Compared with conventional identification methods, DNA-based genetic approaches such as single nucleotide polymorphisms (SNPs) and satellites are much more reliable for pig identification and meat traceability. In this study, multiallelic amplification fragments with multiple SNPs, incorporating the advantages of both SNPs and microsatellites, were explored for the first time for pig identification and meat traceability. Primer pairs for multiallelic fragments and their optimal SNPs were successfully selected and used for identification of individuals from Suzhong and Duroc populations. Meanwhile, the combined panel of the above mentioned primer pairs together with their optimal SNPs for Suzhong and/or Duroc pigs were validated for identification of the hybrids (Suzhong×Duroc). Therefore, we have successfully selected multiallelic amplification fragments with multiple SNPs to identify pigs and their meat samples from Suzhong, Duroc or their hybrids. Our study demonstrates that our method is more powerful for pig identification or meat traceability than SNPs or microsatellites.
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