The genetics of overwintering performance in two-year old common carp and its relation to performance until market size

Molecular cloning, tissue distribution, and pharmacologic function of melanocortin-3 receptor in common carp (Cyprinus carpio)

Melanocortin-3 receptor (MC3R) not only regulates energy homeostasis in animals, but also is an important regulator of inflammation. As one of the most widely farmed freshwater fish, common carp has attracted great interest for its feeding and inflammation regulation. In this study, we cloned the coding sequence (CDS) of common carp Mc3r (ccMc3r), examined its tissue expression profile, and investigated the function of this receptor in mediating downstream signaling pathways. The results showed that the CDS of ccMc3r was 975 bp, encoding a putative protein of 324 amino acids. Homology, phylogeny, and chromosomal synteny analyses revealed that ccMc3r is evolutionarily close to the orthologs of cyprinids. Quantitative real-time PCR (qPCR) indicated that ccMc3r was highly expressed in the brain and intestine. The luciferase reporter systems showed that four ligands, ACTH (1-24), α-MSH, β-MSH, and NDP-MSH, were able to activate the cAMP and MAPK/ERK signaling pathways downstream of ccMc3r with different potencies. For the cAMP signaling pathway, ACTH (1-24) had the highest activation potency; while for the MAPK/ERK signaling pathway, β-MSH had the greatest activation effect. In addition, we found that the four agonists were able to inhibit TNF-α-induced NF-κB signaling in approximately the same order of potency as cAMP signaling activation. This study may facilitate future studies on the role of Mc3r in common carp feed efficiency and immune regulation.

Genetically Based Physiological Responses to Overwinter Starvation in Gibel Carp (Carassius gibelio)

Normally, fish will decrease food intake or even stop feeding during the winter. In previous studies, two widely cultured gibel carp strains (strain A and strain F) showed differences in lipid and glucose metabolism. Therefore, we hypothesized that the physiological changes during the overwintering period would be different between the two strains. Thus, the two strains were starved for 77 days, after which the levels of glucose and lipid metabolism, ER stress, autophagy, and apoptosis were determined. The starvation increased hepatic glycogenolysis and fatty acid β-oxidation but suppressed lipogenesis in both strains overwintering. Considering the effects of genotype, strain F had higher levels of ER stress and autophagy but lower levels of apoptosis than strain A, suggesting that strain F might be more resistant to overwintering starvation. The interactions between strains and starvation periods were observed in plasma triglyceride contents and the mRNA levels of pyruvate kinase (pk), sterol regulatory element binding protein 1 (srebp1), activating transcription factor 4 (atf4), and autophagy protein 12 (atg12). In conclusion, long-term starvation during winter could induce hepatic glycogenolysis and fatty acid β-oxidation but suppress lipogenesis, ER stress, autophagy, and apoptosis in gibel carp, and strain F may be more resistant to starvation during winter. Taken together, these results discovered the responses to prolonged starvation stress during winter in two strains of gibel carp and could provide information for genotype selection, especially for selecting strains better adapted to winter.

Optimizing Genomic Prediction of Host Resistance to Koi Herpesvirus Disease in Carp

Genomic selection (GS) is increasingly applied in breeding programs of major aquaculture species, enabling improved prediction accuracy and genetic gain compared to pedigree-based approaches. Koi Herpesvirus disease (KHVD) is notifiable by the World Organization for Animal Health and the European Union, causing major economic losses to carp production. GS has potential to breed carp with improved resistance to KHVD, thereby contributing to disease control. In the current study, Restriction-site Associated DNA sequencing (RAD-seq) was applied on a population of 1,425 common carp juveniles which had been challenged with Koi herpes virus, followed by sampling of survivors and mortalities. GS was tested on a wide range of scenarios by varying both SNP densities and the genetic relationships between training and validation sets. The accuracy of correctly identifying KHVD resistant animals using GS was between 8 and 18% higher than pedigree best linear unbiased predictor (pBLUP) depending on the tested scenario. Furthermore, minor decreases in prediction accuracy were observed with decreased SNP density. However, the genetic relationship between the training and validation sets was a key factor in the efficacy of genomic prediction of KHVD resistance in carp, with substantially lower prediction accuracy when the relationships between the training and validation sets did not contain close relatives.

A Novel Dietary Source of EPA and DHA: Metabolic Engineering of an Important Freshwater Species-Common Carp by fat1-Transgenesis

Omega-3 polyunsaturated fatty acids (n-3 PUFAs), such as eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA), are essential for neural development and human health. The n-3 PUFAs are mainly obtained from marine fish by dietary intake. Freshwater fish species usually contain low level of n-3 PUFAs due to the lack of n-3 PUFAs in their food chain. In this study, we report on the substantial production of EPA and DHA in a globally important freshwater fish species, common carp (Cyprinus carpio). This was achieved by introducing an "all-fish" transgene CA:fat1 containing the fish codon-optimized omega-3 desaturase gene (fat1) driven by the common carp β-actin promoter (CA). Through a sperm sample screening method, we successfully generated fat1-positive F1 transgenic population with high efficiency. In F1 population, the muscle contents of ALA (18:3n-3), EPA and DHA were significantly increased when compared with non-transgenic siblings. Thereafter, four independent F2 heterozygous lines were obtained from 4 F1 transgenic males and a detailed comparison of fatty acids profile and growth performance was carried out for these 4 lines. All fat1-transgenic common carps from 4 lines showed an evident decrease in n-6 PUFA contents and a substantial increase in n-3 PUFA contents, among which line 4 stands out, showing a statistically significant increase in all 4 types of n-3 PUFAs including ALA (4.4-fold increase, p < 0.001), EPA (4.8-fold increase, p < 0.01), C22:5n-3 (DPA, 2.4-fold increase, p < 0.05), and DHA (1.9-fold increase, p < 0.05). Therefore, the line 4 was selected as the optimized breeding stock for further study, and the proximate nutrition composition and PUFA synthesis pathway were analyzed. Our study demonstrates that in the transgenic group, the muscular lipid content did not change, while fat accumulations in the internal organs and especially in the liver were significantly decreased as a result of hyperactivation of fatty acid oxidation process. Finally, we conclude that the "all-fish" CA:fat1-transgenic freshwater fish-common carp-can serve as a novel healthy dietary source of n3-PUFAs, especially EPA and DHA.

Mapping and Sequencing of a Significant Quantitative Trait Locus Affecting Resistance to Koi Herpesvirus in Common Carp

Cyprinids are the most highly produced group of fishes globally, with common carp being one of the most valuable species of the group. Koi herpesvirus (KHV) infections can result in high levels of mortality, causing major economic losses, and is listed as a notifiable disease by the World Organization for Animal Health. Selective breeding for host resistance has the potential to reduce morbidity and losses due to KHV. Therefore, improving knowledge about host resistance and methods of incorporating genomic data into breeding for resistance may contribute to a decrease in economic losses in carp farming. In the current study, a population of 1,425 carp juveniles, originating from a factorial cross between 40 sires and 20 dams was challenged with KHV. Mortalities and survivors were recorded and sampled for genotyping by sequencing using Restriction Site-Associated DNA sequencing (RADseq). Genome-wide association analyses were performed to investigate the genetic architecture of resistance to KHV. A genome-wide significant QTL affecting resistance to KHV was identified on linkage group 44, explaining approximately 7% of the additive genetic variance. Pooled whole genome resequencing of a subset of resistant (n = 60) and susceptible animals (n = 60) was performed to characterize QTL regions, including identification of putative candidate genes and functional annotation of associated polymorphisms. The TRIM25 gene was identified as a promising positional and functional candidate within the QTL region of LG 44, and a putative premature stop mutation in this gene was discovered.

Potential for Genetic Improvement of the Main Slaughter Yields in Common Carp With in vivo Morphological Predictors

Common carp is a major aquaculture species worldwide, commonly sold alive but also as processed headless carcass or filets. However, recording of processing yields is impossible on live breeding candidates, and alternatives for genetic improvement are either sib selection based on slaughtered fish, or indirect selection on correlated traits recorded in vivo. Morphological predictors that can be measured on live fish and that correlate with real slaughter yields hence remain a possible alternative. To quantify the power of morphological predictors for genetic improvement of yields, we estimated genetic parameters of slaughter yields and various predictors in 3-year-old common carp reared communally under semi-intensive pond conditions. The experimental stock was established by a partial factorial design of 20 dams and 40 sires, and 1553 progenies were assigned to their parents using 12 microsatellites. Slaughter yields were highly heritable (h² = 0.46 for headless carcass yield, 0.50 for filet yield) and strongly genetically correlated with each other (r_g = 0.96). To create morphological predictors, external (phenotypes, 2D digitization) and internal measurements (ultrasound imagery) were recorded and combined by multiple linear regression to predict slaughter yields. The accuracy of the phenotypic prediction was high for headless carcass yield (R² = 0.63) and intermediate for filet yield (R² = 0.49). Interestingly, heritability of predicted slaughter yields (0.48–0.63) was higher than that of the real yields to predict, and had high genetic correlations with the real yields (r_g = 0.84–0.88). In addition, both predicted yields were highly phenotypically and genetically correlated with each other (0.95 for both), suggesting that using predicted headless carcass yield in a breeding program would be a good way to also improve filet yield. Besides, two individual predictors (P₁ and P₂) included in the prediction models and two simple internal measurements (E4 and E23) exhibited intermediate to high heritability estimates (h² = 0.34 – 0.72) and significant genetic correlations to the slaughter yields (r_g = |0.39 – 0.83|). The results show that there is a solid potential for genetic improvement of slaughter yields by selecting for predictor traits recorded on live breeding candidates of common carp.