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Genetic Research in Aquaculture

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (10 April 2021) | Viewed by 35989

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Dr. Antonio Figueras

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Instituto de Investigaciones Marinas, IIM-CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
Interests: aquaculture; fish; shellfish; genetics; genomics; transcriptomic; epigenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Overfishing is an important concern, mainly due to the on-going increase in the size of the human population. Fortunately, aquaculture has emerged as an alternative supply of fish and shellfish. In recent years, although capture fishery production has been flat at approximately 90 million tonnes per year, aquaculture has continued to show sustained growth, amounting to 80 million tonnes in recent years. Therefore, fish and shellfish aquaculture represent a powerful economic sector all around the world.

The lowering cost of next-generation sequencing (NGS) strategies during the last years has enabled the genome sequencing of numerous fish and shellfish species with relevance in the aquaculture industry. This represents an important tool for geneticists, since whole-genome availability facilitates the search for genetic markers or genes associated with different traits of interest. Massive transcriptome analyses have also become indispensable to study different questions of interest (nutrition, growth, disease resistance, reproduction, etc.). More recently, the study of the epigenome is being rapidly expanded to aquaculture research.

This Special Issue welcomes papers in the field of the genetics and genomics of fish and shellfish species of interest in aquaculture, including the identification of genetic markers, gene variants, genome sequencing, and transcriptome and epigenome analyses. Manuscripts focusing on high-throughput methodologies will be appreciated, although the topic covers all aspects related to genetic research in aquaculture.

Dr. Antonio Figueras
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

aquaculture
fish
shellfish
genetics
genomics
transcriptomics
epigenomics
high-throughput methodologies

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Published Papers (10 papers)

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Research

18 pages, 5410 KiB

Open AccessArticle

Differential Expression of Long Non-Coding RNA (lncRNA) in Mediterranean Mussel (Mytilus galloprovincialis) Hemocytes under Immune Stimuli

by Patricia Pereiro, Rebeca Moreira, Beatriz Novoa and Antonio Figueras

Genes 2021, 12(9), 1393; https://doi.org/10.3390/genes12091393 - 9 Sep 2021

Cited by 10 | Viewed by 2473

Abstract

The Mediterranean mussel is one of the most economically relevant bivalve mollusk species in Europe and China. The absence of massive mortalities and their resistance to pathogens affecting other cultured bivalves has been under study in recent years. The transcriptome response of this species to different immune stimuli has been extensively studied, and even the complexity of its genome, which has recently been sequenced, has been suggested as one of the factors contributing to this resistance. However, studies concerning the non-coding RNA profiles remain practically unexplored—especially those corresponding to the lncRNAs. To the best of our knowledge, this is the second characterization and study of lncRNAs in this bivalve species. In this work, we identified the potential repertoire of lncRNAs expressed in mussel hemocytes, and using RNA-Seq we analyzed the lncRNA profile of mussel hemocytes stimulated in vitro with three different immune stimuli: LPS, poly I:C, and β-glucans. Compared to unstimulated hemocytes, LPS induced the highest modulation of lncRNAs, whereas poly I:C and β-glucans induced a similar discrete response. Based on the potential cis-regulatory activity of the lncRNAs, we identified the neighboring protein-coding genes of the regulated lncRNAs to estimate—at least partially—the processes in which they are implicated. After applying correlation analyses, it seems that—especially for LPS—the lncRNAs could participate in the regulation of gene expression, and substantially contribute to the immune response. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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23 pages, 2515 KiB

Open AccessArticle

Intestinal Transcriptome Analysis Reveals Enrichment of Genes Associated with Immune and Lipid Mechanisms, Favoring Soybean Meal Tolerance in High-Growth Zebrafish (Danio Rerio)

by Luis Valenzuela, Sebastian Pacheco, Gonzalo Rincón, Leonardo Pavez, Natalia Lam, Adrián J. Hernández, Patricio Dantagnan, Felipe González, Felipe Jilberto, M. Cristina Ravanal, Cecilia Ramos, Héctor Garcia, Cristian Araneda and Pilar E. Ulloa

Genes 2021, 12(5), 700; https://doi.org/10.3390/genes12050700 - 8 May 2021

Cited by 8 | Viewed by 4063

Abstract

The molecular mechanisms underlying fish tolerance to soybean meal (SBM) remain unclear. Identifying these mechanisms would be beneficial, as this trait favors growth. Two fish replicates from 19 experimental families were fed fishmeal-(100FM) or SBM-based diets supplemented with saponin (50SBM + 2SPN) from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (HG-50SBM + 2SPN, 170 ± 18 mg) or lower (LG-50SBM + 2SPN, 76 ± 10 mg) weight gain on 50SBM + 2SPN for intestinal transcriptomic analysis. A histological evaluation confirmed middle intestinal inflammation in the LG- vs. HG-50SBM + 2SPN group. Enrichment analysis of 665 differentially expressed genes (DEGs) identified pathways associated with immunity and lipid metabolism. Genes linked to intestinal immunity were downregulated in HG fish (mpx, cxcr3.2, cftr, irg1l, itln2, sgk1, nup61l, il22), likely dampening inflammatory responses. Conversely, genes involved in retinol signaling were upregulated (rbp4, stra6, nr2f5), potentially favoring growth by suppressing insulin responses. Genes associated with lipid metabolism were upregulated, including key components of the SREBP (mbtps1, elov5l, elov6l) and cholesterol catabolism (cyp46a1), as well as the downregulation of cyp7a1. These results strongly suggest that transcriptomic changes in lipid metabolism mediate SBM tolerance. Genotypic variations in DEGs may become biomarkers for improving early selection of fish tolerant to SMB or others plant-based diets. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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14 pages, 5450 KiB

Open AccessArticle

Responses to Mineral Supplementation and Salmon Lice (Lepeophtheirus salmonis) Infestation in Skin Layers of Atlantic Salmon (Salmo salar L.)

by Lene Sveen, Aleksei Krasnov, Gerrit Timmerhaus and Andrè Sture Bogevik

Genes 2021, 12(4), 602; https://doi.org/10.3390/genes12040602 - 19 Apr 2021

Cited by 6 | Viewed by 3095

Abstract

The crustacean ectoparasite salmon louse (Lepeophtheirus salmonis), which severely affects Atlantic salmon health and welfare is one of the main problems of commercial aquaculture. In the present study, fish were fed a diet supplemented with extra minerals through the inclusion of a commercial additive (Biofeed Forte Salmon), substituting wheat in the control diet, before experimental infestation with salmon lice. Lice counts reduced with time but with no apparent effect of the diets. Further, fish fed the mineral diet had an overall higher number of blue (acidic) mucous cells, while the ratio of purple mucous cells was higher in the mineral diet. The transcriptional response in skin was enhanced at 7 dpc (copepodite life stage) in fish fed the mineral diet including immune and stress responses, while at 21 dpc (pre-adult life stage), the difference disappeared, or reversed with stronger induction in the control diet. Overall, 9.3% of the genes affected with lice also responded to the feed, with marked differences in outer (scale + epidermis) and inner (dermis) skin layers. A comparison of transcriptome data with five datasets from previous trials revealed common features and gene markers of responses to lice, stress, and mechanically induced wounds. Results suggested a prevalence of generic responses in wounded skin and lice-infected salmon. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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23 pages, 4374 KiB

Open AccessArticle

Molecular Pathways and Pigments Underlying the Colors of the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus 1758)

by Pierre-Louis Stenger, Chin-Long Ky, Céline Reisser, Julien Duboisset, Hamadou Dicko, Patrick Durand, Laure Quintric, Serge Planes and Jeremie Vidal-Dupiol

Genes 2021, 12(3), 421; https://doi.org/10.3390/genes12030421 - 15 Mar 2021

Cited by 13 | Viewed by 4843

Abstract

The shell color of the Mollusca has attracted naturalists and collectors for hundreds of years, while the molecular pathways regulating pigment production and the pigments themselves remain poorly described. In this study, our aim was to identify the main pigments and their molecular pathways in the pearl oyster Pinctada margaritifera—the species displaying the broadest range of colors. Three inner shell colors were investigated—red, yellow, and green. To maximize phenotypic homogeneity, a controlled population approach combined with common garden conditioning was used. Comparative analysis of transcriptomes (RNA-seq) of P. margaritifera with different shell colors revealed the central role of the heme pathway, which is involved in the production of red (uroporphyrin and derivates), yellow (bilirubin), and green (biliverdin and cobalamin forms) pigments. In addition, the Raper–Mason, and purine metabolism pathways were shown to produce yellow pigments (pheomelanin and xanthine) and the black pigment eumelanin. The presence of these pigments in pigmented shell was validated by Raman spectroscopy. This method also highlighted that all the identified pathways and pigments are expressed ubiquitously and that the dominant color of the shell is due to the preferential expression of one pathway compared with another. These pathways could likely be extrapolated to many other organisms presenting broad chromatic variation. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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16 pages, 1572 KiB

Open AccessArticle

Sensitivity to Dietary Wheat Gluten in Atlantic Salmon Indicated by Gene Expression Changes in Liver and Intestine

by Amritha Johny, Gerd Marit Berge, André S. Bogevik, Aleksei Krasnov, Bente Ruyter, Christiane Kruse Fæste and Tone-Kari Knutsdatter Østbye

Genes 2020, 11(11), 1339; https://doi.org/10.3390/genes11111339 - 12 Nov 2020

Cited by 7 | Viewed by 3124

Abstract

Feed safety is a necessity for animal health and welfare as well as prerequisite for food safety and human health. Wheat gluten (WG) is considered as a valuable protein source in fish feed due to its suitability as a feed binder, high digestibility, good amino acid profile, energy density and most importantly, due to its relatively low level of anti-nutritional factors (ANFs). The main aim of this study was to identify the impact of dietary WG on salmon health by analysing growth, feed efficiency and the hepatic and intestinal transcriptomes. The fish were fed either control diet with fishmeal (FM) as the only source of protein or diets, where 15% or 30% of the FM were replaced by WG. The fish had a mean initial weight of 223 g and approximately doubled their weight during the 9-week experiment. Salmon fed on 30% WG showed reduced feed intake compared to the 15% and FM fed groups. The liver was the less affected organ but fat content and activities of the liver health markers in plasma increased with the inclusion level of WG in the diet. Gene expression analysis showed significant changes in both, intestine and liver of fish fed with 30% WG. Especially noticeable were changes in the lipid metabolism, in particular in relation to the intestinal lipoprotein transport and sterol metabolism. Moreover, the intestinal transcriptome of WG-fed fish showed shifts in the expression of a large number of genes responsible for immunity and tissue structure and integrity. These observations implied that the fish receiving WG-containing diet were undergoing nutritional stress. Overall, the study provided evidence that a high dietary level of WG can have a negative impact on the intestinal and liver health of salmon with symptoms similar to gluten sensitivity in humans. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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19 pages, 33941 KiB

Open AccessArticle

Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes

by Ling-Yu Wang, Yuan Tian, Hai-Shen Wen, Peng Yu, Yang Liu, Xin Qi, Zhi-Chao Gao, Kai-Qiang Zhang and Yun Li

Genes 2020, 11(11), 1271; https://doi.org/10.3390/genes11111271 - 28 Oct 2020

Cited by 11 | Viewed by 3086

Abstract

The solute carrier 4 (SLC4) family is a class of cell membranes transporters involved in base transport that plays crucial roles in diverse physiological processes. In our study, 15 slc4 genes were identified and annotated in spotted sea bass, including five members of Cl⁻/HCO₃⁻ exchangers, eight genes coding Na⁺-dependent HCO₃⁻ transporters, and two copies of Na⁺-coupled borate transporters. The gene sequence and structure, chromosomal and syntenic arrangement, phylogenetic and evolution profiles were analyzed. Results showed that the slc4 gene in teleosts obviously expanded compared with higher vertebrates, arising from teleost-specific whole genome duplication event. Most gene sites of slc4 in spotted sea bass were under strong purifying selection during evolution, while positive selection sites were only detected in slc4a1b, slc4a8, and slc4a10b. Additionally, qRT-PCR results showed that different slc4 genes exhibited distinct branchial expression patterns after alkalinity and salinity stresses, of which the strongly responsive members may play essential roles during these physiological processes. Our study provides the systemic overview of the slc4 gene family in spotted sea bass and enables a better understanding for the evolution of this family and further deciphering the biological roles in maintaining ion and acid–base homeostasis in teleosts. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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11 pages, 1403 KiB

Open AccessArticle

Multigene Expression Assay for Assessment of the Immune Status of Atlantic Salmon

by Aleksei Krasnov, Sergey Afanasyev, Stian Nylund and Alexander Rebl

Genes 2020, 11(11), 1236; https://doi.org/10.3390/genes11111236 - 22 Oct 2020

Cited by 18 | Viewed by 3461

Abstract

We report the development of a multigene gene expression assay on the BioMark HD platform for the evaluation of immune competence (ImCom) in farmed Atlantic salmon. The first version of the assay included 92 genes selected on the basis of transcriptome analyses in 54 trials that challenged the immune system; annotations were taken into account to represent the key pathways of innate and adaptive immunity. ImCom was tested on samples collected from seven independent projects. Fish were reared from the start feeding to eight months in the sea at eight units in different parts of Norway. Several tissues were analyzed. Linear discriminant analysis (LDA) showed that no more than 10 genes were required to separate groups, and a set of 46 immune genes was sufficient for any task. The second version of the assay was tested in the gills of two groups of high-performing healthy smolts and in groups with intermediate and high mortality rates (IM and HM, respectively). A set of 645 gill samples from clinically healthy Atlantic salmon was used as a reference. The IM group showed general suppression of immunity. All HM group salmon were above the threshold by the squared deviation from the reference. This group showed marked upregulation of genes involved in acute stress and inflammation: mmp-9, mmp-13, hsp70, il-1b, lect2, and cathelicidin. Further work will clarify the boundaries of the norm and explore various cases of impaired immunity. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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19 pages, 4343 KiB

Open AccessArticle

Tackling the Molecular Drug Sensitivity in the Sea Louse Caligus rogercresseyi Based on mRNA and lncRNA Interactions

by Gustavo Núñez-Acuña, Constanza Sáez-Vera, Valentina Valenzuela-Muñoz, Diego Valenzuela-Miranda, Gabriel Arriagada and Cristian Gallardo-Escárate

Genes 2020, 11(8), 857; https://doi.org/10.3390/genes11080857 - 27 Jul 2020

Cited by 6 | Viewed by 3239

Abstract

Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. This pathogen is mainly controlled by immersion baths with delousing drugs, which can lead to resistant traits selection in lice populations. Bioassays are commonly used to assess louse drug sensitivity, but the current procedures may mask relevant molecular responses. This study aimed to discover novel coding genes and non-coding RNAs that could evidence drug sensitivity at the genomic level. Sea lice samples from populations with contrasting sensitivity to delousing drugs were collected. Bioassays using azamethiphos, cypermethrin, and deltamethrin drugs were conducted to evaluate the sensitivity and to collect samples for RNA-sequencing. Transcriptome sequencing was conducted on samples exposed to each drug to evaluate the presence of coding and non-coding RNAs associated with the response of these compounds. The results revealed specific transcriptome patterns in lice exposed to azamethiphos, deltamethrin, and cypermethrin drugs. Enrichment analyses of Gene Ontology terms showed specific biological processes and molecular functions associated with each delousing drug analyzed. Furthermore, novel long non-coding RNAs (lncRNAs) were identified in C. rogercresseyi and tightly linked to differentially expressed coding genes. A significant correlation between gene transcription patterns and phenotypic effects was found in lice collected from different salmon farms with contrasting drug treatment efficacies. The significant correlation among gene transcription patterns with the historical background of drug sensitivity suggests novel molecular mechanisms of pharmacological resistance in lice populations. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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16 pages, 2149 KiB

Open AccessArticle

Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout (Oncorhynchus mykiss) Breeding Strains by Using Next-Generation Sequencing

by Lidia de los Ríos-Pérez, Ronald Marco Brunner, Frieder Hadlich, Alexander Rebl, Carsten Kühn, Dörte Wittenburg, Tom Goldammer and Marieke Verleih

Genes 2020, 11(8), 841; https://doi.org/10.3390/genes11080841 - 24 Jul 2020

Cited by 5 | Viewed by 3059

Abstract

Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (Oncorhynchus mykiss), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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20 pages, 2453 KiB

Open AccessArticle

Shedding the Light on Litopenaeus vannamei Differential Muscle and Hepatopancreas Immune Responses in White Spot Syndrome Virus (WSSV) Exposure

by Camilla A. Santos, Sónia C. S. Andrade, Jorge M. O. Fernandes and Patrícia D. Freitas

Genes 2020, 11(7), 805; https://doi.org/10.3390/genes11070805 - 16 Jul 2020

Cited by 15 | Viewed by 3870

Abstract

White Spot Syndrome Virus (WSSV) is one of the main threats to farming Litopenaeus vannamei, the most important crustacean commercialized in aquaculture worldwide. Here, we performed RNA-seq analyses in hepatopancreas and muscle from WSSV-negative (healthy) and WSSV-positive (unhealthy) L. vannamei, previously exposed to the virus, to obtain new insights about the molecular basis of resistance to WSSV. We detected 71% of our reads mapped against the recently described L. vannamei genome. This is the first report mapping RNA-seq transcripts from shrimps exposed to WSSV against the species reference genome. Differentially expressed gene (DEG) analyses were performed for four independent comparisons, and 13,338 DEGs were identified. When the redundancies and isoforms were disregarded, we observed 8351 and 6514 DEGs, respectively. Interestingly, after crossing the data, we detected a common set of DEGs for hepatopancreas and healthy shrimps, as well as another one for muscle and unhealthy shrimps. Our findings indicate that genes related to apoptosis, melanization, and the Imd pathway are likely to be involved in response to WSSV, offering knowledge about WSSV defense in shrimps exposed to the virus but not infected. These data present potential to be applied in further genetic studies in penaeids and other farmed shrimp species. Full article

(This article belongs to the Special Issue Genetic Research in Aquaculture)

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