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

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• 作者：Kyoung-Tag Do ; Joon-Ho Lee ; Hak-Kyo Lee&#8230
• 关键词：Jeju horse ; Linkage disequilibrium (LD) ; Effective population size
• 刊名：Journal of Animal Science and Technology
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：56
• 期：1
• 全文大小：443KB
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• 作者单位：Kyoung-Tag Do (7)
  Joon-Ho Lee (8)
  Hak-Kyo Lee (8)
  Jun Kim (9)
  Kyung-Do Park (8)
  
  7. Department of Equine Sciences, Sorabol College, Gyeongju, 780-711, Republic of Korea
  8. The Animal Genomics and Breeding Center, Hankyong National University, Anseong, 456-749, Republic of Korea
  9. Provincial Livestock Promotion, Jeju, 690-802, Republic of Korea
  
• 刊物类别：Animal Genetics and Genomics; Agriculture;
• 刊物主题：Animal Genetics and Genomics; Agriculture;
• 出版者：BioMed Central
• ISSN：2055-0391

文摘

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鈥揥einberg equilibrium test P-value of <10鈥?) 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 (r2) between SNP pairs, were calculated for each allele and the effective population size was determined based on r2 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 r2 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 r2 between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r2 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鈥墌鈥? generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse鈥檚 population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size. Keywords Jeju horse Linkage disequilibrium (LD) Effective population size