ArticleHeredity2014
Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions.
Article in Heredity, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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Who cites it
106 citing papers in PubMed.
- Resolving Cattle GWAS Loci: Current Progress, Persistent Challenges and Future Directions.Current issues in molecular biology · 2026Review
- Opportunities and computational challenges in large-scale whole-genome sequencing data analysis.Journal of animal science · 2026Review
- Claudin and Rab proteins are key molecular components involved in coccidiosis resistance in Portuguese Merino sheep.Genetics, selection, evolution : GSE · 2025Article
- Low-Coverage Whole-Genome Sequencing (lcWGS) in Cattle: Analysis of Potential and Prospects for Application.Animals : an open access journal from MDPI · 2025Review
- Effect of using preselected markers from imputed whole-genome sequence for genomic prediction in Angus cattle.Genetics, selection, evolution : GSE · 2025Article
- GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.Genomics, proteomics & bioinformatics · 2025Article
- Evaluation of genomic selection models using whole genome sequence data and functional annotation in Belgian Blue cattle.Genetics, selection, evolution : GSE · 2025Article
- Mendelian randomisation to uncover causal associations between conformation, metabolism, and production as potential exposure to reproduction in German Holstein dairy cattle.Genetics, selection, evolution : GSE · 2025Article
- Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle.Communications biology · 2025Article
- Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants.Nature communications · 2025Article
- Estimating evolutionary and demographic parameters via ARG-derived IBD.PLoS genetics · 2025Article
- Genomic Prediction of Semen Traits in Boars Incorporating Biological Interactions.International journal of molecular sciences · 2024Article
- Genetic and genomic analysis of reproduction traits in holstein cattle using SNP chip data and imputed sequence level genotypes.BMC genomics · 2024Article
- Exploring the genetic basis of resistance to Neopestalotiopsis species in strawberry.The plant genome · 2024Article
- Novel SNP markers for flowering and seed quality traits in faba bean (Frontiers in plant science · 2024Article
- Increased Accuracy of Genomic Prediction Using Preselected SNPs from GWAS with Imputed Whole-Genome Sequence Data in Pigs.Animals : an open access journal from MDPI · 2023Article
- Preselecting Variants from Large-Scale Genome-Wide Association Study Meta-Analyses Increases the Genomic Prediction Accuracy of Growth and Carcass Traits in Large White Pigs.Animals : an open access journal from MDPI · 2023Article
- Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools.BMC genomics · 2023Article
- Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals.Genetics, selection, evolution : GSE · 2023Article
- Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.Genetics, selection, evolution : GSE · 2023Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic prediction from whole-genome sequence data is attractive, as the accuracy of genomic prediction is no longer bounded by extent of linkage disequilibrium between DNA markers and causal mutations affecting the trait, given the causal mutations are in the data set. A cost-effective strategy could be to sequence a small proportion of the population, and impute sequence data to the rest of the reference population. Here, we describe strategies for selecting individuals for sequencing, based on either pedigree relationships or haplotype diversity. Performance of these strategies (number of variants detected and accuracy of imputation) were evaluated in sequence data simulated through a real Belgian Blue cattle pedigree. A strategy (AHAP), which selected a subset of individuals for sequencing that maximized the number of unique haplotypes (from single-nucleotide polymorphism panel data) sequenced gave good performance across a range of variant minor allele frequencies. We then investigated the optimum number of individuals to sequence by fold coverage given a maximum total sequencing effort. At 600 total fold coverage (x 600), the optimum strategy was to sequence 75 individuals at eightfold coverage. Finally, we investigated the accuracy of genomic predictions that could be achieved. The advantage of using imputed sequence data compared with dense SNP array genotypes was highly dependent on the allele frequency spectrum of the causative mutations affecting the trait. When this followed a neutral distribution, the advantage of the imputed sequence data was small; however, when the causal mutations all had low minor allele frequencies, using the sequence data improved the accuracy of genomic prediction by up to 30%.
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