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).
Highlights
Linkage disequilibrium (LD), defined as the degree of non-random association of allele between loci or correlation between genotypes of markers, is an important concept in the understanding of gene mapping and its application in genetic studies
Results from their study revealed that moderate linkage disequilibrium (LD) (r2 = 0.20) were extended to
A total 43,821 autosomal SNPs were available for downstream analysis
Summary
Linkage disequilibrium (LD), defined as the degree of non-random association of allele between loci or correlation between genotypes of markers, is an important concept in the understanding of gene mapping and its application in genetic studies. The LD between markers provides insight in exploring the level of diversity between different breeds, inferring the frequency of recombination events, investigating the change in effective population size across generations, and identifying genomic regions to improve economically important traits [1,2,3]. The accuracy and precision of the genomic studies rely on the level and pattern of linkage disequilibrium (LD) between markers across genome [7]. The LD between markers has been studied in the genome of several taurine and indicine cattle breeds [2, 8].
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