below ∼0.96. High imputation accuracy for the parent translated to no impact on offspring imputation.
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影响因子：
2.9
作者：
VanRaden PM;Sun C;O'Connell JR
通讯作者：
O'Connell JR
DOI：
10.1186/1297-9686-43-12
发表时间：
2011-03-10
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Hickey JM;Kinghorn BP;Tier B;Wilson JF;Dunstan N;van der Werf JH
通讯作者：
van der Werf JH
影响因子：
2.3
作者：
Hickey, John M.;Dreisigacker, Susanne;Gorjanc, Gregor
通讯作者：
Gorjanc, Gregor
影响因子：
2.3
作者：
Jacobson, Amy;Lian, Lian;Bernardo, Rex
通讯作者：
Bernardo, Rex
影响因子：
2.3
作者：
Bernardo, Rex;Yu, Jianming
通讯作者：
Yu, Jianming