Genotyping-by-Sequencing Reveals the Impact of Restocking on Wild Common Carp Populations of the Southern Caspian Basin

Abstract

Understanding the population structure and level of genetic diversity of wild populations is fundamental for appropriate stock management and species conservation. The common carp (Cyprinus carpio) is one of the most important bony fish throughout the Southern coastline of the Caspian Sea, but captures of this species have seen a dramatic reduction during the last decade. As a consequence, a restocking program has been put in place to maintain C. carpio populations, but its impact is not clear. In the present study, the population structure and genetic diversity of C. carpio in the Southern Caspian basin was determined using 17,828 single-nucleotide polymorphism (SNP) markers. A total of 117 individuals collected from four different locations in the southern Caspian basin and a farm were genotyped by genotyping-by-sequencing. The overall Fst obtained was 0.04, indicating a low level of differentiation between populations, and most genetic diversity was attributed to within population variation (97%). The low Fst values suggest that frequent migration events between different locations occur, and three migration events were inferred in the present study. However, each population still showed a distinct genetic profile, which allowed distinguishing the origin of the fish. This indicates that the ongoing restocking program is maintaining the differences between populations to some extent. Nonetheless, high inbreeding and low heterozygosity were detected in all populations, suggesting that additional conservation efforts are required to protect C. carpio populations in the Southern coast of the Caspian Sea.

Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius

“…The method for GBS library preparation and sequencing is fully described in the paper on common carp ( Cyprinus carpio ) [ 19 ]. The paired-end GBS sequencing of the samples was done at BGI company in China ( https://www.bgi.com/global ).…”

“…Nowadays, because of the impressive advances in sequencing technologies known as Next Generation Sequencing (NGS), researchers are able to have accessibility to the genomic information of both model and nonmodel organisms [ 17 , 18 ]. Genotyping-by sequencing (GBS) is a technique on the basis of genome complexity reduction by restriction enzymes which has been widely applied in fish population studies and aquaculture activities [ 19 , 20 ]. For example, large scale SNP obtained from GBS were successfully used in separation wild and cultured populations of Cynoglossus semilaevis [ 21 ] and significant QTL affecting resistance to Koi Herpesvirus was detected through a genome-wide association study (GWAS) in Common Carp [ 22 ].…”

Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars

“…The GBS technique can be used simultaneously for marker discovery and genotyping, allowing many samples to be multiplexed in order to reduce the cost per sample [18]. A modern genomics approach such as GBS can be used to analyze cultivated potato samples in order to gain insight into the genomic diversity of extant germplasm, to identify historic introgressions and hybridizations, and to identify genes that were targeted during domestication that are responsible for agricultural traits [2,19]. Several studies have identified GBS as a highly…”