ArticleGenetics, selection, evolution : GSE2015
Empirical and deterministic accuracies of across-population genomic prediction.
Article in Genetics, selection, evolution : GSE, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Dissecting the Predictive Accuracy of Polygenic Indexes for Behavioral Phenotypes Across Genetic Ancestries.bioRxiv : the preprint server for biology · 2026Article
- Optimizing genomic predictions in maize using a diversity panel and a multiparental population.The plant genome · 2026Article
- Sharing approaches in predictive genomics across animals, plants and humans.Nature genetics · 2026Review
- Leveraging Fst and Genetic Distance to Optimize Reference Sets for Enhanced Cross-Population Genomic Prediction.Animals : an open access journal from MDPI · 2026Article
- Dissecting the Predictive Accuracy of Polygenic Indexes for Behavioral Phenotypes Across Genetic Ancestries.Research square · 2025Article
- Genomic Prediction for Germplasm Improvement Through Inter-Heterotic-Group Line Crossing in Maize.International journal of molecular sciences · 2025Article
- Enhancing Across-Population Genomic Prediction for Maize Hybrids.Plants (Basel, Switzerland) · 2024Article
- TrG2P: A transfer-learning-based tool integrating multi-trait data for accurate prediction of crop yield.Plant communications · 2024Article
- Genomic Prediction of Growth Traits in Yorkshire Pigs of Different Reference Group Sizes Using Different Estimated Breeding Value Models.Animals : an open access journal from MDPI · 2024Article
- Expected values for the accuracy of predicted breeding values accounting for genetic differences between reference and target populations.Genetics, selection, evolution : GSE · 2024Article
- Article
- Principles and methods for transferring polygenic risk scores across global populations.Nature reviews. Genetics · 2024Review
- Multibreed genomic prediction using summary statistics and a breed-origin-of-alleles approach.Heredity · 2023Article
- Article
- Stacked kinship CNN vs. GBLUP for genomic predictions of additive and complex continuous phenotypes.Scientific reports · 2022Article
- Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple.G3 (Bethesda, Md.) · 2022Article
- Assessment of genomic prediction reliability and optimization of experimental designs in multi-environment trials.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Review: optimizing genomic selection for crossbred performance by model improvement and data collection.Journal of animal science · 2021Review
- Genomic prediction using a reference population of multiple pure breeds and admixed individuals.Genetics, selection, evolution : GSE · 2021Article
- Factors affecting accuracy of estimated effective number of chromosome segments for numerically small breeds.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2021Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundDifferences in linkage disequilibrium and in allele substitution effects of QTL (quantitative trait loci) may hinder genomic prediction across populations. Our objective was to develop a deterministic formula to estimate the accuracy of across-population genomic prediction, for which reference individuals and selection candidates are from different populations, and to investigate the impact of differences in allele substitution effects across populations and of the number of QTL underlying a trait on the accuracy.
methodsA deterministic formula to estimate the accuracy of across-population genomic prediction was derived based on selection index theory. Moreover, accuracies were deterministically predicted using a formula based on population parameters and empirically calculated using simulated phenotypes and a GBLUP (genomic best linear unbiased prediction) model. Phenotypes of 1033 Holstein-Friesian, 105 Groninger White Headed and 147 Meuse-Rhine-Yssel cows were simulated by sampling 3000, 300, 30 or 3 QTL from the available high-density SNP (single nucleotide polymorphism) information of three chromosomes, assuming a correlation of 1.0, 0.8, 0.6, 0.4, or 0.2 between allele substitution effects across breeds. The simulated heritability was set to 0.95 to resemble the heritability of deregressed proofs of bulls.
resultsAccuracies estimated with the deterministic formula based on selection index theory were similar to empirical accuracies for all scenarios, while accuracies predicted with the formula based on population parameters overestimated empirical accuracies by ~25 to 30%. When the between-breed genetic correlation differed from 1, i.e. allele substitution effects differed across breeds, empirical and deterministic accuracies decreased in proportion to the genetic correlation. Using a multi-trait model, it was possible to accurately estimate the genetic correlation between the breeds based on phenotypes and high-density genotypes. The number of QTL underlying the simulated trait did not affect the accuracy.
conclusionsThe deterministic formula based on selection index theory estimated the accuracy of across-population genomic predictions well. The deterministic formula using population parameters overestimated the across-population genomic accuracy, but may still be useful because of its simplicity. Both formulas could accommodate for genetic correlations between populations lower than 1. The number of QTL underlying a trait did not affect the accuracy of across-population genomic prediction using a GBLUP method.
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