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Extent of linkage disequilibrium and effective population size of Korean Yorkshire swine

  • Shin, Donghyun (Department of Animal Biotechnology, Chonbuk National University) ;
  • Won, Kyeong-Hye (Department of Animal Biotechnology, Chonbuk National University) ;
  • Kim, Sung-Hoon (PigGene Korea Inc.) ;
  • Kim, Yong-Min (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)
  • Received : 2017.03.31
  • Accepted : 2018.06.22
  • Published : 2018.12.01

Abstract

Objective: We aimed to characterize linkage disequilibrium (LD) and effective population size ($N_e$) in a Korean Yorkshire population using genomic data from thousands of individuals. Methods: We genotyped 2,470 Yorkshire individuals from four major Grand-Grand-Parent farms in Korea using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 single nucleotide polymorphisms (SNPs) located across all chromosomes and mitochondria. We estimated the expected LD and inferred current $N_e$ as well as ancestral $N_e$. Results: We identified 61,565 SNP from autosomes, mitochondria, and sex chromosomes and characterized the LD of the Yorkshire population, which was relatively high between closely linked markers (>0.55 at 50 kb) and declined with increasing genetic distance. The current $N_e$ of this Korean Yorkshire population was 122.87 (106.90; 138.84), while the historical $N_e$ of Yorkshire pigs suggests that the ancestor $N_e$ has decreased by 99.6% over the last 10,000 generations. Conclusion: To maintain genetic diversity of a domesticated animal population, we must carefully consider appropriate breed management methods to avoid inbreeding. Although attenuated selection can affect short-term genetic gain, it is essential for maintaining the long-term genetic variability of the Korean Yorkshire population. Continuous and long-term monitoring would also be needed to maintain the pig population to avoid an unintended reduction of $N_e$. The best way to preserve a sustainable population is to maintain a sufficient $N_e$.

Keywords

Linkage Disequilibrium;Yorkshire;Effective Population Size;Single Nucleotide Polymorphism

Acknowledgement

Supported by : National Research Foundation of Korea (NRF), Rural Development Administration

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