Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data

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...

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Bibliographic Details
Published in:PloS one 2021-11, Vol.16 (11), p.e0259572-e0259572
Main Authors: Singh, Akansha, Kumar, Amit, Mehrotra, Arnav, A, Karthikeyan, Pandey, Ashwni Kumar, Mishra, B P, Dutt, Triveni
Format: Article
Language:English
Subjects:
Alleles
Analysis
Animals
Beef cattle
Biology and Life Sciences
Cattle
Chromosomes
Data Collection
Ecological balance
Evaluation
Female
Frequency distribution
Gene frequency
Gene Frequency - genetics
Genetic aspects
Genetic Variation
Genetics
Genetics, Population
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Genotype
Haplotypes
Inbreeding
Linkage disequilibrium
Linkage Disequilibrium - genetics
Markers
Models, Statistical
Mutation
Polymorphism, Single Nucleotide - genetics
Population
Population number
Quality control
Sample Size
Single nucleotide polymorphisms
Single-nucleotide polymorphism
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Summary: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).
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0259572