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Genetic Divergence of Cattle Populations Based on Genomic Information

Abstract The aim of this study was to analyze the extent of linkage disequilibrium (LD) and estimate the effective population size in three divergent cattle breeds. In total 19 Pinzgau, 30 Brown Swiss, and 30 Nelore bulls were genotyped using Illumina BovineSNP50 v2 BeadChip. The level of LD was assessed only for syntenic adjacent autosomal loci. The extent of LD significantly varied across the analyzed groups and autosomes. The highest average value of r2, which was used as measure of LD extent, was found in Brown Swiss (0.27). The r2 values were averaged into 50 kb distance bins to estimate their relationship to SNP physical positions. With the increasing genetic distance a decay of LD was found by each of the analyzed breeds. Moreover, the decrease in relation to the distance was observed also in effective population size (Ne) estimation. Thus, the long distances in genome produced a signal of the recent history of population. The observed values of recent Ne across evaluated cattle breeds were above the minimum number required to maintain genetic diversity and indicated a sufficient animal basis for the future management of breeding programs for each of the populations.