How could fully scaled carps appear in natural waters in Madagascar?

The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the 'mirror' reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms.

Immune responses of resistant and sensitive common carp families following experimental challenge with Aeromonas hydrophila.

Parameters of non-specific immune response and level of specific and natural antibodies were investigated after an experimental challenge with Aeromonas hydrophila in genetically different common carp (Cyprinus carpio) families. Ten resistant and ten sensitive families were used for the experiment, which had been selected out of 96 families, based on the results of a preliminary challenge test. Blood samples were collected 12 h, one week and 21 days following the challenge. Phagocytic and respiratory burst activities of phagocytic cells, lysozyme activity of the blood plasma were determined. Level of specific antibodies against A. hydrophila and level of natural antibodies were measured in the samples taken on the 28th day. Non-infected fish from resistant and sensitive families were used as controls. Significant differences of phagocytic and lysozyme activities were measured between the challenged resistant and sensitive families. The level of specific antibodies between the same families was also found to be significantly different. There were no significant differences of the studied parameters between the control groups. Based on our results, phagocytic activity of leukocytes, plasma lysozyme activity and specific antibody titre were found to be higher in the resistant families than in the sensitive ones following infection with A. hydrophila.

A new strain group of common carp: The genetic differences and admixture events between Cyprinus carpio breeds.

Common carp (Cyprinus carpio) has an outstanding economic importance in freshwater aquaculture due to its high adaptive capacity to both food and environment. In fact, it is the third most farmed fish species worldwide according to the Food and Agriculture Organization. More than four million tons of common carp are produced annually in aquaculture, and more than a hundred thousand tons are caught from the wild. Historically, the common carp was also the first fish species to be domesticated in ancient China, and now, there is a huge variety of domestic carp strains worldwide. In the present study, we used double digestion restriction site-associated DNA sequencing to genotype several European common carp strains and showed that they are divided into two distinct groups. One of them includes central European common carp strains as well as Ponto-Caspian wild common carp populations, whereas the other group contains several common carp strains that originated in the Soviet Union, mostly as cold-resistant strains. We believe that breeding with wild Amur carp and subsequent selection of the hybrids for resistance to adverse environmental conditions was the attribute of the second group. We assessed the contribution of wild Amur carp inheritance to the common carp strains and discovered discriminating genes, which differed in allele frequencies between groups. Taken together, our results improve our current understanding of the genetic variability of common carp, namely the structure of natural and artificial carp populations, and the contribution of wild carp traits to domestic strains.

Differences in the antibody response and survival of genetically different varieties of common carp (Cyprinus carpio L.) vaccinated with a commercial Aeromonas salmonicida/A. hydrophila vaccine and challenged with A. hydrophila.

Males of two strains of carp, wild Duna (D), and inbred Szarvas 22 (22), were selected for high and low stress response. Two purebreds of D and 22, from randomly chosen parents and four crosses, 22 x 22-L (low stress response), 22 x 22-H (high stress response), 22 x D-L (low stress response) and 22 x D-H (high stress response) from selected stress response parents were produced and vaccinated with a commercial Aeromonas salmonicida/Aeromonas hydrophila vaccine and their circulating antibody response evaluated 1, 3, 5, and 7 weeks post-vaccination by ELISA. Significantly higher titres of circulatory antibodies against A. hydrophila were found in the families 22 and cross 22 x 22-L compared to other groups. The development of circulatory antibodies against A. hydrophila in all crosses having at least one D parent was low and remained low throughout the experiment. The level of circulatory antibodies against atypical A. salmonicida in the inbred strain increased following a booster vaccination with the highest values measured in inbred strain 22 and cross 22 x 22 L. The different varieties of carp had different levels of survival against experimental challenge with A. hydrophila. The greatest survival was obtained in strain 22 and cross 22 x 22-L, while ~90% of D wild carp and cross 22 x D (independent of their stress response) died. Survival results correlated well with the antibody response of the different groups: 22 and 22 x 22-L had the highest antibody titres against A. hydrophila and the greatest level of survival.

Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes.

Common carp (Cyprinus carpio L.) is one of the oldest, most widely farmed commercially important freshwater fish in the world. However, many undetermined phylogenetic relationships and origins of common carp lineages remain, which are obstacles to conservation and genetic breeding of this species. Phylogenetic analyses based on molecular tools are helpful to distinguish the origin of species, understand and clarify their evolutionary history, and provide a genetic basis for selective breeding. In this study, we demonstrated a method to extract complete mitochondrial genome sequences from whole-genome resequencing data using the Illumina platform. The complete mitochondrial genome sequences of 26 individuals representing nine strains were obtained and subjected to a phylogenetic analysis. We reconstructed the phylogenetic topologies of the nine strains and analyzed the haplotypes. Results from both analyses suggested that the genome sequences belonged to two distinct subspecies from Europe and East Asia. We also estimated the time of divergence of the nine strains, which was up to 100 KYA. The phylogenetic results clarified the breeding history of Songpu mirror carp and suggest that this species may be hybrid of paternal European mirror carp and maternal Xingguo red carp. The results also support a previous hypothesis that koi may have originated from or have close ancestry with Oujiang color carp in China.

Effect of pulp and paper mill effluent (BKME) on physiological parameters of roach (Rutilus rutilus) infected by the digenean Rhipidocotyle fennica.

Physiological parameters were measured after experimental infection of roach (Rutilus rutilus L.) with Rhipidocotyle fennica Gibson, Valtonen et Taskinen, 1992 (Digenea) cercariae. The fish were caught from two lakes: a eutrophic bleached kraft mill effluent (BKME)-contaminated lake and an oligotrophic unpolluted lake. The intensity of infection was followed up to 10 days post infection (p.i.) and physiological parameters indicating non-specific stress responses and the condition of fish were examined simultaneously. The mean abundance, the number of parasites per fish, of R. fennica was significantly higher in the fish from the contaminated water during the first two days p.i., probably reflecting the decreased resistance of these fish to infection. The decrease of leukocrit, as well as the increase of the activity of transaminases (GOT and GPT) in infected fish of both groups are suggestive of pathological processes caused by cercariae penetrating the fish. A significantly lower leukocrit value, as well as higher alkaline phosphatase activity and plasma chloride levels were noted in fish originating from the contaminated lake compared to those from the unpolluted lake. No significant differences were noted in haematocrit, plasma protein and calcium values between the fish from the uncontaminated and contaminated lakes, or between the infected and uninfected control fish.

Genome sequence and genetic diversity of the common carp, Cyprinus carpio.

The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.

Disappearing scales in carps: re-visiting Kirpichnikov's model on the genetics of scale pattern formation.

The body of most fishes is fully covered by scales that typically form tight, partially overlapping rows. While some of the genes controlling the formation and growth of fish scales have been studied, very little is known about the genetic mechanisms regulating scale pattern formation. Although the existence of two genes with two pairs of alleles (S&s and N&n) regulating scale coverage in cyprinids has been predicted by Kirpichnikov and colleagues nearly eighty years ago, their identity was unknown until recently. In 2009, the 'S' gene was found to be a paralog of fibroblast growth factor receptor 1, fgfr1a1, while the second gene called 'N' has not yet been identified. We re-visited the original model of Kirpichnikov that proposed four major scale pattern types and observed a high degree of variation within the so-called scattered phenotype due to which this group was divided into two sub-types: classical mirror and irregular. We also analyzed the survival rates of offspring groups and found a distinct difference between Asian and European crosses. Whereas nude × nude crosses involving at least one parent of Asian origin or hybrid with Asian parent(s) showed the 25% early lethality predicted by Kirpichnikov (due to the lethality of the NN genotype), those with two Hungarian nude parents did not. We further extended Kirpichnikov's work by correlating changes in phenotype (scale-pattern) to the deformations of fins and losses of pharyngeal teeth. We observed phenotypic changes which were not restricted to nudes, as described by Kirpichnikov, but were also present in mirrors (and presumably in linears as well; not analyzed in detail here). We propose that the gradation of phenotypes observed within the scattered group is caused by a gradually decreasing level of signaling (a dose-dependent effect) probably due to a concerted action of multiple pathways involved in scale formation.

Genetic characterization of 18 novel microsatellite loci in northern pike (Esox lucius L.).

The northern pike (Esox lucius L.), an important predatory freshwater species, is undergoing significant population decline. In this study, 18 novel polymorphic microsatellite loci were isolated and used for assessing genetic variation in the Chinese Ulungur and Hungarian Balaton populations of the species. The number of alleles ranged from 2 to 13, observed heterozygosity from 0.154 to 0.920 and expected heterozygosity from 0.145 to 0.921, thereby indicating the specific usefulness of these suites of markers for investigating genetic variability.

Genetic characterization of 18 novel microsatellite loci in northern pike (Esox lucius L)

The northern pike (Esox lucius L.), an important predatory freshwater species, is undergoing significant population decline. In this study, 18 novel polymorphic microsatellite loci were isolated and used for assessing genetic variation in the Chinese Ulungur and Hungarian Balaton populations of the species. The number of alleles ranged from 2 to 13, observed heterozygosity from 0.154 to 0.920 and expected heterozygosity from 0.145 to 0.921, thereby indicating the specific usefulness of these suites of markers for investigating genetic variability.