Assessment of genetic diversity and inbreeding in the Okinawa indigenous Agu pig through pedigree analysis.

Objective: The objective of this study was to clarify the changes in genetic diversity and inbreeding over the years as well as to identify the causes of genetic diversity loss using the pedigree of Okinawa indigenous Agu pigs.

Methods: The pedigree of the Agu population consisted of 1,997 animals from 1997 to 2020. The equivalent complete generations (ECG), inbreeding coefficient (F), and effective population size (Ne) were computed using ENDOG v4.8. Genetic diversity parameters, including founders (f), the effective number of founders (fe), the effective number of ancestors (fa), and the founder genome equivalent (fge), were derived from the probability of gene origin. The study also investigated changes in genetic diversity indices over time.

Results: ECG increased from 0.1 in 2003 to 3.87 by 2020, indicating an improved pedigree depth. The F has been on a downward trend since it peaked at 10.5% in 2015. However, the Ne in the reference population was 14.6, which is below the recommended levels. The f, fe, fa and fge of the reference population were 86, 26, 19, and 11.5, respectively. These values decrease in the order of f>fe>fa>fge. This indicates that all factors of genetic diversity loss played a role, including the unbalanced contributions of founders, bottlenecks, and random gene losses. Although in recent years efforts have been made to maintain genetic diversity and reduce inbreeding, the Agu pig population exhibited a 5% decrease in genetic diversity over the past 18 years, with both unequal founder contributions and genetic drift identified as significant contributing factors.

Conclusion: This study reveals that more favorable breeding strategies (such as optimal contribution and population size expansion) are required to maintain genetic diversity and increase the Ne of the Agu pig population.