Detection of Haplotypic Structure for Genome of Azerbaijani Buffalo Using High Density SNP Markers

Abstract

The aim of this study was to determine genome-wide haplotype block structure, extent of linkage disequilibrium (LD) and effective population size using the information obtained from 243 Azerbaijani buffalo (Axiom® Buffalo Genotyping 90 K) using a high density SNP panel. After quality control, 62,141 SNP markers remained for population structure analysis and identification of haplotype blocks. The extent of LD was measured by the square of correlation coefficient (r²) between alleles. The maximum LD varied from 0.25 to 0.29 at a distance of <2.5 kb, and the minimum average values of r² varied from 0.012 to 0.014 at distances ranging from 900 to 1000 kb. Overall, 1693 blocks were observed through the genome. Eleven percent of all SNPs were clustered into haplotype blocks, covering 202 ± 3.4 Mb of the total autosomal genome size. Using formula which relate expected LD to effective population size (N_e), and assuming a constant actual population size, N_e was 422 in our population.