Insights into mitochondrial DNA variation of common carp Cyprinus carpio strains in the Centre of Carpathian Basin

Abstract

The assessment of genetic reserves is extremely important for the conservation of rich genetic stocks. Artificial selection can be considered as the main evolutionary force in domesticated species, which can influence the development of the genetic diversity and spatial patterns of the genetic structure of a species. Understanding the extent of genetic differentiation between breeds provides insight into breeding work and domestication processes. In this study, we examined the maternal genetic diversity and spatial pattern of genetic structures of 13 Hungarian common carp strains of six hatchery populations based on two datasets of the mitochondrial DNA: 1) a concatenated fragment (2551 bp) including 12S rRNA, tRNA-Val, 16S rRNA, cytochrome b, and control region (the first dataset), and 2) a 687 bp fragment of cytochrome b (the second dataset). Altogether 250 sequences were used in both datasets comprising 138 own samples and 112 Genbank sequences from previous studies. A total of 43 haplotypes were detected among the 138 new sequences for the second dataset, including 40 novel haplotypes and three previously recorded haplotypes. Haplotype diversity levels were relatively high (average = 0.566 ± 0.052) in most common carp strains, whereas nucleotide diversity values were moderate to low (average = 0.00474 ± 0.00083). Based on Bayesian clustering analysis using STRUCTURE, K = 3 was the most likely grouping of strains. Seven of the studied strains were grouped with high membership coefficients in the same cluster, while individuals from the other strains showed a mix. Differences in the genetic diversity of stocks between hatcheries reflect historical facts and anthropogenic events as well. Our results reveal the genetic structure of strains that reflect founding practices as well as the movements of individuals and strains between hatcheries. Our findings may have an impact on fisheries professionals as well as fish farmers who are involved in introductions, restorations, strains design, and development.