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Fishes
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The Applications of Genome Editing and Genomics in Aquaculture
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The Applications of Genome Editing and Genomics in Aquaculture

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (20 March 2023) | Viewed by 14150

Special Issue Editors

Dr. Ahmed Elaswad

E-Mail Website
Guest Editor
1. School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
2. Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
Interests: genetics; genome editing; gene transfer; genomics; aquaculture
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Rex Dunham

E-Mail Website
Guest Editor
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
Interests: selective breeding; hybridization; gene transfer; gene mapping and genomics; reproductive physiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genome editing opens avenues for targeted genome modifications. This technology can be applied in aquaculture to manipulate almost all genes by means of gene insertion, modification, or  knockout. In aquaculture, genome editing provides an efficient approach to study functional genomics. Gene knockout helps to identify candidate genes that are important for the development of particular economically important traits. Understanding gene function can also assist in selecting the best individuals for selective breeding programs and commercial production. Genome editing can also be used for gene insertion at specific genomic targets to generate transgenic fish in a more precise and effective way, as well as to illuminate molecular mechanisms of biological processes and generate fish models to study diseases.

Genomic tools have provided extensive genomic information for many aquaculture species. This allows the investigation of complex biological processes, especially those playing an important role in reproduction, production, and disease resistance. Genomics have also enhanced selective breeding via providing genetic and genomic markers for marker-assisted selection. Genome-wide association studies have facilitated the discovery of genomic markers and their association with economically important traits such as growth, carcass traits, and disease resistance.

This Special Issue focuses on genome editing and genomics, and their applications in aquaculture including—but not limited to—gene knockout, gene insertion, gene correction or modification, study of functional genomics, gene interactions with other genes and the environment, transcriptomics, genome-wide association studies, genomic selection, functional genomics, and the development of genome-scale technologies and their applications in aquaculture.

Dr. Ahmed Elaswad
Dr. Rex Dunham
Guest Editors

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. Fishes 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

  • genome editing
  • genomics
  • selection
  • transgenics
  • aquaculture

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Related Special Issue

Published Papers (5 papers)

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Research

16 pages, 3024 KiB  
Article
Antimicrobial Activity of Identified Ubiquitin-40S Ribosomal Protein S27a (RPS27A), Ubiquitin-like Protein Fubi, and Ribosomal Protein (S30FAU) in the Starry Flounder (Platichthys stellatus)
by Ha-Jeong Son, Gyoungsik Kang, Won-Sik Woo, Kyung-Ho Kim, Min-Young Sohn, Jong-Won Park, Dain Lee and Chan-Il Park
Fishes 2023, 8(4), 187; https://doi.org/10.3390/fishes8040187 - 30 Mar 2023
Viewed by 2594
Abstract
Ubiquitin-40S ribosomal protein S27a (RPS27A), ubiquitin-like protein Fubi, and ribosomal protein (S30FAU) are ubiquitin-related proteins that are involved in the regulation of immune-related functions such as cell cycle, protein expression, and apoptosis. This study aimed to confirm the molecular characteristics, gene expression analysis, [...] Read more.
Ubiquitin-40S ribosomal protein S27a (RPS27A), ubiquitin-like protein Fubi, and ribosomal protein (S30FAU) are ubiquitin-related proteins that are involved in the regulation of immune-related functions such as cell cycle, protein expression, and apoptosis. This study aimed to confirm the molecular characteristics, gene expression analysis, and antibacterial activity of RPS27A and S30FAU identified from the starry flounder (15 starry flounders of 128.7 ± 18.2 g). An expression analysis using a normal fish showed that RPS27A was highly expressed in the head kidney, heart, and stomach. In contrast, S30FAU exhibited high expression in the stomach, heart, and head kidney. Upon simulating an artificial pathogen infection, RPS27A was highly expressed in the heart at 1 h and 3 days post-viral hemorrhagic septicemia (VHSV) infection, and had a high expression in the kidney, liver, and heart at 7 days post-Streptococcus parauberis (S. parauberis) infection. S30FAU was highly expressed in the spleen and gills at 1 day and 12 h post-VHSV infection, respectively, and exhibited a high expression in the kidney at 7 days post-S. parauberis infection. In an MIC analysis, RPS27A and S30FAU showed antimicrobial activity against all bacteria used in this study. In the biofilm assay, S30FAU was removed from S. parauberis in a concentration-dependent manner, and the cytotoxicity test showed no hemolytic activity in both RPS27A and S30FAU. Therefore, RPS27A and S30FAU of the starry flounder were confirmed to possess antimicrobial peptide abilities without limitations of cytotoxicity. This study provides valuable information on the antibacterial ability and molecular biology of the ubiquitin family isolated from the starry flounder. Full article
(This article belongs to the Special Issue The Applications of Genome Editing and Genomics in Aquaculture)
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12 pages, 2577 KiB  
Article
CRISPR/Cas9-Mediated Disruption of Endo16 Cis-Regulatory Elements in Sea Urchin Embryos
by Lili Xing, Lingyu Wang, Femke Roos, Michelle Lee and Gregory A. Wray
Fishes 2023, 8(2), 118; https://doi.org/10.3390/fishes8020118 - 20 Feb 2023
Viewed by 2501
Abstract
Sea urchins have become significant mariculture species globally, and also serve as invertebrate model organisms in developmental biology. Cis-regulatory elements (enhancers) control development and physiology by regulating gene expression. Mutations that affect the function of these sequences may contribute to phenotypic diversity. Cis-regulatory [...] Read more.
Sea urchins have become significant mariculture species globally, and also serve as invertebrate model organisms in developmental biology. Cis-regulatory elements (enhancers) control development and physiology by regulating gene expression. Mutations that affect the function of these sequences may contribute to phenotypic diversity. Cis-regulatory targets offer new breeding potential for the future. Here, we use the CRISPR/Cas9 system to disrupt an enhancer of Endo16 in developing Lytechinus variegatus embryos, in consideration of the thorough research on Endo16’s regulatory region. We designed six gRNAs against Endo16 Module A (the most proximal region of regulatory sequences, which activates transcription in the vegetal plate and archenteron, specifically) and discovered that Endo16 Module A-disrupted embryos failed to undergo gastrulation at 20 h post fertilization. This result partly phenocopies morpholino knockdowns of Endo16. Moreover, we conducted qPCR and clone sequencing experiments to verify these results. Although mutations were not found regularly from sequencing affected individuals, we discuss some potential causes. In conclusion, our study provides a feasible and informative method for studying the function of cis-regulatory elements in sea urchins, and contributes to echinoderm precision breeding technology innovation and aquaculture industry development. Full article
(This article belongs to the Special Issue The Applications of Genome Editing and Genomics in Aquaculture)
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20 pages, 11310 KiB  
Article
Editing the Melanocortin-4 Receptor Gene in Channel Catfish Using the CRISPR-Cas9 System
by Karim Khalil, Ahmed Elaswad, Hisham Abdelrahman, Maximillian Michel, Wenbiao Chen, Shikai Liu, Ramjie Odin, Zhi Ye, David Drescher, Khoi Vo, William S. Bugg, Guyu Qin, Yujia Yang, Nathan J. C. Backenstose, Zhanjiang Liu, Roger D. Cone and Rex Dunham
Fishes 2023, 8(2), 116; https://doi.org/10.3390/fishes8020116 - 18 Feb 2023
Cited by 6 | Viewed by 3462
Abstract
The melanocortin-4 receptor (MC4R) plays a critical role in homeostasis and the regulation of body weight. Polymorphisms in the mc4r gene have been discovered and linked to growth, carcass composition, and meat quality traits. Therefore, we used the CRISPR-Cas9 system to target the [...] Read more.
The melanocortin-4 receptor (MC4R) plays a critical role in homeostasis and the regulation of body weight. Polymorphisms in the mc4r gene have been discovered and linked to growth, carcass composition, and meat quality traits. Therefore, we used the CRISPR-Cas9 system to target the mc4r gene in the most important freshwater aquaculture species in the USA, channel catfish, Ictalurus punctatus. Guide RNAs were designed to direct the Cas9 to the coding sequence of the channel catfish mc4r gene. gRNA(s)-Cas9 mixtures were delivered into one-cell embryos using electroporation and microinjection. For each treatment, the nature and rate of mutations were analyzed. Hatching and survival rates were calculated. The overall mutation rates were 30.6% and 66.7–90.6% for electroporation and microinjection, respectively. Mutated fish generated via electroporation or microinjection exhibited 38% and 20% improvement in body weight, respectively, when compared with the full-sib control. The mean feed conversion ratio of the mutants was 1.18 compared with 1.57 in the control fish. The improved growth and feed conversion indicate that the generation of mc4r-edited fish could economically benefit aquaculture production. Full article
(This article belongs to the Special Issue The Applications of Genome Editing and Genomics in Aquaculture)
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21 pages, 5144 KiB  
Article
Genome-Wide Identification, Phylogenetic Analysis and Expression Pattern Profiling of the Aquaporin Family Genes in Leuciscus waleckii
by Feifei Zhan, Liqun Liang, Shuangyi Wang, Honjung Liew, Yumei Chang and Limin Zhang
Fishes 2023, 8(2), 107; https://doi.org/10.3390/fishes8020107 - 11 Feb 2023
Cited by 2 | Viewed by 2450
Abstract
Aquaporin (Aqp) is a transmembrane-specific channel for small molecules that help in regulating homeostasis in fishes when adapting to changing environments, but its role in Amur ide’s response to alkaline stress is yet to be revealed. Therefore, the purpose of this study is [...] Read more.
Aquaporin (Aqp) is a transmembrane-specific channel for small molecules that help in regulating homeostasis in fishes when adapting to changing environments, but its role in Amur ide’s response to alkaline stress is yet to be revealed. Therefore, the purpose of this study is to investigate the response of the Aqp gene exposed to alkaline water in Amur ide (Leuciscus waleckii) using a genome-transcriptional assay. Based on the results, we classified the Aqps of the L. waleckii (LwAqps) genome and analyzed its transcriptional expression profile and genetic evolution under carbonate alkalinity stress. A total of 18 Aqp genes were identified in four grades in L. waleckii. The highest Aqp gene expression was found in the gill and kidney of L. waleckii from the Wusuli River (WSL) in comparison to those in the Dali Lake (DL), whereas aqp3a, -3ap1, -7, and -9a expressions were found at intensively higher levels in the gill rather than in the kidneys and livers. The experiment of L. waleckii under alkalinity stress (carbonate alkalinity 50 mmol·L−1) and its recovery showed that the expressions of aqp0a, -3a, -3ap1, -7, -8aa, and -9a were upregulated in alkaline water and downregulated in freshwater. We identified 1460 single nucleotide polymorphism (SNP) markers in the Aqp genes. The average value of Fst of SNP markers in the CDS region was 0.177 ± 0.256, and the first 5% SNPs were identified at aqp3a and -11b. Residue Ser66 does not bring about an overall change in the three-dimensional structure of Aqp3a, but may change the penetration of solutes across the membrane. This indicates that Aqp genes are involved in the response of L. waleckii to alkaline stress, and aqp3a is one of the key genes involved in regulating L. waleckii’s adaptation to alkaline environments. Full article
(This article belongs to the Special Issue The Applications of Genome Editing and Genomics in Aquaculture)
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16 pages, 4076 KiB  
Article
Genomic Analysis of the Proteasome Subunit Gene Family and Their Response to High Density and Saline-Alkali Stresses in Grass Carp
by Guo Hu, Yongjun Shu, Peixian Luan, Tianxiang Zhang, Feng Chen and Xianhu Zheng
Fishes 2022, 7(6), 350; https://doi.org/10.3390/fishes7060350 - 26 Nov 2022
Cited by 3 | Viewed by 1883
Abstract
The proteasome is a highly conserved polycatalytic enzyme that is required for cellular processes and is widely present in the nucleus and cytoplasm of archaea, as well as all eukaryotes. A total of 22 members of the proteasome subunit (CiPS) gene family were [...] Read more.
The proteasome is a highly conserved polycatalytic enzyme that is required for cellular processes and is widely present in the nucleus and cytoplasm of archaea, as well as all eukaryotes. A total of 22 members of the proteasome subunit (CiPS) gene family were identified and characterized by scanning the grass carp (Ctenopharyngodon idella) genome. These genes were classified into two subfamilies, CiPSA and CiPSB, based on phylogenetic analysis, which was consistent with the results from other species. We examined the response of this gene family to high density and saline-alkali stresses in aquaculture using publicly available transcriptome data resources. In grass carp, CiPS member transcripts were detected in all tested tissues, with the highest expression level in the head kidney and the lowest in the liver. According to transcriptome-based expression analysis, CiPS genes play a role in response to environmental stresses in grass carp, mainly in the form of negative regulation. Interestingly, a cluster of members belonging to the CiPSB subfamily on a 15 kb region on chromosome segment CI01000319, including CiPSB8, 9, 9b, and 10, showed marked responses to high density and saline-alkali stress. It appears that CiPS genes confer stress tolerance through the regulation of common genes, as well as specific genes. In summary, our genome-wide characterization, evolutionary, and transcriptomic analysis of CiPS genes in grass carp provides valuable information for characterizing the molecular functions of these genes and utilizing them to improve stress tolerance in aquaculture. Full article
(This article belongs to the Special Issue The Applications of Genome Editing and Genomics in Aquaculture)
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