ArticleBMC genomics2008
Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Predicting phenotypes from novel genomic markers using deep learning.Bioinformatics advances · 2023Article
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species.Frontiers in plant science · 2022Review
- Performing parentage analysis for polysomic inheritances based on allelic phenotypes.G3 (Bethesda, Md.) · 2021Article
- PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.Genome research · 2019Article
- Tools for Genetic Studies in Experimental Populations of Polyploids.Frontiers in plant science · 2018Review
- Dominant Allele Phylogeny and Constitutive Subgenome Haplotype Inference in Bananas Using Mitochondrial and Nuclear Markers.Genome biology and evolution · 2017Article
- SHEsisPlus, a toolset for genetic studies on polyploid species.Scientific reports · 2016Article
- Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing.BMC research notes · 2012Article
- High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.).Molecular breeding : new strategies in plant improvement · 2012Article
- Inferring haplotypes of copy number variations from high-throughput data with uncertainty.G3 (Bethesda, Md.) · 2011Article
- Natural diversity of potato (Solanum tuberosum) invertases.BMC plant biology · 2010Article
- Inferring combined CNV/SNP haplotypes from genotype data.Bioinformatics (Oxford, England) · 2010Article
- Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- GabiPD: the GABI primary database--a plant integrative 'omics' database.Nucleic acids research · 2009Article
- Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions.BMC bioinformatics · 2008Article
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8 authors.
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Abstract
backgroundHaplotype 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.
resultsHere we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlotyper 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.
conclusionOur 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 http://www.gabipd.org/projects/satlotyper/. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.
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