ArticleGenetics, selection, evolution : GSE2010
Dynamics of long-term genomic selection.
Article in Genetics, selection, evolution : GSE, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers.
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111 citing papers in PubMed.
- The effect of selection on allele frequencies and diversity in wheat (Triticum aestivum).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genomic selection in timothy (Phleum pratense L.): a comprehensive evaluation of prediction models, multi-trait strategies, and forward validation across Norwegian environments.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genomic selection strategies and their potential to maintain rare alleles and de-novo mutations: a long-term assessment.Genetics, selection, evolution : GSE · 2026Article
- Optimum recombination rates for genetic gains in simulated recurrent selection in empirical maize populations.The plant genome · 2026Article
- Strategies to improve on selection based on estimated breeding values.Genetics, selection, evolution : GSE · 2026Article
- Genomic prediction for grain yield and biotic stress resistance in field pea (Frontiers in plant science · 2026Article
- Optimizing genomic selection models for wheat breeding under contrasting water regimes in a mediterranean environment.Plant methods · 2025Article
- DiffBreed: automatic differentiation enables efficient gradient-based optimization of breeding strategies.Bioinformatics (Oxford, England) · 2025Article
- Genomic prediction-aided incorporation of genetic resources into elite breeding: lessons from a collaborative multiparental design in flint maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Optimization of recurrent rapid cycle breeding in maize for sustained long-term genetic improvement via stochastic simulations.G3 (Bethesda, Md.) · 2025Article
- Optimal Combination of Different Selection and Mating Strategies on Exploiting Genetic Diversity and Genetic Gain in Small Pig Conservation Populations.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2025Article
- Genomic selection: Essence, applications, and prospects.The plant genome · 2025Review
- Maximizing the accuracy of genetic variance estimation and using a novel generalized effective sample size to improve simulations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- SimpleMating: R-package for prediction and optimization of breeding crosses using genomic selection.The plant genome · 2025Article
- Optimal implementation of genomic selection in clone breeding programs exemplified in potato: II. Effect of selection strategy and cross-selection method on long-term genetic gain.The plant genome · 2025Article
- Changes in allele frequencies and genetic architecture due to selection in two pig populations.Genetics, selection, evolution : GSE · 2024Article
- Leveraging genomic prediction to surpass current yield gains in spring barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- PyBrOpS: a Python package for breeding program simulation and optimization for multi-objective breeding.G3 (Bethesda, Md.) · 2024Article
- Genomic-inferred cross-selection methods for multi-trait improvement in a recurrent selection breeding program.Plant methods · 2024Article
- Genomic selection optimization in blueberry: Data-driven methods for marker and training population design.The plant genome · 2024Article
51 more citing papers are in PubMed but not listed here.
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Abstract
backgroundSimulation and empirical studies of genomic selection (GS) show accuracies sufficient to generate rapid gains in early selection cycles. Beyond those cycles, allele frequency changes, recombination, and inbreeding make analytical prediction of gain impossible. The impacts of GS on long-term gain should be studied prior to its implementation.
methodsA simulation case-study of this issue was done for barley, an inbred crop. On the basis of marker data on 192 breeding lines from an elite six-row spring barley program, stochastic simulation was used to explore the effects of large or small initial training populations with heritabilities of 0.2 or 0.5, applying GS before or after phenotyping, and applying additional weight on low-frequency favorable marker alleles. Genomic predictions were from ridge regression or a Bayesian analysis.
resultsAssuming that applying GS prior to phenotyping shortened breeding cycle time by 50%, this practice strongly increased early selection gains but also caused the loss of many favorable QTL alleles, leading to loss of genetic variance, loss of GS accuracy, and a low selection plateau. Placing additional weight on low-frequency favorable marker alleles, however, allowed GS to increase their frequency earlier on, causing an initial increase in genetic variance. This dynamic led to higher long-term gain while mitigating losses in short-term gain. Weighted GS also increased the maintenance of marker polymorphism, ensuring that QTL-marker linkage disequilibrium was higher than in unweighted GS.
conclusionsLosing favorable alleles that are in weak linkage disequilibrium with markers is perhaps inevitable when using GS. Placing additional weight on low-frequency favorable alleles, however, may reduce the rate of loss of such alleles to below that of phenotypic selection. Applying such weights at the beginning of GS implementation is important.
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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.