Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
9.0
4.9
Journals
IJMS
Special Issues
Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs...
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges (2nd Edition)

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 April 2026 | Viewed by 2773

Special Issue Editor

Prof. Dr. Hongyan Xu

E-Mail Website
Guest Editor
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & College of Fisheries, Southwest University, Chongqing 402460, China
Interests: molecular biology and genetic breeding of aquatic animals; biodiversity and conservation of aquatic animals; sustainable development of fishery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquatic animals are important for ensuring the aquatic product supply in terms of high levels of proteins, unsaturated fatty acids, vitamins, and microelements. Recently, the increasing demands for aquatic products have resulted in the rapid depletion of fishery stocks all over the world. With decreasing water resources, it has become urgent to improve the aquaculture industry’s efficiency and sustainability. Thus, to obtain new breeds with desirable traits such as a rapid growth, a high meat quality, and stress resistance, a variety of technologies have been developed by the molecular biology and genetic breeding fields. The present Special Issue will focus on aquaculture industry improvements in molecular biology, such as genomic sequencing and gene-editing technologies, as well as genetic breeding, such as markers’ assistant selective, integration, and modification breeding. We welcome original research article and review submissions that contribute to progress in molecular biology and the genetic breeding of aquatic animals.

Prof. Dr. Hongyan Xu
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 250 words) can be sent to the Editorial Office for assessment.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • transgenic
  • genetic breeding
  • omics
  • gene expression and regulation
  • aquatic animals

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

22 pages, 2703 KB  
Article
Multi-Omics Insights into the Effects of Long-Term Faba Bean Feeding on Muscle Quality and Metabolic Reprogramming in Nile Tilapia (Oreochromis niloticus)
by Rongni Li, Saisai Wang, Yansheng Sun and Xin Zhang
Int. J. Mol. Sci. 2025, 26(22), 10819; https://doi.org/10.3390/ijms262210819 - 7 Nov 2025
Viewed by 406
Abstract
While short-term faba bean feeding is known to improve fish texture, its long-term systemic effects and the underlying molecular mechanisms in Nile tilapia remain rarely explored. This knowledge gap is critical, given the potential for extended feeding to induce distinct metabolic reprogramming and [...] Read more.
While short-term faba bean feeding is known to improve fish texture, its long-term systemic effects and the underlying molecular mechanisms in Nile tilapia remain rarely explored. This knowledge gap is critical, given the potential for extended feeding to induce distinct metabolic reprogramming and trade-offs. Here, we present the first comprehensive study investigating the 180-day impact of a 60% FB-based diet (FBD) on Nile tilapia through an integrated analysis of phenotypic traits, muscle histology, metabolome, and transcriptome. Our results revealed a fundamental trade-off: FBD feeding induced hyperplasia-driven muscle remodeling, significantly enhancing textural properties (hardness, gumminess, chewiness) and increasing intramuscular fat and collagen content, but at the cost of suppressed growth and hepatosomatic index. Metabolomics identified 243 significantly altered metabolites, outlining a systemic metabolic shift characterized by activated lipid synthesis but inhibited amino acid and energy metabolism. This multi-omics integration nominated the chac1 gene as a novel key regulator for FB-induced muscle hyperplasia, a finding not previously reported in this context. We propose a mechanistic model wherein long-term FBD feeding coordinates lipid deposition, collagen accumulation, and chac1-mediated hyperplastic growth to remodel muscle texture. Our work provides new insights into the long-term metabolic trade-offs and molecular drivers of FB-induced flesh quality improvement, offering a theoretical foundation for developing optimized aquafeeds. Full article
(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges (2nd Edition))
►▼ Show Figures

Figure 1

30 pages, 3096 KB  
Article
Comparative Analysis of CRISPR/Cas9 Delivery Methods in Marine Teleost Cell Lines
by Álvaro J. Arana, Sara Veiga-Rua, Diego Cora, Manuel A. Gónzalez-Gómez, Ana Seijas, Maialen Carballeda, David Polo, Alberto Cuesta, Yolanda Piñeiro, José Rivas, Mercedes Novo, Wajih Al-Soufi, Paulino Martínez, Laura Sánchez and Diego Robledo
Int. J. Mol. Sci. 2025, 26(21), 10703; https://doi.org/10.3390/ijms262110703 - 3 Nov 2025
Viewed by 889
Abstract
Gene editing technologies such as CRISPR/Cas9 have revolutionized functional genomics, yet their application in marine fish cell lines remains limited by inefficient delivery. This study compares three delivery strategies—electroporation, lipid nanoparticles (LNPs), and magnetofection using gelatin-coated superparamagnetic iron oxide nanoparticles (SPIONs)—for CRISPR/Cas9-mediated editing [...] Read more.
Gene editing technologies such as CRISPR/Cas9 have revolutionized functional genomics, yet their application in marine fish cell lines remains limited by inefficient delivery. This study compares three delivery strategies—electroporation, lipid nanoparticles (LNPs), and magnetofection using gelatin-coated superparamagnetic iron oxide nanoparticles (SPIONs)—for CRISPR/Cas9-mediated editing of the ifi27l2a gene in DLB-1 and SaB-1 cell lines. We evaluated transfection and editing efficiency, intracellular Cas9 localization, and genomic stability of the target locus. Electroporation achieved up to 95% editing in SaB-1 under optimized conditions, but only 30% in DLB-1, which exhibited locus-specific genomic rearrangements. Diversa LNPs enabled intracellular delivery and moderate editing (~25%) in DLB-1 but yielded only minimal editing in SaB-1, while SPION-based magnetofection resulted in efficient uptake but no detectable editing, highlighting post-entry barriers. Confocal imaging and fluorescence correlation spectroscopy suggested that nuclear localization and Cas9 aggregation may influence editing success, highlighting the importance of intracellular trafficking in CRISPR/Cas9 delivery. Our findings demonstrate that CRISPR/Cas9 delivery efficiency is cell line-dependent and governed by intracellular trafficking and genomic integrity. These insights provide a practical framework for optimizing gene editing in marine teleosts, advancing both basic research and selective breeding in aquaculture. Full article
(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges (2nd Edition))
►▼ Show Figures

Graphical abstract

19 pages, 2953 KB  
Article
Independent Mutations in the LRP2 Gene Mediating Telescope Eyes and Celestial Eyes in Goldfish
by Rongni Li, Bo Zhang, Yansheng Sun and Jingyi Li
Int. J. Mol. Sci. 2025, 26(21), 10625; https://doi.org/10.3390/ijms262110625 - 31 Oct 2025
Viewed by 445
Abstract
After intensive artificial selection, the development of celestial eyes in goldfish involves the eyeballs protuberating and turning upwards. Thus, the celestial eye goldfish is an excellent model for both evolutionary and human ocular disease studies. Here, two mapping populations of goldfish with segregating [...] Read more.
After intensive artificial selection, the development of celestial eyes in goldfish involves the eyeballs protuberating and turning upwards. Thus, the celestial eye goldfish is an excellent model for both evolutionary and human ocular disease studies. Here, two mapping populations of goldfish with segregating eye phenotypes in the offspring were constructed. Through whole-genome sequencing and RNA-seq for eyeball samples, a premature stop codon in Exon 38 of the LRP2 gene was identified as the top candidate mutation for the celestial eye in goldfish. Fatty acid metabolism and epidermal cells, especially keratocyte-related functions, were inhibited in the eyeballs of celestial eye goldfish, while inflammatory reactions and extracellular matrix secretions were stimulated. These results suggest the dysfunction of the cornea in the celestial eye goldfish, and the same for the retina, which could be the results of the truncated LRP2 protein. In addition, the same gene, LRP2, is in charge of similar phenotypes (celestial eye and telescope eye) in goldfish, but these phenotypes have no shared mutations. In conclusion, the candidate mutation for the celestial eye in goldfish was identified by this study for the first time, and parallel evolutions of similar phenotypes at the molecular level under artificial selection were observed. These findings provide insights into the developmental and evolutionary processes of morphological changes in the eyes of goldfish. Full article
(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges (2nd Edition))
►▼ Show Figures

Figure 1

31 pages, 15266 KB  
Article
Crustacean Protein Kinases A and C: Bioinformatic Characterization in Decapods and Other Non-Model Organisms
by Talia B. Head, Jorge L. Pérez-Moreno, Laura E. Antizzo, David S. Durica and Donald L. Mykles
Int. J. Mol. Sci. 2025, 26(21), 10585; https://doi.org/10.3390/ijms262110585 - 30 Oct 2025
Viewed by 709
Abstract
The AGC kinases constitute a large and ancient gene superfamily with origins that coincided with the appearance of multicellularity. Three AGC kinase families—protein kinase A (PKA), protein kinase G (PKG), and protein kinase C (PKC)—mediate the actions of neuropeptide hormones, biogenic amines, and [...] Read more.
The AGC kinases constitute a large and ancient gene superfamily with origins that coincided with the appearance of multicellularity. Three AGC kinase families—protein kinase A (PKA), protein kinase G (PKG), and protein kinase C (PKC)—mediate the actions of neuropeptide hormones, biogenic amines, and other ligands on various physiological processes in metazoans. Metazoans express two PKG types. Jawed vertebrates express three PKA catalytic (C) subunits, four regulatory (R) subunits, and twelve PKCs, organized into conventional, novel delta-like, novel epsilon-like, atypical, and protein kinase N (PKN) subfamilies. By contrast, invertebrate PKA and PKC sequences are not well characterized. Consequently, limited database resources can result in misidentification or mischaracterization of proteins and can lead to misinterpretation of experimental data. A broad phylogenetic and sequence analysis of CrusTome transcriptome and GenBank databases was used to characterize 640 PKA-C sequences, 1122 PKA-R sequences, and 1844 PKC sequences distributed among the Annelida, Arthropoda, Chordata, Cnidaria, Nematoda, Mollusca, Echinodermata, Porifera, Platyhelminthes, and Tardigrada. Phylogenetic analysis and multiple sequence alignments revealed conservation of certain PKA-C, PKA-R and PKC isoforms across metazoans, as well as diversification of additional taxon-specific isoforms. Decapods expressed four PKA-C isoforms, designated PKA-C1, -CD1, -CGLY1, and -CGLY2; five PKA-R isoforms, designated PKA-RI1, -RID1, -RIIGLY, and -RIID1; and five PKC isoforms, designated PKND1-3, conventional cPKCD1, novel nPKCD1δ and nPKCD1ε, and atypical aPKCD1. PKA-CGLY1, -CGLY2, and -RIIGLY had glycine-rich N-terminal sequences that were unique to crustaceans. These data suggest lineage-specific diversification that retained the core catalytic function of each kinase, while regions outside of the kinase domain may provide specialized regulatory mechanisms and/or spatiotemporal subcellular localization in invertebrate tissues. Full article
(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges (2nd Edition))
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop