Home Equine Research Bank J Anim Sci Technol Estimation of effective population size using single-nucleot...

Journal of animal science and technology2014; 56; 28; doi: 10.1186/2055-0391-56-28

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

Do, KT
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Lee, JH
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Lee, HK
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Kim, J
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Park, KD

Abstract: 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 Ne 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.

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Publication Date: 2014-12-05 PubMed ID: 26290717PubMed Central: PMC4540288DOI: 10.1186/2055-0391-56-28Google Scholar: Lookup

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The research study is about the estimation of the effective population size in Jeju horses by using single-nucleotide polymorphism (SNP) data derived from 240 horses that had participated in races.

Research Process

The research deployed SNP data from 240 Jeju horses that had participated in races at the Jeju racing park.
The complete set of genotyped autosomal SNPs was 61,746 but after undergoing quality control procedures, 17,320 SNPs were discarded. The cut-offs used for quality set at greater than 10% for missing genotype, less than 0.05 for minor allele frequency, and Hardy-Weinberg equilibrium test P-value of less than 10(-6).
The SNPs from the X and Y chromosomes were also eliminated along with genotyped individuals with a missing genotype rate of over 10%. Finally, only 44,426 (71.9%) SNPs were used in further analysis.

Analysis of Linkage Disequilibrium and Population Size

The Linkage Disequilibrium (LD), which measures the non-random association of alleles at different loci, was measured via the square of correlation coefficient (r(2)) between SNP pairs. This was computed for each allele.
Based on these r(2) measures, the effective population size was determined.
The polymorphism information contents (PIC) and expected heterozygosity (HE) were reported to be 0.27 and 0.34, respectively.
In the pattern of LD, the researchers noticed a rapid decline over the first 1 Mb. The r(2) then decreased more slowly with increasing distance, becoming constant after 2 Mb of distance. The decline was almost linear with a log-transformed distance.
The average r(2) of adjacent SNP pairs ranged between 0.20 and 0.31 in each chromosome with an overall average at 0.26. The average r(2) of all SNP pairs was 0.02.