Article

Anim Biosci. 2025; 38(6): 1105-1115.

Published online February 27, 2025.

DOI: https://doi.org/10.5713/ab.24.0646

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

Shihei Touma1 , Kyota Fusho2 , and Aisaku Arakawa3
1Okinawa Prefectural Farming Support Department, Naha, Okinawa, Japan
2Okinawa Prefectural Livestock and Grassland Research Center, Nakijin, Okinawa, Japan
3Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
Corresponding Author: Email: toumashh@pref.okinawa.lg.jp
Received September 14, 2024;    Accepted January 7, 2025.
Abstract
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.
Keywords : Agu Population; Effective Population Size; Genetic Diversity; Inbreeding; Indigenous Pig; Pedigree Analysis