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ISSN : 1225-2964(Print)
ISSN : 2287-3317(Online)
Annals of Animal Resource Sciences Vol.28 No.2 pp.46-55

Linkage Disequilibrium and Association Analysis of Hanwoo Steer in Gangwon Region using Bovine SNP50K BeadChip

Min-Wook Hong, So-Young Choi, Hun Kim, Song-Yi Yang, Kyeongrok Kwak, Jong-Bok Kim, Sung-Jin Lee


This study was conducted with DNA chip analysis to investigate genotypes of SNPs in genome wide association (GWA) of Korean native cattle (Hanwoo) in Gangwon region and extent of linkage disequilibrium (LD) among SNP markers. Genomic DNA for genotyping was extracted from the tissue samples of Hanwoo steers (n=139). A total of 54,609 SNPs were screened using Bovine SNP50K BeadChip. The filtering resulted in 35,769 useful SNPs, which were used for LD analysis. The total length of the SNP markers used in the analysis was 2499.26 Mb, the mean of minor allele frequency was 0.273 and the average interval distances of adjacent SNP markers by each chromosome was 60 to 82 Kb in GWA. The results of this study which confirmed by using Hanwoo steer in Gangwon, showed a pattern similar to previously reported studies for Hanwoo. Greater than 0.2 of LD value (r2) observed 34 percentage at adjacent SNP markers within 50 Kb. Also graph showed an exponential trend the decay of LD with physical distance. When the decay of r2 with a distance was plotted separately for each chromosome, the average r2 values were lower than 0.2 on BTA 13, 15, 19, 23, 25, 28, and 29 in the less than 40 Kb when compared to all other chromosomes. Therefore this study could be utilized as baseline data using genetic improvement, helpful in a genetic breeding system for Gangwon Hanwoo.