ArticleCrop science
Phasing and imputation of single nucleotide polymorphism data of missing parents of biparental plant populations.
Article in Crop science. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost.G3 (Bethesda, Md.) · 2025Article
- Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance.BMC genomics · 2025Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.