Recent and Past Effective Population Size Estimation by Genome Wide SNP Dataset in Equine

The detrimental effects of homozygosity and inbreeding on performance and reproduction traits in equine have been reported, so here we present genome-wide estimates of horse effective population size (Ne) and inbreeding (F) from LD data in Turkmen, Caspian and Thoroughbred. For this purpose we used 40,934 biallelic SNPs after quality control and excluding the X chromosome. Estimated present Ne was 50, 40 and 25 for Turkmen, Caspian and Thoroughbred respectively and also the past Ne in 1000 generation ago was 2590, 2070 and 1355 for Turkmen, Caspian and Thoroughbred respectively. The average F was 0.0125, 0.010 and 0.020 for Turkmen, Caspian and Thoroughbred respectively. It was interesting that the Ne in recent generation for all population drops down to 50, this result showed that horse breeders and responsible association have focused on some specific blood line in the recent generation as an artificial selection forces. These parameters can be highly effective for analyzing population structure and designing the horse breeding strategies.