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16 pages, 2160 KiB

Open AccessArticle

Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming

by Dimitrios Tsaparis, Thomas Lecocq, Dimitrios Kyriakis, Katerina Oikonomaki, Pascal Fontaine and Costas S. Tsigenopoulos

Animals 2022, 12(9), 1178; https://doi.org/10.3390/ani12091178 - 4 May 2022

Cited by 7 | Viewed by 2095

Abstract

The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations [...] Read more.

The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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20 pages, 3574 KiB

Open AccessArticle

Genomic Predictions of Phenotypes and Pseudo-Phenotypes for Viral Nervous Necrosis Resistance, Cortisol Concentration, Antibody Titer and Body Weight in European Sea Bass

by Sara Faggion, Daniela Bertotto, Valentina Bonfatti, Matteo Freguglia, Luca Bargelloni and Paolo Carnier

Animals 2022, 12(3), 367; https://doi.org/10.3390/ani12030367 - 2 Feb 2022

Cited by 2 | Viewed by 1710

Abstract

In European sea bass (Dicentrarchus labrax L.), the viral nervous necrosis mortality (MORT), post-stress cortisol concentration (HC), antibody titer (AT) against nervous necrosis virus and body weight (BW) show significant heritability, which makes selective breeding a possible option for their improvement. An [...] Read more.

In European sea bass (Dicentrarchus labrax L.), the viral nervous necrosis mortality (MORT), post-stress cortisol concentration (HC), antibody titer (AT) against nervous necrosis virus and body weight (BW) show significant heritability, which makes selective breeding a possible option for their improvement. An experimental population (N = 650) generated by a commercial broodstock was phenotyped for the aforementioned traits and genotyped with a genome-wide SNP panel (16,075 markers). We compared the predictive accuracies of three Bayesian models (Bayes B, Bayes C and Bayesian Ridge Regression) and a machine-learning method (Random Forest). The prediction accuracy of the EBV for MORT was approximately 0.90, whereas the prediction accuracies of the EBV and the phenotype were 0.86 and 0.21 for HC, 0.79 and 0.26 for AT and 0.71 and 0.38 for BW. The genomic prediction of the EBV for MORT used to classify the phenotype for the same trait showed moderate classification performance. Genome-wide association studies confirmed the polygenic nature of MORT and demonstrated a complex genetic structure for HC and AT. Genomic predictions of the EBV for MORT could potentially be used to classify the phenotype of the same trait, though further investigations on a larger experimental population are needed. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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18 pages, 1241 KiB

Open AccessArticle

Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass

by Stavroula Oikonomou, Athanasios Samaras, Maria Tekeoglou, Dimitrios Loukovitis, Arkadios Dimitroglou, Lefteris Kottaras, Kantham Papanna, Leonidas Papaharisis, Costas S. Tsigenopoulos, Michail Pavlidis and Dimitrios Chatziplis

Animals 2022, 12(3), 277; https://doi.org/10.3390/ani12030277 - 23 Jan 2022

Cited by 7 | Viewed by 3280

Abstract

The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its [...] Read more.

The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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17 pages, 6475 KiB

Open AccessArticle

Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

by Menelaos Kavouras, Emmanouil E. Malandrakis, Ewout Blom, Kyriaki Tsilika, Theodoros Danis, Panagiota Panagiotaki and Athanasios Exadactylos

Animals 2021, 11(8), 2273; https://doi.org/10.3390/ani11082273 - 1 Aug 2021

Cited by 2 | Viewed by 3150

Abstract

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented [...] Read more.

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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13 pages, 1457 KiB

Open AccessArticle

Association between the Polymorphisms of fads2a and fads2b and Poly-Unsaturated Fatty Acids in Common Carp (Cyprinus carpio)

by Yan Zhang, Xiao-Qing Sun, Yu-Qing Ye, Qi Wang, Qing-Song Li, Ran Zhao, Hong-Wei Wang and Jiong-Tang Li

Animals 2021, 11(6), 1780; https://doi.org/10.3390/ani11061780 - 15 Jun 2021

Cited by 5 | Viewed by 3799

Abstract

Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in PUFAs biosynthesis. Compared with the diploid fish encoding one fads2, the allo-tetraploid common carp, one most important food fish, encodes two fads2 genes (fads2a and fads2b). [...] Read more.

Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in PUFAs biosynthesis. Compared with the diploid fish encoding one fads2, the allo-tetraploid common carp, one most important food fish, encodes two fads2 genes (fads2a and fads2b). The associations between the contents of different PUFAs and the polymorphisms of fads2a and fads2b have not been studied. The contents of 12 PUFAs in common carp individuals were measured, and the polymorphisms in the coding sequences of fads2a and fads2b were screened. We identified five coding single nucleotide polymorphisms (cSNPs) in fads2a and eleven cSNPs in fads2b. Using the mixed linear model and analysis of variance, a synonymous fads2a cSNP was significantly associated with the content of C20:3n-6. One non-synonymous fads2b cSNP (fads2b.751) and one synonymous fads2b cSNP (fads2b.1197) were associated with the contents of seven PUFAs and the contents of six PUFAs, respectively. The heterozygous genotypes in both loci were associated with higher contents than the homozygous genotypes. The fads2b.751 genotype explained more phenotype variation than the fads2b.1197 genotype. These two SNPs were distributed in one haplotype block and associated with the contents of five common PUFAs. These results suggested that fads2b might be the major gene responding to common carp PUFA contents and that fads.751 might be the main effect SNP. These cSNPs would be potential markers for future selection to improve the PUFA contents in common carp. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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14 pages, 1273 KiB

Open AccessArticle

A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus)

by Xinghua Lin, Dayan Zhou, Xiaomin Zhang, Guangli Li, Yulei Zhang, Cailin Huang, Zhixin Zhang and Changxu Tian

Animals 2021, 11(4), 1131; https://doi.org/10.3390/ani11041131 - 15 Apr 2021

Cited by 16 | Viewed by 2654

Abstract

Hong Kong catfish (Clarias fuscus) exhibit sexual dimorphism, particularly in body size. Due to the fast growth rate of males, the sexual size dimorphism of Hong Kong catfish has become an economically important trait. However, limited knowledge is known about the [...] Read more.

Hong Kong catfish (Clarias fuscus) exhibit sexual dimorphism, particularly in body size. Due to the fast growth rate of males, the sexual size dimorphism of Hong Kong catfish has become an economically important trait. However, limited knowledge is known about the molecular mechanisms of sex determination and sex differentiation in this species. In this study, a first de novo transcriptome sequencing analysis of testes and ovaries was performed to identify sex-biased genes in Hong Kong catfish. The results showed that a total of 290,291 circular consensus sequences (CCSs) were obtained, from which 248,408 full-length non-chimeric (FLNC) reads were generated. After non-redundant analysis, a total of 37,305 unigenes were predicted, in which 34,342 unigenes were annotated with multiple public databases. Comparative transcriptomic analysis identified 5750 testis-biased differentially expressed genes (DEGs) and 6991 ovary-biased DEGs. The enrichment analysis showed that DEGs were classified into 783 Gene Ontology (GO) terms and 16 Kyoto Encyclopedia of Gene and Genome (KEGG) pathways. Many DEGs were involved with sex-related GO terms and KEGG pathways, such as oocyte maturation, androgen secretion, gonadal development and steroid biosynthesis pathways. In addition, the expression levels of 23 unigenes were confirmed to validate the transcriptomic data by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first investigation into the transcriptome of Hong Kong catfish testes and ovaries. This study provides an important molecular basis for the sex determination and sex control breeding of Hong Kong catfish. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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20 pages, 2345 KiB

Open AccessArticle

Comparison of Gonadal Transcriptomes Uncovers Reproduction-Related Genes with Sexually Dimorphic Expression Patterns in Diodon hystrix

by Huapu Chen, Zhiyuan Li, Yaorong Wang, Hai Huang, Xuewei Yang, Shuangfei Li, Wei Yang and Guangli Li

Animals 2021, 11(4), 1042; https://doi.org/10.3390/ani11041042 - 7 Apr 2021

Cited by 11 | Viewed by 2035

Abstract

Diodon hystrix is a new and emerging aquaculture species in south China. However, due to the lack of understanding of reproductive regulation, the management of breeding and reproduction under captivity remains a barrier for the commercial aquaculture of D. hystrix. More genetic [...] Read more.

Diodon hystrix is a new and emerging aquaculture species in south China. However, due to the lack of understanding of reproductive regulation, the management of breeding and reproduction under captivity remains a barrier for the commercial aquaculture of D. hystrix. More genetic information is needed to identify genes critical for gonadal development. Here, the first gonadal transcriptomes of D. hystrix were analyzed and 151.89 million clean reads were generated. All reads were assembled into 57,077 unigenes, and 24,574 could be annotated. By comparing the gonad transcriptomes, 11,487 differentially expressed genes were obtained, of which 4599 were upregulated and 6888 were downregulated in the ovaries. Using enrichment analyses, many functional pathways were found to be associated with reproduction regulation. A set of sex-biased genes putatively involved in gonad development and gametogenesis were identified and their sexually dimorphic expression patterns were characterized. The detailed transcriptomic data provide a useful resource for further research on D. hystrix reproductive manipulation. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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14 pages, 2416 KiB

Open AccessArticle

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

by Fotis Pappas and Christos Palaiokostas

Animals 2021, 11(3), 899; https://doi.org/10.3390/ani11030899 - 21 Mar 2021

Cited by 3 | Viewed by 4992

Abstract

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments [...] Read more.

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding. Full article

(This article belongs to the Special Issue Aquaculture Genetics and Genomics)

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