Genome-Wide Detection of Genetic Diversity and Genomic Structure in Hanwoo Cows

This study aimed to utilize genomic information to elucidate the genetic diversity and structure of Hanwoo cows and develop a more efficient improvement system. Genomic DNA was extracted from hair root samples of 7273 Hanwoo cows, and genotypes were determined using a customized Illumina Hanwoo SNP50k BeadChip. A total of 41,884 single-nucleotide polymorphisms (SNPs) covering approximately 2500 Mb of the genome were selected for analysis, along with 7166 Hanwoo cows that passed quality control. The mean observed and expected heterozygosity were 0.358 ± 0.125 and 0.357 ± 0.124, respectively. A total of 94,560 runs of homozygosity (ROHs) were observed, with an average of 13.2 per animal. Linkage disequilibrium (LD) was estimated using two parameters, D’ and r2, which were found to be 0.381 ± 0.309 and 0.054 ± 0.126, respectively, on autosomes. LD declined sharply from< 50 kb to 50–100 kb. In addition, 1818 haplotype blocks were identified on autosomes, totaling 88.27 Mb (3.53% of the autosomal length). The most common haplotype block size was two SNPs, with 1101 blocks. Finally, the effective population size (Ne) was 2853 at 1691 generations but decreased to 277 at 13 generations. These results provide genomic information for further studies and will be helpful for Hanwoo breeding programs.