ArticleG3 (Bethesda, Md.)2019
polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids.
Article in G3 (Bethesda, Md.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 117 citations in OpenAlex.
- Balancing gain and diversity: Optimal contribution selection for sustainable genetic improvement in sugarcane.The plant genome · 2026Review
- 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
- Genomic selection in timothy (Phleum pratense L.): a comprehensive evaluation of prediction models, multi-trait strategies, and forward validation across Norwegian environments.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
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- Local Genetic Signatures of a Global Weed: Population Structure and Ecological Drivers ofEcology and evolution · 2026Article
- A public mid-density genotyping platform for pecan [Carya illinoinensis (Wangenh.) K. Koch].The plant genome · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Molecular identification and diversity assessment of Tyrrhenian Romulea species (Iridaceae).PloS one · 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
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- A public mid-density genotyping platform for cultivated cranberry (Vaccinium macrocarpon Aiton).The plant genome · 2025Article
- Imputef: imputation of polyploid genotype classes and allele frequencies.BMC genomics · 2025Article
- Niche expansion of polyploid cytotypes shaped the phylogeographical history of the Salix retusa complex in the European Alpine System.Annals of botany · 2025Article
- Genetic architecture and genomic prediction for yield, winter damage, and digestibility traits in timothy (Phleum pratense L.) using genotyping-by-sequencing data.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Combining genome-wide association and genomic prediction to unravel the genetic architecture of carotenoid accumulation in carrot.The plant genome · 2025Article
- Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers.Scientific reports · 2025Article
- A low-cost dpMIG-seq method for elucidating complex inheritance in polysomic crops: a case study in tetraploid blueberry.Horticulture research · 2024Article
- Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis.npj biodiversity · 2024Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates, heterozygotes miscalled as homozygotes, and uncertainty of allele copy number in heterozygous polyploids. Bayesian genotype calling can mitigate these issues, but previously has only been implemented in software that requires a reference genome or uses priors that may be inappropriate for the population. Here we present several novel Bayesian algorithms that estimate genotype posterior probabilities, all of which are implemented in a new R package, polyRAD. Appropriate priors can be specified for mapping populations, populations in Hardy-Weinberg equilibrium, or structured populations, and in each case can be informed by genotypes at linked markers. The polyRAD software imports read depth from several existing pipelines, and outputs continuous or discrete numerical genotypes suitable for analyses such as genome-wide association and genomic prediction.
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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.