ArticleGenetics2018
Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence.
Article in Genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 43 citations in OpenAlex.
- Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- A Multi-Approach for In Silico Detection of Chromosome Inversions in Mosquito Vectors.Microorganisms · 2025Article
- Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding.The plant genome · 2023Article
- Reliable genotyping of recombinant genomes using a robust hidden Markov model.Plant physiology · 2023Article
- GBScleanR: robust genotyping error correction using a hidden Markov model with error pattern recognition.Genetics · 2023Article
- A genetic linkage map and improved genome assembly of the termite symbiont Termitomyces cryptogamus.BMC genomics · 2023Article
- Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.The plant genome · 2022Article
- Hybridization is strongly constrained by salinity during secondary contact between silverside fishes (Odontesthes, Atheriniformes).Heredity · 2022Article
- Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex.Molecular biology and evolution · 2022Article
- A generic hidden Markov model for multiparent populations.G3 (Bethesda, Md.) · 2022Article
- Genotyping, the Usefulness of Imputation to Increase SNP Density, and Imputation Methods and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Rapid genotype imputation from sequence with reference panels.Nature genetics · 2021Article
- Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations.G3 (Bethesda, Md.) · 2021Article
- Impact of pre- and post-variant filtration strategies on imputation.Scientific reports · 2021Article
- Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding.Heredity · 2020Review
- AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data.Bioinformatics (Oxford, England) · 2020Article
- Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach.Genetics, selection, evolution : GSE · 2019Article
- Article
Corrections and comments
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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
Many different types of multiparental populations have recently been produced to increase genetic diversity and resolution in QTL mapping. Low-coverage, genotyping-by-sequencing (GBS) technology has become a cost-effective tool in these populations, despite large amounts of missing data in offspring and founders. In this work, we present a general statistical framework for genotype imputation in such experimental crosses from low-coverage GBS data. Generalizing a previously developed hidden Markov model for calculating ancestral origins of offspring DNA, we present an imputation algorithm that does not require parental data and that is applicable to bi- and multiparental populations. Our imputation algorithm allows heterozygosity of parents and offspring as well as error correction in observed genotypes. Further, our approach can combine imputation and genotype calling from sequencing reads, and it also applies to called genotypes from SNP array data. We evaluate our imputation algorithm by simulated and real data sets in four different types of populations: the F
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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.