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

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).