Abstract：Small Meishan pig (Sus scrofa) is a unique local pig breed in the Taihu River Basin which has the characteristics of delicious meat. There is the problem of counterfeiting meat products in the market, while the traditional identification technology has some limitations in practical application. The present study is to develop a new method to distinguish Small Meishan pig from other pig breeds or strains of Taihu Basin and common western pig breeds by using the third generation molecular marker called Single Nucleotide Polymorphism (SNP). The data of genotyping by genome reducing and sequencing (GGRS) of 7 local breeds (strains) in Taihu Basin (Middle Meishan pig, Small Meishan pig, Erhualian pig, Mi pig, Jiaxinghei pig, Fengjing pig and Shawutou pig) and 5 imported pig breeds (Duroc, Landrace, Yorkshire, Piltland, and Baxia) was used. Five SNP sites only in Small Meishan pig were selected and Sanger sequencing was used to verify the results. It was showed that the 5 SNP sites had high mutation rate in Small Meishan pig. By using the combination of 5 candidate sites, the identification probability could be up to 99.35% and the accuracy was 100% with no false positive identification. The present study provides a basic principle for the protection of genetic resources and identification of fake and inferior pork products in Small Meishan pig.
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