Investigation of Genomic Structure of Okinawan Pig Population

Agu is a domestic pig breed in Okinawa Island, located in south-west region of Japan. The ancestor of Agu pig was reportedly introduced from China in Min dynasty about 600 years ago. In 1950’s, the population size of Agu momentarily decreased to several dozen in a few years. The population size has recovered to around 1,000 individuals from 1980’s. Here, we sought to compare genetic structure of Agu to 16 pig breeds including 9 Western, 2 Asian, 2 Miniature, and 2 wild boars, in order to estimate differences in genomic structure among pig breeds using SNPs from porcine60k Beadchip. The 37,449 SNPs exceeded a minor allele frequency 0.2 was used in this study. Principal components analysis (PCA) was conducted using EigenStrat to identify the genetic relationship among the pig breeds. Genomic structure of the pig breeds was inferred using FRAPPE. According to the result of PCA, 3 major clusters which consisted of Agu, Western, and Asian pigs were constructed by PC1 and PC2. By PC3 and PC4, 4 clusters were constructed as follows: Asian pigs including Agu, Large White-originated breeds which are from northern England, Hampshire/Berkshire–originated breeds (southern England), and Duroc (American). When the number of ancestor group was assumed to 3, Agu population was set to be the independent group from the Western pig breeds and Asian pigs. The remarkable genomic structure of Agu was possibly caused by the strong bottleneck in the past.