Invistigation of effictive populatioin, linkage disequilibrium and haplotype block structure in Azarbaijani breed buffalo using high density SNP markers

The aim of this study was to determine genomewide linkage disequilibrium (LD), Haplotype block and effective population size using the information obtained from 243 Azarbaijani breed buffalo using a high density SNP panel (Axiom® Buffalo Genotyping 90K). After quality control of SNP markers data, 62,141 SNP markers remained for identification of linkage disequiliberum, haplotype blocks and effective population size. LD was measured by the square of the correlation coefficient (r2) between alleles. The maximum LD measured by r2 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, clearly showing that the average r2 reduced with the increase in SNP pair distances. 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. Effective population size (Ne) was estimated based on expected linkage disequilibrium. Ne was estimated to be 422 in our population.