ArticleBMC genomics2010
Characteristics of linkage disequilibrium in North American Holsteins.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 135 citations in OpenAlex.
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- Long-range linkage disequilibrium in French beef cattle breeds.Genetics, selection, evolution : GSE · 2021Article
- High-throughput genotype-based population structure analysis of selected buffalo breeds.Translational animal science · 2021Article
- Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico.Animals : an open access journal from MDPI · 2021Article
- Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data.PloS one · 2021Article
- Linkage Disequilibrium and Effective Population Size of Buffalo Populations of Iran, Turkey, Pakistan, and Egypt Using a Medium Density SNP Array.Frontiers in genetics · 2021Article
- A Comprehensive Comparison of Haplotype-Based Single-Step Genomic Predictions in Livestock Populations With Different Genetic Diversity Levels: A Simulation Study.Frontiers in genetics · 2021Article
- LDscaff: LD-based scaffolding of de novo genome assemblies.BMC bioinformatics · 2020Article
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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
backgroundEffectiveness of genomic selection and fine mapping is determined by the level of linkage disequilibrium (LD) across the genome. Knowledge of the range of genome-wide LD, defined as a non-random association of alleles at different loci, can provide an insight into the optimal density and location of single-nucleotide polymorphisms (SNPs) for genome-wide association studies and can be a keystone for interpretation of results from QTL mapping.
resultsLinkage disequilibrium was measured by /D'/ and r2 between 38,590 SNPs (spaced across 29 bovine autosomes and the X chromosome) using genotypes of 887 Holstein bulls. The average level of /D'/ and r2 for markers 40-60 kb apart was 0.72 and 0.20, respectively in Holstein cattle. However, a high degree of heterogeneity of LD was observed across the genome. The sample size and minor allele frequency had an effect on /D'/ estimates, however, r2 was not noticeably affected by these two factors. Syntenic LD was shown to be useful for verifying the physical location of SNPs. No differences in the extent of LD and decline of LD with distance were found between the intragenic and intergenic regions.
conclusionsA minimal sample size of 444 and 55 animals is required for an accurate estimation of LD by /D'/ and r2, respectively. The use of only maternally inherited haplotypes is recommended for analyses of LD in populations consisting of large paternal half-sib families. Large heterogeneity in the pattern and the extent of LD in Holstein cattle was observed on both autosomes and the X chromosome. The extent of LD was higher on the X chromosome compared to the autosomes.
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