ArticleBMC genetics2015
Using selection index theory to estimate consistency of multi-locus linkage disequilibrium across populations.
Article in BMC genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 24 citations in OpenAlex.
- Improving multibreed genomic prediction for breeds with small populations by modeling heterogeneous genetic (co)variance blockwise accounting for linkage disequilibrium.Journal of animal science and biotechnology · 2025Article
- Genomic selection with GWAS-identified QTL markers enhances prediction accuracy for quantitative traits in poplar (Populus deltoides).Communications biology · 2025Article
- Enhancing Across-Population Genomic Prediction for Maize Hybrids.Plants (Basel, Switzerland) · 2024Article
- Multi-line ssGBLUP evaluation using preselected markers from whole-genome sequence data in pigs.Frontiers in genetics · 2023Article
- Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize.Genome biology · 2022Article
- Genomic Prediction of Complex Traits, Principles, Overview of Factors Affecting the Reliability of Genomic Prediction, and Algebra of the Reliability.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Predicting the accuracy of genomic predictions.Genetics, selection, evolution : GSE · 2021Article
- Genomic selection efficiency and a priori estimation of accuracy in a structured dent maize panel.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Genomic prediction for numerically small breeds, using models with pre-selected and differentially weighted markers.Genetics, selection, evolution : GSE · 2018Article
- Utility of whole-genome sequence data for across-breed genomic prediction.Genetics, selection, evolution : GSE · 2018Article
- Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein-Friesian cattle.Genetics, selection, evolution : GSE · 2016Article
- An Equation to Predict the Accuracy of Genomic Values by Combining Data from Multiple Traits, Populations, or Environments.Genetics · 2016Article
- Across population genomic prediction scenarios in which Bayesian variable selection outperforms GBLUP.BMC genetics · 2015Article
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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
backgroundThe potential of combining multiple populations in genomic prediction is depending on the consistency of linkage disequilibrium (LD) between SNPs and QTL across populations. We investigated consistency of multi-locus LD across populations using selection index theory and investigated the relationship between consistency of multi-locus LD and accuracy of genomic prediction across different simulated scenarios. In the selection index, QTL genotypes were considered as breeding goal traits and SNP genotypes as index traits, based on LD among SNPs and between SNPs and QTL. The consistency of multi-locus LD across populations was computed as the accuracy of predicting QTL genotypes in selection candidates using a selection index derived in the reference population. Different scenarios of within and across population genomic prediction were evaluated, using all SNPs or only the four neighboring SNPs of a simulated QTL. Phenotypes were simulated using different numbers of QTL underlying the trait. The relationship between the calculated consistency of multi-locus LD and accuracy of genomic prediction using a GBLUP type of model was investigated.
resultsThe accuracy of predicting QTL genotypes, i.e. the measure describing consistency of multi-locus LD, was much lower for across population scenarios compared to within population scenarios, and was lower when QTL had a low MAF compared to QTL randomly selected from the SNPs. Consistency of multi-locus LD was highly correlated with the realized accuracy of genomic prediction across different scenarios and the correlation was higher when QTL were weighted according to their effects in the selection index instead of weighting QTL equally. By only considering neighboring SNPs of QTL, accuracy of predicting QTL genotypes within population decreased, but it substantially increased the accuracy across populations.
conclusionsConsistency of multi-locus LD across populations is a characteristic of the properties of the QTL in the investigated populations and can provide more insight in underlying reasons for a low empirical accuracy of across population genomic prediction. By focusing in genomic prediction models only on neighboring SNPs of QTL, multi-locus LD is more consistent across populations since only short-range LD is considered, and accuracy of predicting QTL genotypes of individuals from another population is increased.
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