ArticleBMC bioinformatics2019
FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Genome-wide detection of selection signatures in roses.BMC plant biology · 2026Article
- Genome-wide association studies and genomics-informed breeding for tuber dormancy in tetraploid potatoes.The plant genome · 2026Article
- High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination.The plant genome · 2025Article
- Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis.The plant genome · 2024Article
- GenoTriplo: A SNP genotype calling method for triploids.PLoS computational biology · 2024Article
- Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.The plant genome · 2024Article
- Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- A multiplexed plant-animal SNP array for selective breeding and species conservation applications.G3 (Bethesda, Md.) · 2023Article
- Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genomic selection and genome-wide association studies in tetraploid chipping potatoes.The plant genome · 2023Article
- Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit.Plant biotechnology journal · 2023Article
- Effective omics tools are still lacking for improvement of stress tolerance in polyploid crops.Frontiers in plant science · 2023Article
- Potato Cultivar Identification in South Africa Using a Custom SNP Panel.Plants (Basel, Switzerland) · 2022Article
- Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Cells · 2021Review
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
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- Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty.Heredity · 2021Article
- Using probabilistic genotypes in linkage analysis of polyploids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms.Ecology and evolution · 2021Article
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5 authors.
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Abstract
backgroundGenetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data.
resultsOur upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60 k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated.
conclusionOur updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.
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