ArticleBMC bioinformatics2011
Genotype calling in tetraploid species from bi-allelic marker data using mixture models.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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96 citing papers in PubMed.
- From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- The curious case of sporadic nematode susceptibility in "Tifguard" peanut (Arachis hypogaea): seed mixture or genetic instability?G3 (Bethesda, Md.) · 2026Article
- A k-mer-based genome-wide association study approach empowering gene mining in polyploids.Nature genetics · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Genome-wide association studies and genomics-informed breeding for tuber dormancy in tetraploid potatoes.The plant genome · 2026Article
- First genomic insights into the introgression of almond PPV-Marcus resistance into peach.Frontiers in plant science · 2026Article
- Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing.BMC plant biology · 2025Article
- High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination.The plant genome · 2025Article
- Surprisingly frequent chromosomal instability in cultivated peanut.The Plant journal : for cell and molecular biology · 2025Article
- From bottleneck to boom: Polyploidy, genetic instability and response to artificial selection resolve the peanut paradox.The Plant journal : for cell and molecular biology · 2025Article
- Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers.G3 (Bethesda, Md.) · 2025Article
- Exploring chromosomal variations in garden roses: Insights from high-density SNP array data and a new tool, Qploidy.The plant genome · 2025Article
- Beyond bloom: validated marker-trait discovery for polyploid roses via GWAS.Frontiers in plant science · 2025Article
- Unraveling the genetic basis of Rhizobium rhizogenes-mediated transformation and hairy root formation in rose using a genome-wide association study.Plant cell reports · 2024Article
- Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis.The plant genome · 2024Article
- Development of a robust SNP marker set for genotyping diverse gene bank collections of polyploid roses.BMC plant biology · 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
- Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Use of continuous genotypes for genomic prediction in sugarcane.The plant genome · 2024Article
36 more citing papers are in PubMed but not listed here.
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Abstract
backgroundAutomated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex).
resultsWe present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence.
conclusionsWe have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from http://www.plantbreeding.wur.nl/UK/software_fitTetra.html and as Additional files with this article.
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