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Fishes
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Molecular Design Breeding in Aquaculture
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Molecular Design Breeding in Aquaculture

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

Deadline for manuscript submissions: 15 September 2025 | Viewed by 1232

Special Issue Editors

Dr. Peng Yu

E-Mail Website
Guest Editor
State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
Interests: molecular breeding; goldfish; evolution; aquaculture; efficient breeding
Dr. Shuting Xiong

E-Mail Website
Guest Editor
Fisheries College, Hunan Agricultural University, Changsha 410128, China
Interests: aquatic animals; gene editing; selective and genetic breeding; innate immune regulation
Dr. ChunHong Nie

E-Mail Website
Guest Editor
Key Laboratory of Freshwater Animal Breeding, College of Fisheries, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
Interests: molecular breeding; gene edit; intermuscular bone; fish; development; omics; bone; gene function

Special Issue Information

Dear Colleagues,

In the burgeoning domain of aquaculture, the advent of precision molecular design breeding and bio-breeding technologies has positioned itself at the vanguard, heralding an epoch of unprecedented efficiency and specificity. This thematic issue is dedicated to the elucidation of the latest advances in the identification of key genes that govern the economically significant traits in aquatic species, leveraging multi-omics strategies such as resequencing and transcriptomics. These traits, which include growth, disease resistance, coloration, reproduction, sex control, and ploidy regulation, are paramount for the economic feasibility of aquaculture. We delve into the innovative development of molecular markers, gene editing, transgenic technologies, germline stem cell transplantation, and chromosomal engineering, which are pivotal for the expedited generation of superior germplasm. Concurrently, the research presented in this Issue also addresses the development of monosex and sterile breeding techniques, which are critical for mitigating the potential ecological risks associated with the application of gene editing and other precision molecular design breeding technologies. By integrating these cutting-edge strategies, this thematic issue aspires to provide a holistic understanding of the current state and future prospects of bio-breeding technologies in aquaculture. This endeavor is aimed not only at maximizing economic benefits but also at ensuring ecological sustainability, thereby contributing to the responsible advancement of the aquaculture industry.

Dr. Peng Yu
Dr. Shuting Xiong
Dr. ChunHong Nie
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

  • molecular breeding
  • gene edting
  • sex control
  • transgenosis
  • molecular marker

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Published Papers (2 papers)

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Research

23 pages, 11176 KiB  
Article
Multi-Omics Investigation of Fatty Acid Content Variations in Common Carp (Cyprinus carpio) Muscle: Integrating Genome, Transcriptome, and Lipid Profiling Data
by Kaikuo Wang, Qi Wang, Yingjie Chen, Yiming Cao, Ran Zhao, Shuangting Yu, Xiaoqing Sun, Yan Zhang and Jiongtang Li
Fishes 2025, 10(5), 234; https://doi.org/10.3390/fishes10050234 - 16 May 2025
Viewed by 154
Abstract
Fatty acids (FAs), especially the polyunsaturated fatty acids (PUFAs), play pivotal roles in growth and development. Fish possess a remarkable ability to synthesize PUFAs, rendering them a crucial and significant source of these essential FAs for human consumption. Despite extensive research on the [...] Read more.
Fatty acids (FAs), especially the polyunsaturated fatty acids (PUFAs), play pivotal roles in growth and development. Fish possess a remarkable ability to synthesize PUFAs, rendering them a crucial and significant source of these essential FAs for human consumption. Despite extensive research on the metabolic processes of FAs, the primary processes underlying FA content variation and corresponding regulatory mechanisms remain largely unexplored. We quantified the muscular FA profiles of 304 common carp samples. High variation in muscle FA content among samples was observed, with the coefficients of variation ranging from 0.36 to 0.92. With genome-wide association studies (GWAS), we identified 1410 SNPs significantly associated with the FA content. The genetic variation at genes participating in oxidation, ubiquitination, and transcriptional factors was associated with the content of multiple FAs, while few variants were observed in the FA-synthesis genes. For the total PUFA (TPUFA) content, transcriptome analysis of groups with the highest and lowest TPUFA content identified 715 differentially expressed genes (DEGs), including genes involved in oxidation and ubiquitination. Using multiple genomic selection programs with the associated SNPs for FA content, we obtained high and positive correlations ranging from 0.65 to 0.92 between the real FA contents and estimated breeding values. These findings manifested the major-effect processes governing the differences in muscular FA content and their regulatory mechanisms. The optimal genomic selection programs provide novel and feasible perspectives to enhance FA content in common carp. Full article
(This article belongs to the Special Issue Molecular Design Breeding in Aquaculture)
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13 pages, 2280 KiB  
Article
RIOK1/2 Negatively Regulates the Antiviral Response by Targeting TBK1 in Yellow Catfish (Pelteobagrus fulvidraco)
by Kejun Liu, Jiayang Huang, Yuting Gui, Qian Li, Lei Zhang and Shuting Xiong
Fishes 2025, 10(1), 6; https://doi.org/10.3390/fishes10010006 - 27 Dec 2024
Viewed by 674
Abstract
The yellow catfish (Pelteobagrus fulvidraco) industry has expanded to a certain scale and is an important part of aquaculture in China, but frequent diseases have caused huge economic losses. Comprehending the fish’s immune mechanisms, particularly the regulation of the interferon (IFN) [...] Read more.
The yellow catfish (Pelteobagrus fulvidraco) industry has expanded to a certain scale and is an important part of aquaculture in China, but frequent diseases have caused huge economic losses. Comprehending the fish’s immune mechanisms, particularly the regulation of the interferon (IFN) response, is of paramount importance for future drug development and disease-resistant molecular breeding. Notably, the role of atypical protein kinases, such as the RIO kinase family, in immune regulation is poorly defined. Here, we investigated the roles of yellow catfish RIO kinases, PfRIOK1 and PfRIOK2, in modulating the IFN response through their interaction with PfTBK1, a key player in the RLR signaling pathway. Mechanically, PfRIOK1 and PfRIOK2 negatively regulate the IFN response by interacting with the RIO domains to target and degrade PfTBK1. Our findings reveal that the overexpression of PfRIOK1 and PfRIOK2 led to the decreased expression of IFN-related genes and enhanced viral replication in vitro. Additionally, PfRIOK1 and PfRIOK2 could inhibit PfTBK1-mediated antiviral responses in infected cells. These results suggest that PfRIOK1 and PfRIOK2 act as negative regulators of the IFN response in yellow catfish, providing new insights into the regulatory mechanisms of fish innate immunity and offering target molecules for molecular design breeding in aquaculture. Full article
(This article belongs to the Special Issue Molecular Design Breeding in Aquaculture)
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