ArticleBMC genomics2014
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 105 citations in OpenAlex.
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- Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions.Frontiers in plant science · 2023Article
- Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds.PloS one · 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
- SNP- and Haplotype-Based GWAS of Flowering-Related Traits inPlants (Basel, Switzerland) · 2021Article
- Long-range linkage disequilibrium in French beef cattle breeds.Genetics, selection, evolution : GSE · 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
- Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil.Frontiers in genetics · 2021Article
- Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed.Frontiers in genetics · 2021Article
- Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other TwoFrontiers in genetics · 2021Article
- Expression profiles of the MXD3 gene and association of sequence variants with growth traits in Xianan and Qinchuan cattle.Veterinary medicine and science · 2020Article
- Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle.Animals : an open access journal from MDPI · 2019Article
- Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain.Frontiers in genetics · 2019Article
- Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array.PloS one · 2019Article
- Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances.Genetics, selection, evolution : GSE · 2018Article
- Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations.Frontiers in genetics · 2018Article
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.
resultsThe maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.
conclusionsThis study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.
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