ArticleJournal of animal science and technology2015
Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data.
Article in Journal of animal science and technology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Genomic Characterization of Peruvian Creole Goats: Insights into Population Structure and Runs of Homozygosity.Animals : an open access journal from MDPI · 2025Article
- Linkage Disequilibrium Decay in Selected Cattle Breeds.Animals : an open access journal from MDPI · 2024Article
- Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats.Scientific reports · 2024Article
- Genome-wide association study for carcass weight in pasture-finished beef cattle in Hawai'i.Frontiers in genetics · 2023Article
- Unveiling the common loci for six body measurement traits in Chinese Wenshan cattle.Frontiers in genetics · 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
- Genome analyses revealed genetic admixture and selection signatures in Bos indicus.Scientific reports · 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
- Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data.PloS one · 2021Article
- Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed.Genes & genomics · 2020Article
- Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data.Frontiers in genetics · 2020Article
- Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle.Animals : an open access journal from MDPI · 2019Article
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Abstract
backgroundKnowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data.
resultsA total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r(2) criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r(2) above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations.
conclusionsA wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.
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