Dataset Information

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

ABSTRACT:

Objective

We aimed to characterize linkage disequilibrium (LD) and effective population size (Ne) 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 Ne as well as ancestral Ne.

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 Ne of this Korean Yorkshire population was 122.87 (106.90; 138.84), while the historical Ne of Yorkshire pigs suggests that the ancestor Ne 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 Ne. The best way to preserve a sustainable population is to maintain a sufficient Ne.

SUBMITTER: Shin D

PROVIDER: S-EPMC6212734 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Publications

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

Shin Donghyun D Won Kyeong-Hye KH Kim Sung-Hoon SH Kim Yong-Min YM

Asian-Australasian journal of animal sciences. 20180726 12

<h4>Objective</h4>We aimed to characterize linkage disequilibrium (LD) and effective population size (Ne) in a Korean Yorkshire population using genomic data from thousands of individuals.<h4>Methods</h4>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 cur ...[more]

PMID: 30056677

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Dataset Information

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

Objective

Methods

Results

Conclusion

Publications

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

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