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Fishes
Special Issues
Germplasm Resources and Genetic Breeding of Aquatic Animals
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Germplasm Resources and Genetic Breeding of Aquatic Animals

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

Deadline for manuscript submissions: 15 May 2026 | Viewed by 4185

Special Issue Editors

Dr. Yang Liu

E-Mail Website
Guest Editor
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
Interests: fish; genetic; breeding
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yongsheng Tian

E-Mail Website
Guest Editor
Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
Interests: sperm cryopreservation; gynogenesis; selective breeding; crossbreeding; sex control; vitrification cryopreservation for frozen embryos; flounder breeding system; Paralichthys olivaceus; fish

Special Issue Information

Dear Colleagues,

Multifarious taxonomically diverse groups are detected in aquatic animals. Their remarkable evolutionary success is characterized by varied reproductive strategies and multiple genome duplication events throughout their evolutionary history. Investigations into germplasm resources and the genetic breeding of aquatic animals will provide critical insights for understanding growth and development, population diversity, evolutionary trajectories, and molecular breeding applications. Current genetic breeding technologies employed to combat species degeneration encompass hybridization, gynogenesis, androgenesis, selective breeding, transgenic modification, and gene editing technologies. These interventions frequently yield progeny with significant enhancements in commercially important traits including growth performance, survival rates, disease resistance, body color, and environmental stress tolerance. Through advanced genomic approaches, including genome-wide association studies (GWAS), QTL-seq analysis, and transcriptome sequencing, researchers have successfully identified key candidate genes and genetic markers associated with economically valuable traits.

This Special Issue aims to share the latest research trends and applications of “Germplasm Resources and Genetic Breeding of Aquatic Animals” that might shed light on genomic evolution, regulatory mechanism, functional gene, and novel breeding strategies. To advance the knowledge of such intricate issues, contributions from experts in the field, in the form of research papers and critical reviews, are called for.

Dr. Yang Liu
Prof. Dr. Yongsheng Tian
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-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

  • germplasm preservation and utilization
  • genome evolution
  • omics analysis
  • economic traits
  • functional gene
  • mitochondrial genome
  • microsatellite
  • growth and development

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Published Papers (4 papers)

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Research

20 pages, 3383 KB  
Article
Gonadal Transcriptome Analysis Identifies Sex-Related Genes and Regulatory Pathways in Spotted Longbarbel Catfish (Hemibagrus guttatus)
by Kun Zhao, Yuanyuan Wang, Yexin Yang, Yi Liu, Chao Liu, Shandian Zhu, Jinhui Sun and Xidong Mu
Fishes 2026, 11(1), 43; https://doi.org/10.3390/fishes11010043 - 9 Jan 2026
Viewed by 658
Abstract
Hemibagrus guttatus is a large omnivorous fish of significant economic value, listed as a Class II protected species in the National Key Protected Wildlife List in 2021 in China. To provide a theoretical foundation for the artificial breeding of H. guttatus, this [...] Read more.
Hemibagrus guttatus is a large omnivorous fish of significant economic value, listed as a Class II protected species in the National Key Protected Wildlife List in 2021 in China. To provide a theoretical foundation for the artificial breeding of H. guttatus, this study employs high-throughput transcriptome sequencing of testes and ovaries to elucidate the molecular regulatory pathways involved in sex differentiation. Because H. guttatus exhibits no obvious sexual dimorphism even during the breeding season, the distinctive contribution of this study compared with previous gonadal-transcriptomic investigations in other Siluriformes lies not only in documenting sex-biased genes but also in providing a molecular foundation for developing non-lethal sex-identification methods for this morphologically indistinguishable species. A total of 303,192,896 raw reads were obtained, with an effective data rate of 98.4%, indicating high sequencing quality. Differential expression analysis identified 8694 genes, including 6369 upregulated in testes and 2325 upregulated in ovaries. Among these, 88 genes were functionally annotated as sex-related, with 62 testis-biased genes such as spata17, sox9, and dmrt1, and 26 ovary-biased genes including cyp19a, wnt8, and sox12. KEGG pathway enrichment analysis revealed that the TGF-β signaling pathway, insulin secretion, and steroid hormone biosynthesis may play crucial roles in gonadal development and differentiation in H. guttatus. The expression patterns of key genes such as hsd11b1, amh, and insl3 were validated by quantitative real-time PCR, showing consistency with the transcriptome results. These findings lay a molecular foundation for understanding the regulatory mechanisms of sex differentiation in H. guttatus, and provide candidate genes for further investigation into the genetic basis of gonadal development, which is essential for improving artificial reproduction and selective breeding practices. Full article
(This article belongs to the Special Issue Germplasm Resources and Genetic Breeding of Aquatic Animals)
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17 pages, 2330 KB  
Article
Neurotransmitter and Gut–Brain Metabolic Signatures Underlying Individual Differences in Sociability in Large Yellow Croaker (Larimichthys crocea)
by Guan-Yuan Wei, Zheng-Xiang Zhang, Hao-Han Chen, Bao Qiu, Yun-Zhong Wang, Lan Ding, Peng Jin, Xue-Wei-Jie Chen and Zhi-Shuai Hou
Fishes 2025, 10(12), 654; https://doi.org/10.3390/fishes10120654 - 17 Dec 2025
Viewed by 620
Abstract
Teleost social behavior plays an important role in foraging, reproduction, and aquaculture management, yet its physiological basis remains poorly understood. This study investigated individual differences in sociability in the large yellow croaker (Larimichthys crocea) using behavioral assays and metabolomic profiling in [...] Read more.
Teleost social behavior plays an important role in foraging, reproduction, and aquaculture management, yet its physiological basis remains poorly understood. This study investigated individual differences in sociability in the large yellow croaker (Larimichthys crocea) using behavioral assays and metabolomic profiling in the brain–intestine axis. Behavioral tests revealed that high-sociability (HS) fish spent significantly more time near conspecifics than low-sociability (LS) fish, indicating clear behavioral divergence between groups. Targeted metabolomics of brain tissue showed distinct neurotransmitter signatures between HS and LS individuals, including significant differences in acetylcholine, DOPAC, xanthurenic acid, and glutamine. Untargeted intestinal metabolomics identified 65 differential metabolites between groups. Intestinal metabolites such as LEA and CEA exhibited significant group-specific variation and were functionally associated with CB1 and CB2 cannabinoid receptors, suggesting a potential endocannabinoid-mediated contribution to sociability differences. Differential metabolites enriched in amino–sugar and nucleotide–sugar metabolic pathways. Integration of behavioral and metabolomic data suggests that neurotransmitter regulation and gut–brain metabolic signaling jointly contribute to sociability differences in large yellow croaker. These findings provide mechanistic insights into social behavior and offer potential biomarkers for welfare assessment and selective breeding in aquaculture. Full article
(This article belongs to the Special Issue Germplasm Resources and Genetic Breeding of Aquatic Animals)
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15 pages, 12128 KB  
Article
Metabolomic and Transcriptomic Analyses of Soft-Body Coloration in Jinjiang Oyster (Crassostrea ariakensis)
by Zhuanzhuan Li, Shuqi Zhao, Jianing Yu, Biao Wu, Peizhen Ma, Xiujun Sun, Liqing Zhou and Zhihong Liu
Fishes 2025, 10(10), 499; https://doi.org/10.3390/fishes10100499 - 3 Oct 2025
Viewed by 964
Abstract
The coloration of shellfish significantly influences both environmental adaptability and economic value. In the Jinjiang oyster (Crassostrea ariakensis), soft-body color varies between individuals, with an orange-yellow phenotype distinct from the milky white coloration of the wild type. To elucidate the compositional [...] Read more.
The coloration of shellfish significantly influences both environmental adaptability and economic value. In the Jinjiang oyster (Crassostrea ariakensis), soft-body color varies between individuals, with an orange-yellow phenotype distinct from the milky white coloration of the wild type. To elucidate the compositional differences and molecular mechanisms underlying orange-yellow (designated as CaR) versus milky white (CaW) soft-body color in C. ariakensis, we conducted comparative ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) non-targeted and transcriptomic analyses. A total of 280 differential accumulation metabolites (DAMs) and 691 differentially expressed genes (DEGs) were detected between the CaR and CaW groups. The metabolite set enrichment analysis (MSEA) revealed that DAMs were significantly enriched in pigment metabolism pathways, including tyrosine metabolism, porphyrin metabolism, and lipid metabolism. Furthermore, genes associated with melanin synthesis and carotenoids conversions or transports were upregulated in the CaR vs. CaW group. These genes included Cyp4z1, Cyp4f22, Cyp17a1, Cyp1a5, Cyp2d28a, Lrp4, Aldh, and Tyr-3, potentially driving the accumulation of pheomelanin and carotenoids. This study demonstrates the vital roles of melanin and carotenoid metabolism in Jinjiang oyster body color formation, providing key insights into the molecular mechanisms of color determination in shellfish. Full article
(This article belongs to the Special Issue Germplasm Resources and Genetic Breeding of Aquatic Animals)
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15 pages, 1849 KB  
Article
Embryonic and Larval Development of an Interspecific Grouper Backcross Between the Kelp Grouper (Epinephelus moara) ♀ and KGGG (E. moara ♀ × E. lanceolatus ♂) ♂
by Yidan Xu, Yongsheng Tian, Shihao Wang, Tangtang Ding, Linna Wang, Zhentong Li, Linlin Li and Yang Liu
Fishes 2025, 10(10), 488; https://doi.org/10.3390/fishes10100488 - 1 Oct 2025
Cited by 2 | Viewed by 1268
Abstract
Backcrossing serves as an effective tool for interspecific gene introgression, facilitating germplasm improvement. To develop superior grouper aquaculture varieties, in this study, a backcrossed breed was constructed by crossing a male hybrid grouper, KGGG (Epinephelus moara ♀ × E. lanceolatus ♂), with [...] Read more.
Backcrossing serves as an effective tool for interspecific gene introgression, facilitating germplasm improvement. To develop superior grouper aquaculture varieties, in this study, a backcrossed breed was constructed by crossing a male hybrid grouper, KGGG (Epinephelus moara ♀ × E. lanceolatus ♂), with a female parent kelp grouper (KG; E. moara). Here, we observed embryonic, larval development, and morphological changes in KG × KGGG. Additionally, the total length and body weight of the backcrossed breed and maternal parent were compared at 160 d post hatching (dph). The results showed that fertilization and the hatching rate were 73.23 ± 4.23% and 51.74 ± 3.67%, respectively, and the egg size was 0.89 ± 0.03 mm. Hatching occurred 23:19 h after fertilization at 25 ± 1 °C, and the newly hatched larvae were 1.94 ± 0.13 mm in length. Furthermore, at 160 dph, the total length and body weight of the backcrossed breed were 1.2-fold and 1.9-fold greater, respectively, when compared with those of the maternal parent. Importantly, it is possible that backcrossed KG × KGGG could become a dominant strain in grouper aquaculture practices. Full article
(This article belongs to the Special Issue Germplasm Resources and Genetic Breeding of Aquatic Animals)
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