ArticlePloS one2021
Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 24 citations in OpenAlex.
- Genomic diversity and population structure of understudied cattle populations of Sri Lanka in relation to established indigenous breeds.Tropical animal health and production · 2026Article
- Genomic insights into the admixture and diversity of Kerala crossbred cattle.Scientific reports · 2026Article
- Transmission Ratio Distortion Detection Using Microsatellite and Single Nucleotide Polymorphism Markers in Hanwoo of Gyeongnam Province.Animal genetics · 2026Article
- Using Whole-Genome Sequencing Data Reveals the Population Structure and Selection Signatures for Reproduction Traits in Duolang Sheep.Animals : an open access journal from MDPI · 2025Article
- Pedigree-based analysis of population structure and genetic diversity in high-milch Vrindavani crossbred cattle of India.Tropical animal health and production · 2024Article
- Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows.BMC genomics · 2024Article
- Comparative assessment of the effective population size and linkage disequilibrium of Karan Fries cattle revealed viable population dynamics.Animal bioscience · 2024Article
- Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Genomic Prediction Accuracies for Growth and Carcass Traits in a Brangus Heifer Population.Animals : an open access journal from MDPI · 2023Article
- 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
- Population structure, genetic diversity and prolificacy in pishan red sheep under an extreme desert environment.Frontiers in genetics · 2023Article
- Article
- Marker density and statistical model designs to increase accuracy of genomic selection for wool traits in Angora rabbits.Frontiers in genetics · 2022Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was having minor allele frequency of less than 0.20. The extent of LD between autosomal SNPs up to 10 Mb apart across the genome was measured using r2 statistic. The mean r2 value was 0.43, if pairwise distance of marker was less than10 kb and it decreased further to 0.21 for 25-50 kb markers distance. Further, the effect of minor allele frequency and sample size on LD estimate was investigated. The LD value decreased with the increase in inter-marker distance, and increased with the increase of minor allelic frequency. The estimated inbreeding coefficient and effective population size were 0.04, and 46 for present generation, which indicated small and unstable population of Vrindavani cattle. These findings suggested that a denser or breed specific SNP panel would be required to cover all genome of Vrindavani cattle for genome wide association studies (GWAS).
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