Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse
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초록
This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that hadraced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missinggenotype 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 withmissing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used forthe analysis. The measures of the LD, square of correlation coefficient (r2) between SNP pairs, were calculated foreach allele and the effective population size was determined based on r2 measures. The polymorphism informationcontents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline wasobserved over the first 1 Mb. But r2 decreased more slowly with increasing distance and was constant after 2 Mb ofdistance and the decline was almost linear with log-transformed distance. The average r2 between adjacent SNPpairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r2between all SNP pairs was 0.02. We observed an initial pattern of decreasing Ne and estimated values were closerto 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be largeconsidering Jeju horse’s population size (about 2,000 heads), but it should be interpreted with caution because ofthe technical limitations of the methods and sample size.
Abstract
This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that hadraced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missinggenotype 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 withmissing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used forthe analysis. The measures of the LD, square of correlation coefficient (r2) between SNP pairs, were calculated foreach allele and the effective population size was determined based on r2 measures. The polymorphism informationcontents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline wasobserved over the first 1 Mb. But r2 decreased more slowly with increasing distance and was constant after 2 Mb ofdistance and the decline was almost linear with log-transformed distance. The average r2 between adjacent SNPpairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r2between all SNP pairs was 0.02. We observed an initial pattern of decreasing Ne and estimated values were closerto 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be largeconsidering Jeju horse’s population size (about 2,000 heads), but it should be interpreted with caution because ofthe technical limitations of the methods and sample size.
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