Development of Traceability System for Agu - Okinawan Pig - Using Dense SNP Markers

Agu is an economically important pig breed in Okinawa due to its favorable meat quality attributed to tenderness and highly unsaturated fatty acids in the meat. Founders of Agu pigs were presumed to be introduced from China ~600 years ago. Recently, Agu has crossbred with European pig breeds in order to improve the pork meat productivity. The pork meat is highly evaluated compared to the other commercial pork. Therefore it is a challenge for Agu producer to acquire a certain established reputation in the market. Objective of this study is to develop the traceability system of the Agu-branded pork based on DNA marker technology to distinguish Agu specific genotypes using dense single nucleotide polymorphism (SNP) markers. The traceability system using supervised learning was consisted of two parts, a training step and predicting step. In the training step, firstly, the first and second eigenvectors were calculated from SNP×SNP matrix adjusted using minor allele frequencies. Then principal component scores calculated using the eigenvectors were clustered by each breed, and 95% confidence ellipsoid constructed from the scores in order to discriminate each breed. In the prediction step, pigs with unknown breed were assigned their predicted breed group from the principal component scores calculated using their SNP genotypes and the eigenvectors. We performed assignment test using additional 192 animals, and as a result, 98.6% of the animals were correctly assigned to their true breeds. The result indicated that the traceability system would contribute to assurance of Agu branded product identity.