ArticlePloS one2012
Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 156 citations in OpenAlex.
- 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
- A k-mer-based genome-wide association study approach empowering gene mining in polyploids.Nature genetics · 2026Article
- MateR: a novel genomic mating framework.Genetics · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- 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
- Tests for segregation distortion in higher ploidy F1 populations.G3 (Bethesda, Md.) · 2025Article
- Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers.G3 (Bethesda, Md.) · 2025Article
- Tests for segregation distortion in tetraploid F1 populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Demographic history inference and the polyploid continuum.Genetics · 2023Article
- Genetic Analysis of Potato Breeding Collection Using Single-Nucleotide Polymorphism (SNP) Markers.Plants (Basel, Switzerland) · 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
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.GigaScience · 2022Article
- Analysis of genetic diversity and population structure among cultivated potato clones from Korea and global breeding programs.Scientific reports · 2022Article
- Allele expression biases in mixed-ploid sugarcane accessions.Scientific reports · 2022Article
- Genomic prediction with allele dosage information in highly polyploid species.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species.Frontiers in plant science · 2022Review
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
- Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty.Heredity · 2021Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species.
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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.