ArticlePloS one2019
Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- 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
- Estimating Linkage Disequilibrium and Effective Population Size Across Generations in Holstein Cattle.Veterinary medicine and science · 2025Article
- Molecular Characteristics and Processing Technologies of Dairy Products from Non-Traditional Species.Molecules (Basel, Switzerland) · 2024Review
- Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project.GigaScience · 2024Article
- Cytokine profile, differential somatic cell count, and oxidative status of Italian Mediterranean buffalo milk affected by the temperature-humidity index.Frontiers in veterinary science · 2024Article
- Space allowance: a tool for improving behavior, milk and meat production, and reproduction performance of buffalo in different housing systems-a review.Tropical animal health and production · 2022Review
- Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows.Animals : an open access journal from MDPI · 2021Article
- A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes.BMC genomics · 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
- Genetic Parameter Estimation and Genome-Wide Association Study-Based Loci Identification of Milk-Related Traits in Chinese Holstein.Frontiers in genetics · 2021Article
- Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species.G3 (Bethesda, Md.) · 2020Article
- Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis.BMC genetics · 2020Article
- Article
- Review
- On the Extent of Linkage Disequilibrium in the Genome of Farm Animals.Frontiers in genetics · 2019Review
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7 authors.
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Abstract
Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information. A set of 404 individuals from three Iranian buffalo populations were genotyped with the Axiom Buffalo Genotyping 90K Array. Average r2 and |D'| between adjacent SNP pairs across all chromosomes was 0.27 and 0.66 for AZI, 0.29 and 0.68 for KHU, and 0.32 and 0.72 for MAZ. The LD between the SNPs decreased with increasing physical distance from 100Kb to 1Mb between markers, from 0.234 to 0.018 for AZI, 0.254 to 0.034 for KHU, and 0.297 to 0.119 for MAZ, respectively. These results indicate that a density of 90K SNP is sufficient for genomic analyses relying on long range LD (e.g. GWAS and genomic selection). The persistence of LD phase decreased with increasing marker distances across all the populations, but remained above 0.8 for AZI and KHU for marker distances up to 100Kb. For multi-breed genomic evaluation, the 90K SNP panel is suitable for AZI and KHU buffalo breeds. Estimated effective population sizes for AZI, KHU and MAZ were 477, 212 and 32, respectively, for recent generations. The estimated effective population sizes indicate that the MAZ is at risk and requires careful management.
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