ArticleBMC genomics2013
Study of whole genome linkage disequilibrium in Nellore cattle.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 123 citations in OpenAlex.
- A Nelore Cattle Structural Variant Catalog.Animal genetics · 2026Article
- Deciphering genetic diversity and selection footprints in Rathi cattle through ddRAD-based genome-wide analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Genome-wide DAPC-based genetic structure, linkage disequilibrium, and effective population size in indigenous buffaloes of Northeastern and Central India.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Effect of selection for growth on reproductive traits in Nellore females: Genetic parameters and genome-wide association studies.Journal of applied genetics · 2026Article
- Article
- Genotype imputation performance in Nellore cattle across different SNP panels and software tools.Tropical animal health and production · 2026Article
- Single-Step Genomic Predictions for Growth and Carcass Traits in Nordic Charolais and Hereford Cattle.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- A comprehensive genomic characterization of Nellore cattle.BMC genomics · 2026Article
- Exploring genome, transcriptome, and microbiome interactions related to feed efficiency and methane emissions in Bos indicus through multi-omics network analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Estimating Linkage Disequilibrium and Effective Population Size Across Generations in Holstein Cattle.Veterinary medicine and science · 2025Article
- Linkage Disequilibrium Decay in Selected Cattle Breeds.Animals : an open access journal from MDPI · 2024Article
- Genomic diversity study of highly crossbred cattle population in a Low and Middle Tropical environment.Tropical animal health and production · 2024Article
- Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats.Scientific reports · 2024Article
- Comparative assessment of the effective population size and linkage disequilibrium of Karan Fries cattle revealed viable population dynamics.Animal bioscience · 2024Article
- Article
- SNPs-Panel Polymorphism Variations inBiomedicines · 2023Article
- Genome analyses revealed genetic admixture and selection signatures in Bos indicus.Scientific reports · 2021Article
- Genome-wide association analysis identified molecular markers associated with important tea flavor-related metabolites.Horticulture research · 2021Article
- Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data.PloS one · 2021Article
- Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle.Frontiers in immunology · 2021Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundKnowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate the extent of LD in Nellore cattle using a high density SNP panel and 795 genotyped steers.
resultsAfter data editing, 446,986 SNPs were used for the estimation of LD, comprising 2508.4 Mb of the genome. The mean distance between adjacent markers was 4.90 ± 2.89 kb. The minor allele frequency (MAF) was less than 0.20 in a considerable proportion of SNPs. The overall mean LD between marker pairs measured by r(2) and |D'| was 0.17 and 0.52, respectively. The LD (r(2)) decreased with increasing physical distance between markers from 0.34 (1 kb) to 0.11 (100 kb). In contrast to this clear decrease of LD measured by r(2), the changes in |D'| indicated a less pronounced decline of LD. Chromosomes BTA1, BTA27, BTA28 and BTA29 showed lower levels of LD at any distance between markers. Except for these four chromosomes, the level of LD (r(2)) was higher than 0.20 for markers separated by less than 20 kb. At distances < 3 kb, the level of LD was higher than 0.30. The LD (r(2)) between markers was higher when the MAF threshold was high (0.15), especially when the distance between markers was short.
conclusionsThe level of LD estimated for markers separated by less than 30 kb indicates that the High Density Bovine SNP BeadChip will likely be a suitable tool for prediction of genomic breeding values in Nellore cattle.
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