ArticleGenetics2014
The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it, 105 citations in OpenAlex.
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- Study of Genetic Progress in the Context of Disconnection Between Two Originally Connected Populations.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Accessible, Realistic Genome Simulation with Selection Using stdpopsim.Molecular biology and evolution · 2025Article
- Accessible, realistic genome simulation with selection using stdpopsim.bioRxiv : the preprint server for biology · 2025Article
- GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.Genomics, proteomics & bioinformatics · 2025Article
- On ARGs, pedigrees, and genetic relatedness matrices.bioRxiv : the preprint server for biology · 2025Article
- Genomic prediction based on preselected single-nucleotide polymorphisms from genome-wide association study and imputed whole-genome sequence data annotation for growth traits in Duroc pigs.Evolutionary applications · 2024Article
- 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
- Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.eLife · 2023Article
- Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry.The plant genome · 2023Article
- Genomic prediction with whole-genome sequence data in intensely selected pig lines.Genetics, selection, evolution : GSE · 2022Article
- Weighted Single-Step Genomic Best Linear Unbiased Prediction Method Application for Assessing Pigs on Meat Productivity and Reproduction Traits.Animals : an open access journal from MDPI · 2022Article
- Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data.Evolutionary applications · 2022Article
- Evaluation of updated Feed Saved breeding values developed in Australian Holstein dairy cattle.JDS communications · 2022Article
- Genomic Prediction Using LD-Based Haplotypes in Combined Pig Populations.Frontiers in genetics · 2022Article
- The utility of genomic prediction models in evolutionary genetics.Proceedings. Biological sciences · 2021Article
- Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of dense SNPs to predict the genetic value of an individual for a complex trait is often referred to as "genomic selection" in livestock and crops, but is also relevant to human genetics to predict, for example, complex genetic disease risk. The accuracy of prediction depends on the strength of linkage disequilibrium (LD) between SNPs and causal mutations. If sequence data were used instead of dense SNPs, accuracy should increase because causal mutations are present, but demographic history and long-term negative selection also influence accuracy. We therefore evaluated genomic prediction, using simulated sequence in two contrasting populations: one reducing from an ancestrally large effective population size (Ne) to a small one, with high LD common in domestic livestock, while the second had a large constant-sized Ne with low LD similar to that in some human or outbred plant populations. There were two scenarios in each population; causal variants were either neutral or under long-term negative selection. For large Ne, sequence data led to a 22% increase in accuracy relative to ∼600K SNP chip data with a Bayesian analysis and a more modest advantage with a BLUP analysis. This advantage increased when causal variants were influenced by negative selection, and accuracy persisted when 10 generations separated reference and validation populations. However, in the reducing Ne population, there was little advantage for sequence even with negative selection. This study demonstrates the joint influence of demography and selection on accuracy of prediction and improves our understanding of how best to exploit sequence for 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.