Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse

This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy-Weinberg equilibrium test P-value of < $10^{-6}$) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient ($r^2$) between SNP pairs, were calculated for each allele and the effective population size was determined based on $r^2$ measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But $r^2$ decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average $r^2$ between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average $r^2$ between all SNP pairs was 0.02. We observed an initial pattern of decreasing $N_e$ and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse's population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.