ArticleBMC genetics2009
High-resolution haplotype block structure in the cattle genome.
Article in BMC genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers, 1 of them a synthesis that pooled it.
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92 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results.Journal of animal science · 2018Pooled it
- Transmission Ratio Distortion Detection Using Microsatellite and Single Nucleotide Polymorphism Markers in Hanwoo of Gyeongnam Province.Animal genetics · 2026Article
- Genome-wide SNP evidence for the genetic uniqueness of indigenous cattle population.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
- A primer on sequencing and genotype imputation in cattle.Journal of animal science · 2025Review
- Genome-wide scan for signatures of selection in Hanwoo and Angus cattle using whole-genome sequence data.PloS one · 2025Article
- High-density LD-based structural variations analysis in ten Native and Mestizo Mexican populations.PloS one · 2025Article
- Linkage Disequilibrium Decay in Selected Cattle Breeds.Animals : an open access journal from MDPI · 2024Article
- Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation.Genetics, selection, evolution : GSE · 2024Article
- Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India.Tropical animal health and production · 2023Article
- Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle.Animal bioscience · 2023Article
- Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds.PloS one · 2023Article
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- Effect of L3MBTL3/PTPN9 polymorphisms on risk to alcohol-induced ONFH in Chinese Han population.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2022Article
- Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires.Journal of animal science · 2022Article
- Breed of origin of alleles and genomic predictions for crossbred dairy cows.Genetics, selection, evolution : GSE · 2021Article
- High-throughput genotype-based population structure analysis of selected buffalo breeds.Translational animal science · 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
- Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region.Frontiers in genetics · 2021Article
32 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use.
resultsFrom the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1-100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure.
conclusionThis work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1-100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in Bos taurus breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.
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