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

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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 5954

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Prof. Dr. Hongyan Xu

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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
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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

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Keywords

transgenic
genetic breeding
omics
gene expression and regulation
aquatic animals

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Published Papers (6 papers)

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Research

37 pages, 18067 KB

Open AccessArticle

Characterization of the Crustacean Methyl Farnesoate Transcriptional Signaling Genes

by Vanessa L. Bentley, Jorge L. Pérez-Moreno, David S. Durica and Donald L. Mykles

Int. J. Mol. Sci. 2026, 27(3), 1215; https://doi.org/10.3390/ijms27031215 - 26 Jan 2026

Cited by 1 | Viewed by 700

Abstract

Methyl farnesoate (MF) is a sesquiterpenoid hormone that controls a variety of physiological processes in crustaceans, including morphogenesis, development, reproduction, and molting. MF action is mediated by a transcriptional signaling cascade consisting of Methoprene-tolerant (Met), Steroid receptor coactivator (Src), Krüppel homolog 1 (Kr-h1), and Ecdysone response gene 93 (E93) transcription factors (TFs), and transcriptional co-regulators CREB-binding protein (CBP) and C-terminal-binding protein (CtBP). Phylogenetic and sequence analyses revealed that these genes were highly conserved across pancrustacean species. Met and Src were characterized as basic helix-loop-helix, Period (Per)-Aryl Hydrocarbon Nuclear Translocator (ARNT)-Single-minded (Sim) protein (bHLH-PAS) TFs; Kr-h1 was characterized as a C₂H₂ zinc finger TF with seven zinc finger motifs; E93 was characterized as a helix-turn-helix, pipsqueak (HTH_Psq) TF. CBP was identified by several zinc finger-binding regions with Transcription Adaptor Zinc Finger 1 and 2, Really Interesting New Gene, Plant homeodomain, and Z-type zinc finger domains; the Kinase-inducible Domain Interacting-transcription factor docking site; the Bromodomain-acetylated lysine recognition and binding site; the histone acetyltransferase domain; and a C-terminal CREB-binding region containing a nuclear receptor co-activator-binding domain. CtBP had a dehydrogenase domain with arginine-glutamate-histidine catalytic triad. 81 Met contigs, 45 Src contigs, 136 Kr-h1 contigs, 66 E93 contigs, 60 CBP contigs, and 172 CtBP contigs were identified across pancrustacean taxa, including decapod crustaceans. Bioinformatic identification and annotation of these TFs and co-regulators in brachyuran Y-organ (YO) transcriptomes suggests that MF signaling influences YO ecdysteroidogenesis; functional tests in the YO are needed to establish causality. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges (2nd Edition))

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20 pages, 3460 KB

Open AccessArticle

Comparative Thermal Tolerance and Tissue-Specific Responses Patterns to Gradual Heat Stress in Reciprocal Cross Hybrids of Acipenser baerii and A. schrenckii

by Wei Wang, Linan Gao, Xiaoyu Yan, Wenjie Liu, Tian Dong, Hailiang Song, Guoqing Ma and Hongxia Hu

Int. J. Mol. Sci. 2026, 27(1), 132; https://doi.org/10.3390/ijms27010132 - 22 Dec 2025

Viewed by 538

Abstract

The increasing frequency and intensity of heatwaves due to climate change pose significant challenges to sturgeon aquaculture. This study investigated the effects of gradual heat stress (1 °C every 8 h) on two reciprocal hybrid sturgeon strains (Acipenser baerii ♀ × A. schrenckii ♂, (BS hybrid); A. schrenckii ♀ × A. baerii ♂, (SB hybrid)), focusing on their antioxidant defense mechanisms, heat shock protein (HSP) expression, and liver and gill tissue histology. When water temperature raised to 34.3 °C (about 104 h), LOE (loss of equilibrium) individuals appeared. Twenty-four hours after sampling, fifteen BS hybrid sturgeon remained alive, whereas no SB hybrid sturgeon survived. In this study, the slow heat stress significantly elevated the expression of HSP-related genes (hsc70, hsp70, hsp90) in both the liver of BS hybrid sturgeon and the gills of SB hybrid sturgeon. However, in the gills of BS hybrid sturgeon and the liver of SB hybrid sturgeon, the expression of hsp family genes in the experimental groups was either lower than or comparable to the control group. Significant liver damage, including cellular vacuolization and necrosis, was observed in BS hybrids, while SB hybrid sturgeon exhibited more pronounced gill tissue damage. Among the four antioxidant enzymes—superoxide dismutase (SOD), lactate dehydrogenase (LDH), catalase (CAT) glutathione peroxidase (GPx)—only LDH activity was elevated in the hepatic tissue of BS hybrid sturgeon, corresponding to increased serum lactate levels, while gill LDH activity was higher in SB hybrid sturgeon. In both hybrids, LDH activity exhibited an increasing trend in the kidney. However, total antioxidant capacity (T-AOC) remained unchanged across all three tissues. Both plasma cortisol and lactate were substantially affected by thermal stress. MDA remained at a relatively stable level after heat stress and recovery. These results demonstrate differential tissue-specific responses to heat stress in the reciprocal hybrids. More importantly, the BS hybrid sturgeon exhibited significantly higher thermal tolerance and post-stress survival compared to the SB hybrid sturgeon. These findings reveal that the choice of maternal parent is a critical factor influencing heat resistance in these hybrids, providing a key basis for selective breeding programs and optimizing aquaculture management. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges (2nd Edition))

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22 pages, 2703 KB

Open AccessArticle

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 701

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 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))

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30 pages, 3096 KB

Open AccessArticle

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 1633

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 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))

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19 pages, 2953 KB

Open AccessArticle

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 783

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 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))

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31 pages, 15266 KB

Open AccessArticle

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

Cited by 1 | Viewed by 1119

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 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, -C_D1, -C_GLY1, and -C_GLY2; five PKA-R isoforms, designated PKA-RI₁, -RI_D1, -RII_GLY, and -RII_D1; and five PKC isoforms, designated PKN_D1-3, conventional cPKC_D1, novel nPKC_D1δ and nPKC_D1ε, and atypical aPKC_D1. PKA-C_GLY1, -C_GLY2, and -RII_GLY 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))

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