Genetic Investigation of Aral Wild Common Carp Populations (Cyprinus carpio) Using ddRAD Sequencing

Abstract

Common carp (Cyprinus carpio) is a widespread freshwater fish species of the Cyprinidae family, one of the largest and most diverse fish families. The natural habitats of C. carpio extend from Western Europe to South-East Asia. Common carp has remained an economically important fish species in aquaculture for many centuries and its production nowadays exceeds 4 million tons worldwide and continues to grow. The taxonomy of C. carpio is complicated, since this species is usually distinguished in two, three, and even four distinct subspecies. In the present study, we used ddRAD-sequencing to genotype 30 specimens from five wild common carp populations from the Ponto-Caspian, Balkhash-Ile, and Aral Sea geographical regions. It is demonstrated that they differ at the population level according to F-statistics analysis. At the same time, the subspecies status of C. carpio aralensis has not yet been confirmed. We found several loci that can be used as a discriminant for Aral and Ponto-Caspian wild common carp populations. It is suggested that Aral carp (C. carpio aralensis), which inhabits Balkhash-Ile and Aral Sea basins, is related to Ponto-Caspian or European carp (C. carpio carpio). Moreover, Aral carp might be the ancestor for European carp subspecies. Our results can be used to develop population-specific, high-density SNP marker panels, allowing the trade control of common carp production in the Eurasian Economic Union.

Genetic Diversity of Common Olive (Olea europaea L.) Cultivars from Nikita Botanical Gardens Collection Revealed Using RAD-Seq Method

“…For each pool, a target distribution of 600 to 800 nucleotide fragments was collected on a BluePippin instrument (Sage Science Inc., Beverly, MA, USA). Next, PCR was performed to enrich the libraries and to attach external unique TruSeq indices with consequent purification on AMPureXP beads [42]. The quality and concentration of the resulting libraries were checked using a Qubit 2.0 fluorometer (Invitrogen, Carlsbad, CA, USA) and a DNA Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).…”

Aquatic Biodiversity: Evolution, Taxonomy and Conservation

“…Three articles are about taxonomy, genetics, and trophic adaptations of fishes. Genomic ddRAD-sequencing study on wild populations of common carp from the Ponto-Caspian, Balkhash-Ile, and Aral Sea basins by Shalgimbaeva et al [9] revealed that Aral Sea carp C. carpio aralensis inhabiting Balkhash-Ile and Aral Sea basins belongs to Ponto-Caspian or European carp C. carpio carpio. Authors also found several loci that can contribute to developing the population-specific, high-density SNP marker panels allowing the trade control of common carp production.…”