Linkage disequilibrium levels in Fars province native cattle population using high-density SNP data

Knowledge on the extent of linkage disequilibrium (LD) among populations is a useful tool to study the evolutionary history of populations and to detect the genomic regions associated with economically important traits. In recent years, high dense SNP data has been widely applying as the standard tools in LD analysis of livestock populations. In the current study, LD levels in the genome of Fars native cattle were investigated in order to provide basic information required to design genome-wide association studies and to survey on probable changes in the effective size of this population. Moreover, the applicability of the modern genomic technologies such as genomic selection can be evaluated using LD data.
Material and Ten individuals were randomly sampled from Fars native cattle population and were genotyped using Illumina Bovine HD beadchip for 777962 SNP markers. Data quality control was performed based on genotyping call rate, deviation from Hardy-Weinberg equilibrium and minor allele frequency. Thereby, a total of 55,718 SNPs were remained for further analyses.
MAF was calculated using PLINK v1.07 for all autosomal SNPs and the distribution of the allelic frequencies was graphed as the proportion of SNPs represented in 6 different categories of MAF: Number of SNPs located on X, Y, mitochondrial chromosomes and unknown sites were respectively equal to 39367, 1224, 343 and 1735 and all of those were excluded from further analysis. Average distance between adjacent SNPs was equal to 48.1 Kb and the average of MAF was equal to 0.223. Also, 44.5% of sites had MAF Results from this study can be applied to determine the optimum marker density required to achieve enough accuracy in the possible genomic studies on the Fars native cattle. Due to recent intense inbreeding and considerable reduction in effective population size of Fars native cattle population, the high r2 values found in this study were as expected.