Genetic contribution of domestic European common carp (Cyprinus carpio carpio) and Amur carp (Cyprinus carpio haematopterus) to the wild Vietnamese carp population as revealed by ddRAD sequencing

At least three subspecies of the common carp, namely, Cyprinus carpio carpio, C. carpio haematopterus, and C. carpio viridiviolaceus, have been described to date. These subspecies natively inhabit Ponto-Caspian and Far Eastern regions, as well as northern Vietnam, but they have also been introduced into aquaculture in almost every region of the world where the environmental conditions are suitable. Moreover, common carp is one of the most widely cultured freshwater fish species in the world. In northern Vietnam, common carp fisheries and aquacultural production are of great economic importance. Investigation of the subspecies distribution among aquacultured and wild common carps is important for understanding the impact of human economic activity, such as aquaculture production, on the environment. In the present study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) was used to estimate the genetic impact of aquaculture carps on the wild common carp populations of northern Vietnam. Our work reveals that a part of wild carp populations has a significant contribution to farmed fish ancestry. For some populations, this contribution exceeds 25% of the population ancestry, but the ancestry value is distributed across most specimens of the populations, whereas pure aquaculture specimens are quite uncommon for wild habitats.