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Sustainable Aquaculture: A Functional Genomic Perspective
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Sustainable Aquaculture: A Functional Genomic Perspective

A Special Issue of Animals (ISSN 2076-2615) belonging to the section "Aquatic Animals".

Deadline for manuscript submissions: 15 December 2026 | Viewed by 4974

Editors

Dr. Robert Mukiibi

E-Mail Website
Guest Editor
1. Department of Animal Health Behaviour and Welfare, Harper Adams University, Edgmond, Newport TF10 8NB, UK
2. The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
Interests: transcriptomics; epigenomics; genomics; genomic selection; proteomics; metabolomics; sustainable aquaculture
Dr. Yangzhen Li

E-Mail Website
Guest Editor
Yellow Sea Fisheries Research Institute, Chinese Academy of fishery Sciences, Qingdao, 266071, China
Interests: selective breeding; genomic selection; quantitative genetics; pangenomics; structural variation; multi-omics; genetic architecture of complex traits; aquaculture.
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquaculture is a steadily growing human food production industry, contributing to sustaining livelihoods as well as food and nutritional security. Despite this steady growth, the industry faces several challenges that significantly impact the sustainability of aquacultural output in the different production systems and environments. Some of these challenges include infectious diseases, parasites, environmental stressors such as fluctuations in temperature, salinity, pH, and oxygen, and ammonia accumulation. These challenges are greatly exacerbated by the current impacts of climate change. In addition, there is an increasing demand for faster-growing farmed aquatic animal strains with high-quality final consumable products. Interestingly, production and welfare traits such as growth rate, feed utilization efficiency and fillet quality, disease, and parasitic resistance as well as resilience to environmental stressors, are partly controlled by the genetics of the animals and this has facilitated the development of farmed aquatic animals with the desired phenotypes of the important traits through selective breeding. Understanding the precise genetic background of the different traits in different farmed species has been demonstrated to have the potential to significantly accelerate selective breeding of farmed aquatic animals. 

In this Special Issue, we invite original research and review articles in functional genomics as applied to enhance the productivity and welfare of farmed aquatic species. Original research and review articles are welcome in this Special Issue. Areas of research may include (but are not limited to) the following: 

  • Metabolomics in farmed aquatic species;
  • Genome-wide association studies in farmed aquatic species;
  • Single-cell and bulk epigenomics in farmed aquatic species;
  • Single-cell and bulk transcriptomics in farmed aquatic species;
  • Multi-omics integration in farmed aquatic species;
  • Genomic selection or functional genomic enhanced genomic selection in farmed aquatic species;
  • Functional genomics-guided vaccine development in farmed aquatic species;
  • Molecular quantitative trait loci identification in farmed aquatic species;
  • Genome editing in farmed aquatic species.

We look forward to receiving your contributions.

Dr. Robert Mukiibi
Dr. Yangzhen Li
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 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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • transcriptomics
  • epigenomics
  • genomics
  • genomic selection
  • proteomics
  • metabolomics
  • GWAS
  • molecular-QTLs
  • sustainable aquaculture

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Published Papers (5 papers)

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Research

20 pages, 3725 KB  
Article
Genome-Wide Identification of the TRAF Gene Family in Common Carp (Cyprinus carpio) and Analysis of Their Expression in Response to CyHV-3 Challenge
by Yaxin Di, Xiaona Jiang, Chitao Li, Xuesong Hu, Yanlong Ge, Xiaodan Shi, Xinyu Zhao and Zhiying Jia
Animals 2026, 16(18), 2859; https://doi.org/10.3390/ani16182859 - 11 Sep 2026
Viewed by 215
Abstract
Tumor necrosis factor receptor-associated factors (TRAFs) are key signal transduction molecules in innate immunity and are involved in multiple immune pathways, such as TNF receptor and Toll-like receptor signaling. In this study, 16 CcTRAFs were identified from the common carp genome, assigned to [...] Read more.
Tumor necrosis factor receptor-associated factors (TRAFs) are key signal transduction molecules in innate immunity and are involved in multiple immune pathways, such as TNF receptor and Toll-like receptor signaling. In this study, 16 CcTRAFs were identified from the common carp genome, assigned to six subfamilies (TRAF1/2/3/4/6/7), with no TRAF5 found. Significant paralogous expansion was observed in the TRAF2/4 subfamilies. All CcTRAF proteins were predicted to be unstable and hydrophilic by ProtParam analysis; most contain conserved RING, TRAF and MATH domains, whereas CcTRAF7 carries seven WD40 domains. Gene structure and conserved motif analysis revealed high conservation of exon numbers and motif compositions within each subfamily, while the TRAF7 subfamily displayed distinct characteristics. Collinearity analysis further indicated that segmental duplication promotes CcTRAF family expansion. qRT-PCR showed that CcTRAF genes have tissue-specific expression patterns and are preferentially expressed in the liver, spleen, and kidney. Under CyHV-3 infection, the expression levels of CcTRAF3/6/7 in these tissues first increased and then decreased, peaking at 48 h post-challenge. In summary, CcTRAF genes, especially CcTRAF3/6/7, play important roles in the immune response of common carp against CyHV-3. This study provides a molecular basis for understanding innate immune regulation in teleost fish and the functional roles of TRAF genes. Full article
(This article belongs to the Special Issue Sustainable Aquaculture: A Functional Genomic Perspective)
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23 pages, 1812 KB  
Article
Integrated Transcriptome and Methylome Analyses Reveal Sex-Specific Molecular Responses to Chronic Heat Stress in Tongue Sole (Cynoglossus semilaevis)
by Yangzhen Li, Wenteng Xu, Xinqi Wen, Ailing Wu, Hongxiang Zhang, Haien Zhang, Weidong Li and Songlin Chen
Animals 2026, 16(13), 2078; https://doi.org/10.3390/ani16132078 - 5 Jul 2026
Viewed by 526
Abstract
Chronic heat stress poses a major challenge to marine aquaculture, yet its sex-associated molecular basis remains poorly understood in Chinese tongue sole (Cynoglossus semilaevis). Juveniles were exposed to a control temperature (24 °C) or elevated temperature (30 °C) for two months, [...] Read more.
Chronic heat stress poses a major challenge to marine aquaculture, yet its sex-associated molecular basis remains poorly understood in Chinese tongue sole (Cynoglossus semilaevis). Juveniles were exposed to a control temperature (24 °C) or elevated temperature (30 °C) for two months, and liver samples from low-temperature females (LF), high-temperature females (HF), low-temperature males (LM), and high-temperature males (HM) were analyzed by RNA sequencing (RNA-seq) and whole-genome bisulfite sequencing (WGBS). Principal component analysis indicated a strong temperature-associated separation, while sex-related separation under heat stress was smaller and was mainly observed along the second principal component. In high-temperature relative to low-temperature comparisons, females showed a broader set of differentially expressed genes (DEGs; LF vs. HF, 1968) than males (LM vs. HM, 506). Differential methylation analyses indicated that cytosine-guanine (CG) methylation was the predominant heat-associated epigenetic signal. Integrative analysis identified 624 overlapping genes between DEGs and CG-associated differentially methylated genes (CG-DMGs) in females and 177 in males, suggesting broader methylation-associated transcriptional remodeling in females. Functional enrichment associated the female overlap genes with immune response, inflammatory signaling, lipid metabolism, and detoxification, whereas male overlap genes were more closely associated with proteostasis, autophagy, and DNA replication/repair. Correlation analyses suggested modest methylation–expression coupling and highlighted candidate W-linked genes, including H2AZ2 and ANKRD13A. Overall, these results should be regarded as a preliminary baseline for understanding sex-associated molecular responses to chronic heat stress in tongue sole and as a source of candidate genes and pathways for future validation and heat-resilience breeding. Full article
(This article belongs to the Special Issue Sustainable Aquaculture: A Functional Genomic Perspective)
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15 pages, 769 KB  
Article
Evaluation and Selection of Stable Reference Genes for qRT-PCR Analysis in Different Tissues of Mugilogobius chulae Under Pollutant Exposure
by Zhongdian Dong, Jiahao Gao, Xiaobin Li, Zhishan Chen, Jianjun Li, Jian Liao, Yanping Zhang, Zhongduo Wang, Yusong Guo and Ning Zhang
Animals 2026, 16(9), 1412; https://doi.org/10.3390/ani16091412 - 5 May 2026
Viewed by 670
Abstract
Reliable normalization is essential for accurate quantitative real-time PCR (qRT-PCR) analysis, yet suitable reference genes have not been systematically evaluated in Mugilogobius chulae, an emerging marine experimental fish used in physiological and environmental research. In this study, 17 candidate reference genes were [...] Read more.
Reliable normalization is essential for accurate quantitative real-time PCR (qRT-PCR) analysis, yet suitable reference genes have not been systematically evaluated in Mugilogobius chulae, an emerging marine experimental fish used in physiological and environmental research. In this study, 17 candidate reference genes were evaluated in five tissues (brain, gill, gonad, intestine, and liver) of sexually mature male and female M. chulae under solvent control (DMSO), bisphenol A (BPA), cadmium (Cd), and sulfamethazine (SMX) treatment conditions. Gene-expression stability was assessed using the comparative ΔCt method, NormFinder, geNorm, BestKeeper, and the integrated RefFinder ranking. The results showed that reference-gene stability was strongly tissue-specific and analysis-dependent. The integrated RefFinder analysis identified eif3h, rpl7, rps4x, stau1, and ef1y as the most stable genes in the pooled dataset, whereas ube2, hprt1l, and aldob were the least stable. geNorm analysis indicated that two reference genes were sufficient for brain, gill, intestine, and liver, whereas four were required for the gonad and six for cross-tissue comparisons. These findings provide the first systematic basis for reference-gene selection in M. chulae and establish an important methodological foundation for future qRT-PCR studies in this species, particularly in research on endocrine disruption, reproductive physiology, and marine ecotoxicology. Full article
(This article belongs to the Special Issue Sustainable Aquaculture: A Functional Genomic Perspective)
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26 pages, 30041 KB  
Article
Integrative Transcriptome Analysis and WGCNA Uncover the Growth Regulatory Mechanisms in Cephalopholis sonnerati
by Ziyuan Wang, Yu Song, Runkai Sun, Zhenxia Sha, Yang Liu and Songlin Chen
Animals 2026, 16(8), 1128; https://doi.org/10.3390/ani16081128 - 8 Apr 2026
Viewed by 891
Abstract
The tomato hind (Cephalopholis sonnerati) is a marine aquaculture fish species with high economic value. Elucidating the mechanisms underlying its growth regulation is crucial for the development of the aquaculture industry. To analyze the biological mechanisms underlying growth differences, individuals with extreme body [...] Read more.
The tomato hind (Cephalopholis sonnerati) is a marine aquaculture fish species with high economic value. Elucidating the mechanisms underlying its growth regulation is crucial for the development of the aquaculture industry. To analyze the biological mechanisms underlying growth differences, individuals with extreme body sizes at 8 months of age from the same batch were selected in this study. A combined experiment of “body size × feeding status” was constructed, and transcriptome sequencing and weighted gene co-expression network analysis (WGCNA) were performed on brain and muscle tissues. The results showed that 2553 differentially expressed genes (DEGs) were identified between individuals with distinct body sizes, which were significantly enriched in growth regulation pathways such as PI3K–Akt, MAPK, and FoxO. Feeding differences affected 4480 genes, which were significantly enriched in signaling pathways including the insulin signaling pathway. WGCNA further identified co-expression modules (brown4, blue, coral1) significantly correlated with growth, as well as hub genes including pik3r1 and eif4ebp2. Comprehensive analysis demonstrated that the growth regulation of C. sonnerati operates as a cascade network. Brain tissues perceive signals through neuroactive ligand–receptor interactions and integrate and transduce these signals via core pathways including Ras–MAPK and PI3K–Akt. Finally, growth processes are executed in muscle tissues by regulating glycogen metabolism, protein synthesis, and other processes, which are precisely regulated by terminal processes such as cellular senescence. Among them, pik3r1 and eif4ebp2, as key molecular switches, play a central role in integrating upstream signals and precisely regulating downstream growth programs. This study preliminarily clarifies the molecular mechanism network of growth differences in C. sonnerati, providing a theoretical basis and candidate genes for the genetic improvement of its growth traits. Full article
(This article belongs to the Special Issue Sustainable Aquaculture: A Functional Genomic Perspective)
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24 pages, 10948 KB  
Article
Genome-Wide Characterization of the wnt Gene Family Reveals a wnt5b-Mediated Regulatory Mechanism of Testicular Development in Cynoglossus semilaevis
by Zhengjie Li, Junhao Wang, Chao Li and Ying Zhu
Animals 2026, 16(3), 387; https://doi.org/10.3390/ani16030387 - 26 Jan 2026
Viewed by 1623
Abstract
The wnt gene family encodes a group of highly conserved secreted glycoproteins that play essential roles in vertebrate development, including tissue patterning, cell differentiation, and gonadal regulation. However, the genomic organization, evolutionary dynamics, and functional roles of Wnt signaling components in flatfish remain [...] Read more.
The wnt gene family encodes a group of highly conserved secreted glycoproteins that play essential roles in vertebrate development, including tissue patterning, cell differentiation, and gonadal regulation. However, the genomic organization, evolutionary dynamics, and functional roles of Wnt signaling components in flatfish remain poorly understood. In this study, we performed a comprehensive genome-wide identification, evolutionary characterization, expression profiling, and functional analysis of wnt genes in Cynoglossus semilaevis, a flatfish species exhibiting ZW/ZZ sex determination and temperature-induced sex reversal. A total of 20 wnt genes were identified and classified into 13 subfamilies, displaying conserved structural organization and phylogenetic relationships consistent with other teleosts. Chromosomal mapping revealed lineage-specific WNT clusters, including a unique wnt3–wnt7b–wnt5b–wnt16 block, as well as syntenic associations with reproduction-related genes (e.g., adipor2, sema3a, nape-pld, erc2, lamb2), suggesting coordinated genomic regulation. Tissue transcriptome analysis demonstrated strong sex- and tissue-biased expression patterns, with wnt5a predominantly expressed in ovaries and wnt5b specifically upregulated in pseudo-male testes. Functional assays revealed that knockdown of wnt5a or wnt5b induced testis-specific genes (sox9b, tesk1) and suppressed ovarian markers (foxl2, cyp19a1a), indicating antagonistic regulatory roles in gonadal fate determination. Promoter analysis identified yy1a as a selective repressor of wnt5b, but not wnt5a, providing a mechanistic basis for paralog divergence. Furthermore, pull-down combined with LC–MS/MS analysis showed that WNT5b interacts with proteins enriched in ribosome biogenesis and ubiquitin-mediated proteolysis, suggesting a role in translational regulation and protein turnover during spermatogenesis. Together, these findings establish WNT5 signaling—particularly wnt5b—as a key driver of testicular development in C. semilaevis and provide new insights into the molecular mechanisms underlying sex differentiation and sex reversal in flatfish. Full article
(This article belongs to the Special Issue Sustainable Aquaculture: A Functional Genomic Perspective)
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