ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2014
The impact of population structure on genomic prediction in stratified populations.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers, 1 of them a synthesis that pooled it.
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Who cites it
96 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Optimizing Genomic-Enabled Prediction in Small-Scale Maize Hybrid Breeding Programs: A Roadmap Review.Frontiers in plant science · 2021Pooled it
- Enhancing alfalfa breeding through genomic prediction with exotic germplasm resources.BMC plant biology · 2026Article
- A benchmarking of genomic selection models for predicting grain-yield related traits using haplotype-based and genome-wide association study-based markers in rice.The plant genome · 2026Article
- Optimizing genomic predictions in maize using a diversity panel and a multiparental population.The plant genome · 2026Article
- Integrative genomic approaches to unravel genomic regions and candidate genes associated with flag leaf photosynthesis at the reproductive stage in rice.Frontiers in plant science · 2026Article
- Accounting for population structure in genomic prediction of strawberry sweetness at a global scale.Scientific reports · 2025Article
- Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Transferability of genomic prediction models across market segments in potato and the effect of selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass.Plant physiology · 2025Article
- Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples.American journal of human genetics · 2025Article
- Genomic selection: Essence, applications, and prospects.The plant genome · 2025Review
- Genomic Prediction for Germplasm Improvement Through Inter-Heterotic-Group Line Crossing in Maize.International journal of molecular sciences · 2025Article
- Increased genomic predictive ability in mango using GWAS-preselected variants and fixed-effect SNPs.Frontiers in plant science · 2025Article
- Leveraging genomic prediction to surpass current yield gains in spring barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Enhancing Across-Population Genomic Prediction for Maize Hybrids.Plants (Basel, Switzerland) · 2024Article
- Genomic selection for agronomical phenotypes using genome-wide SNPs and SVs in pearl millet.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples.bioRxiv : the preprint server for biology · 2024Article
- Biologically meaningful genome interpretation models to address data underdetermination for the leaf and seed ionome prediction in Arabidopsis thaliana.Scientific reports · 2024Article
- Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection.The plant genome · 2024Article
- Genomic prediction for agronomic traits in a diverse Flax (Linum usitatissimum L.) germplasm collection.Scientific reports · 2024Article
36 more citing papers are in PubMed but not listed here.
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9 authors.
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Abstract
Impacts of population structure on the evaluation of genomic heritability and prediction were investigated and quantified using high-density markers in diverse panels in rice and maize. Population structure is an important factor affecting estimation of genomic heritability and assessment of genomic prediction in stratified populations. In this study, our first objective was to assess effects of population structure on estimations of genomic heritability using the diversity panels in rice and maize. Results indicate population structure explained 33 and 7.5% of genomic heritability for rice and maize, respectively, depending on traits, with the remaining heritability explained by within-subpopulation variation. Estimates of within-subpopulation heritability were higher than that derived from quantitative trait loci identified in genome-wide association studies, suggesting 65% improvement in genetic gains. The second objective was to evaluate effects of population structure on genomic prediction using cross-validation experiments. When population structure exists in both training and validation sets, correcting for population structure led to a significant decrease in accuracy with genomic prediction. In contrast, when prediction was limited to a specific subpopulation, population structure showed little effect on accuracy and within-subpopulation genetic variance dominated predictions. Finally, effects of genomic heritability on genomic prediction were investigated. Accuracies with genomic prediction increased with genomic heritability in both training and validation sets, with the former showing a slightly greater impact. In summary, our results suggest that the population structure contribution to genomic prediction varies based on prediction strategies, and is also affected by the genetic architectures of traits and populations. In practical breeding, these conclusions may be helpful to better understand and utilize the different genetic resources in 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.