GBS-obtained SNP detected divergent genomic loci between farmed and wild common carp

Cyprinus carpio is one of the most important bony fish in the globe-wide aquaculture which also has an endemic distribution in the Caspian Sea. There are some evidences showing the probability of mixing between farmed and wild common carp in the Caspian Sea. The hybridization events between farmed and wild strains are supposed to impose negative effects on historically and functionally important traits such as maturity, success of breeding and age at maturity. Hence, discrimination of wild and farmed animals is of great important in fields of biology and conservation genomics. For this purpose, ۳۴ fin tissues of of common carp were sampled from the Caspian Sea (Miankaleh, ۱۹ specimens) and a farm in Gomishan (۱۵ specimens) and stored at absolute ethanol. After DNA extraction, the GBS libraries were constructed sequenced at BGI sequencing facilities and the SNPs were called. The obtained results based on screening over ۱۷,۰۰۰ SNPs identified eight chromosomal SNPs with Fst values above ۰.۲, indicating divergent behaviour and potential usage to be used as novel markers in conservation genomics of common carp in the Southern basin of the Caspian Sea. The annotation results of the found ۸ loci detected two of the SNPs being related to encoding genes. Hence, new advances in genome sequencing technologies and the provided techniques such as GBS are highly capable to be used in conservation genomics of not only common carp but also other endemic fish species of the Caspian Sea in order to provide a fine-scale stocks management.

Keywords:

Caspian Sea , Conservation genomics , Cyprinus carpio , Genotyping , SNP