Study of linkage disequilibrium and identification of haplotype blocks structure in Sarabi breed cows

This study was conducted to estimate the linkage disequilibrium (LD) and determine haplotype blocks structure in 93 Sarabi cow using SNP-chip 40k of Illumina company. After genotyping and quality control, 27386 SNP markers on autosomal chromosomes remained for analyzing. The LD was measured by r2 and D' statistics. In this study the average of r2 and D' for range less than of 2.5 kb were maximum with 0.505 and 0.927, respectively. The average of r2 and D' were minimum with 0.064 and 0.486, respectively in range of 2-5 Mb. 582 haplotype blocks were observed in the genome of Sarabi cow. 6.73% SNP from all of the SNPs were covered and 0.83% (21.43 Mb) of the autosomal genome were covered by the blocks haplotype. Population effective size was estimated about 40 that refer to four generations ago. The low number of haplotype block and also low LD level in Sarabi cow population showed high variation. In refer to the result and the number of haplotype blocks in this breed, applying the haplotype blocks could be improve results and high precision on genomic selection study so it was recommended that in study of genomic selection applying the haplotype blocks really useful than single SNP study