ArticleBMC genomics2012
Estimation of linkage disequilibrium in four US pig breeds.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 2 of them syntheses that pooled it.
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Who cites it
95 citing papers in PubMed, 2 syntheses or guidelines pooled it, 149 citations in OpenAlex.
- Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs.PloS one · 2018Pooled it
- Meta-analysis of genome-wide association from genomic prediction models.Animal genetics · 2016Pooled it
- Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.Journal of applied genetics · 2026Article
- Methods to detect selection history in a population under ongoing directional selection.Genetics · 2026Article
- Characterizing breed-shared and breed-specific genetic regulatory effects of gene expression across three pig breeds.Journal of animal science and biotechnology · 2026Article
- Genotype imputation performance in Nellore cattle across different SNP panels and software tools.Tropical animal health and production · 2026Article
- Farm animal evolution demonstrates hidden molecular basis of human traits.bioRxiv : the preprint server for biology · 2026Article
- 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
- Characterization of genomic diversity and population structure of worldwide Duroc subpopulations and other pig breeds.Genetics, selection, evolution : GSE · 2025Article
- Exploring transcriptomic and genomic differences between susceptible and resistant fetal pigs to maternal PRRSV infection at late gestation.Veterinary research · 2025Article
- Genome-Wide Association Study for Individual Primal Cut Quality Traits in Canadian Commercial Crossbred Pigs.Animals : an open access journal from MDPI · 2025Article
- Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs.Animals : an open access journal from MDPI · 2025Article
- Technical note: anomaly detection for breed purity analysis in pigs using a single breed genotype panel.Journal of animal science · 2025Article
- Accuracy of genomic prediction using multiple Atlantic salmon populations.Genetics, selection, evolution : GSE · 2024Article
- Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs.Animals : an open access journal from MDPI · 2024Article
- The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations.Genetics · 2023Article
- Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds.PloS one · 2023Article
- Population genomics of American mink using genotype data.Frontiers in genetics · 2023Article
- Linkage Disequilibrium, Haplotype Block Structures, Effective Population Size and Genome-Wide Signatures of Selection of Two Conservation Herds of the South African Nguni Cattle.Animals : an open access journal from MDPI · 2022Article
- Imputation of non-genotyped F1 dams to improve genetic gain in swine crossbreeding programs.Journal of animal science · 2022Article
35 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe success of marker assisted selection depends on the amount of linkage disequilibrium (LD) across the genome. To implement marker assisted selection in the swine breeding industry, information about extent and degree of LD is essential. The objective of this study is to estimate LD in four US breeds of pigs (Duroc, Hampshire, Landrace, and Yorkshire) and subsequently calculate persistence of phase among them using a 60 k SNP panel. In addition, we report LD when using only a fraction of the available markers, to estimate persistence of LD over distance.
resultsAverage r2 between adjacent SNP across all chromosomes was 0.36 for Landrace, 0.39 for Yorkshire, 0.44 for Hampshire and 0.46 for Duroc. For markers 1 Mb apart, r2 ranged from 0.15 for Landrace to 0.20 for Hampshire. Reducing the marker panel to 10% of its original density, average r2 ranged between 0.20 for Landrace to 0.25 for Duroc. We also estimated persistence of phase as a measure of prediction reliability of markers in one breed by those in another and found that markers less than 10 kb apart could be predicted with a maximal accuracy of 0.92 for Landrace with Yorkshire.
conclusionsOur estimates of LD, although in good agreement with previous reports, are more comprehensive and based on a larger panel of markers. Our estimates also confirmed earlier findings reporting higher LD in pigs than in American Holstein cattle, especially at increasing marker distances (> 1 Mb). High average LD (r2 > 0.4) between adjacent SNP found in this study is an important precursor for the implementation of marker assisted selection within a livestock species.Results of this study are relevant to the US purebred pig industry and critical for the design of programs of whole genome marker assisted evaluation and selection. In addition, results indicate that a more cost efficient implementation of marker assisted selection using low density panels with genotype imputation, would be feasible for these breeds.
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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.