ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2018
A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Assessing the potential of genetic resource introduction into elite germplasm: a collaborative multiparental population for flint maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Development of molecular inversion probes for soybean progeny genomic selection genotyping.The plant genome · 2023Article
- Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.The plant genome · 2022Article
- Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs.The plant genome · 2022Article
- Genotype imputation for soybean nested association mapping population to improve precision of QTL detection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Implementing within-cross genomic prediction to reduce oat breeding costs.The plant genome · 2020Article
- Combining Partially Overlapping Multi-Omics Data in Databases Using Relationship Matrices.Frontiers in plant science · 2020Article
- Family-specific genotype arrays increase the accuracy of pedigree-based imputation at very low marker densities.Genetics, selection, evolution : GSE · 2019Article
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6 authors.
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Abstract
Key message New fast and accurate method for phasing and imputation of SNP chip genotypes within diploid bi-parental plant populations. This paper presents a new heuristic method for phasing and imputation of genomic data in diploid plant species. Our method, called AlphaPlantImpute, explicitly leverages features of plant breeding programmes to maximise the accuracy of imputation. The features are a small number of parents, which can be inbred and usually have high-density genomic data, and few recombinations separating parents and focal individuals genotyped at low density (i.e. descendants that are the imputation targets). AlphaPlantImpute works roughly in three steps. First, it identifies informative low-density genotype markers in parents. Second, it tracks the inheritance of parental alleles and haplotypes to focal individuals at informative markers. Finally, it uses this low-density information as anchor points to impute focal individuals to high density. We tested the imputation accuracy of AlphaPlantImpute in simulated bi-parental populations across different scenarios. We also compared its accuracy to existing software called PlantImpute. In general, AlphaPlantImpute had better or equal imputation accuracy as PlantImpute. The computational time and memory requirements of AlphaPlantImpute were tiny compared to PlantImpute. For example, accuracy of imputation was 0.96 for a scenario where both parents were inbred and genotyped at 25,000 markers per chromosome and a focal F
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