Estimation of linkage disequilibrium and effective population size using whole genome single nucleotide polymorphisms in Korean native pig and Landrace

Abstract Text: The linkage disequilibrium and effective population size in a closed population of Landrace purebred and Korean native pig crossbred were compared using a whole genomic single nucleotide polymorphism panel. Genotypic data consisted of 661 of Landrace and 1,266 of native pigs born in 2006 to 2012. After controlling SNP quality, linkage disequilibrium measures (r²) were estimated for over 40,000 SNP. Average distance of SNP pairs was 2.3 Mb for both breeds. From the analysis using SNP, average r² between adjacent SNP pairs were 0.34 and 0.48 for native pig and Landrace, respectively. Effective population size estimates based on r² with the SNP distance were 27 and 33 for Landrace and native pig, respectively. This result suggests that two breeds in Korea have smaller effective population size than other countries. Crossbreds showed lager genetic diversity than closed populations in Korea.

Keywords: Linkage Disequilibrium, Effective population size, Single Nucleotide Polymorphism, Pig