Annual trends in heterozygosity of Korea native cattle (Hanwoo) based on microsatellite markers

High-qulity Hanwoo (Korean native cattle) semen yields calves with better genetics, significantly enhancing farm profits. However, the repeated use of this semen can reduce heterozygosity and genetic diversity in the Hanwoo population, potentially compromising parentage verification accuracy. This study was conducted to analyze large-scale microsatellite (MS) marker data to evaluate the heterozygosity of Hanwoo cows and the discriminatory power of the MS marker set currently used for parentage verification.

The study involved Hanwoo cows from farms participating in the Hanwoo cow improvement project, utilizing MS marker data from 778,544 heads collected for parentage verification since 2012. Heterozygosity (HObs), expected heterozygosity (HExp), polymorphism information content (PIC), and the inbreeding coefficient within populations (FIS) were estimated using R version 4.3.3 and Cervus version 3.0.7.

The results showed average values of HObs, HExp, and PIC were 0.771, 0.768, and 0.736, respectively. Heterozygosity by marker suggested a gradual decrease in variability for most markers post-2010. After 2010, the analysis of over 10,000 animals led to a decrease in variance of sample statistics, improving the accuracy of estimates. The FIS values suggest that the population is approaching Hardy-Weinberg equilibrium and that inbreeding risk is being effectively managed through planned breeding programs. To assess trends in genetic differentiation over time, we grouped individuals by birth year (2001-23) and calculated pairwise genetic differentiation values. The values ranged from 0.0003 to 0.0081, indicating low genetic differentiation and suggesting temporal genetic stability.

This study shows that the Hanwoo population has high genetic diversity and low fixation, and that the current MS marker set remains reliable for future parentage verification.