Molecular species identification of commercially important penaeid shrimp from the Gulf of Mexico using a multiplex haplotype-specific PCR assay

This study describes a multiplex PCR assay based on the 16S rRNA mitochondrial gene to identify the penaeid shrimp Farfantepenaeus aztecus, Farfantepenaeus duorarum, Farfantepenaeus brasiliensis and Litopenaeus setiferus, all native to the Gulf of Mexico, and the exotic Litopenaeus vannamei. The assay was validated using positively identified adult shrimp and confirmed by direct sequencing. Samples of postlarvae and early juveniles collected in the eastern and western Gulf of Mexico were tested yielding 119 F. aztecus, 78 F. duorarum and five L. setiferus. Reliable identification of the morphologically similar early life stages of F. aztecus and F. duorarum has important implications for management and conservation. Similarly, the ability to identify L. vannamei is relevant as early detection could help minimize the ecological impact if this species escapes to the wild.