Submit to Fishes Review for Fishes Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Genetics and Breeding of Fishes

Print Special Issue Flyer
Editor
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A Special Issue of Fishes (ISSN 2410-3888) belonging to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (10 September 2026) | Viewed by 7188

Share This Special Issue

Editor

Dr. Wuhui Li

E-Mail Website
Guest Editor

Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China
Interests: fish; reproduction and breeding; genetics and genomics; heterosis; sustainable aquaculture

Special Issue Information

Dear Colleagues,

Fish and aquatic products with high-quality protein and high-quality fat are an important human food source. However, the traditional aquaculture model is faced with resource-based and environmental constraints, a lack of technological innovation ability in the seed-production industry, and the degradation of germplasm, which restricts the development of sustainable aquaculture practices. Germplasm innovation and efficient aquaculture practices are important in ensuring the sustainable development of aquatic products; therefore, there is a need to consolidate the latest information regarding fish breeding and aquaculture development. This Special Issue aims to provide the latest information on fish breeding technologies and sustainable aquaculture. Submissions may take the form of original research, full or mini-reviews, and perspectives on topics including, but not limited to, the following:

Genetic breeding techniques (selective breeding, hybridization, gynogenesis, gene editing, etc.), more generally for aquatic animals;
The evaluation of phenotype and genetic traits;
The evaluation of important characteristics (growth, disease resistance, stress tolerance, etc.);
Nutrition and metabolism;
New technology or systems for sustainable aquaculture;
Precision feeding, waste reduction strategies, and water quality management.

Dr. Wuhui Li
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-anonymized 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

fish breeding techniques
reproduction
genetics and genomics
sustainable aquaculture

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 (7 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

18 pages, 6196 KB

Open AccessArticle

Divergent Expression and Stress Responsiveness of mitfa and mitfb in Congjiang Golden-Backed Crucian Carp

by Sheng Zeng, Jinli Hu, Qinglan Zhou, Feng Chen, Ning Qin, Zhou Zhou and Xianbo Zhang

Fishes 2026, 11(9), 494; https://doi.org/10.3390/fishes11090494 - 22 Aug 2026

Viewed by 284

Abstract

The microphthalmia-associated transcription factor (Mitf) family is central to melanocyte biology. Teleosts possess two mitf paralogs, mitfa and mitfb, yet their functional divergence remains incompletely understood. Here, we characterized the coding sequences, phylogeny, tissue distribution, developmental expression, cellular localization, and stress responsiveness of mitfa and mitfb in Congjiang natural mutant crucian carp (NMCC). Both genes encoded proteins containing the characteristic bHLH-ZIP domain. Phylogenetic analysis revealed that teleost mitfb clustered with the tetrapod mitf clade, indicating closer evolutionary affinity than mitfa. mitfa was predominantly expressed in skin and eyes, whereas mitfb showed broad tissue distribution. Both paralogs were constitutively expressed in skin across developmental stages; mitfa levels remained consistently lower than mitfb. Both transcripts were localized to melanocyte-containing regions of the skin. Transcriptomic analysis following high temperature (34 °C), UV radiation, and combined stress (48 h) revealed that mitfa was significantly upregulated by thermal stress, while mitfb showed no significant changes. Profiling of DNA damage response pathways uncovered extensive, stress-specific transcriptional remodeling. High temperature broadly suppressed apoptotic genes while upregulating tsc2, gadd45b, and cdip1; UV triggered widespread apoptotic gene activation. Combined stress elicited a hybrid signature. Notably, robust DNA Damage Response pathway remodeling contrasted with muted mitf responses, suggesting that DNA Damage Response-to-pigmentation signaling may operate predominantly at post-transcriptional levels. These findings reveal a substantial regulatory divergence between mitfa and mitfb, with mitfa maintaining a conserved melanogenic role while mitfb has been co-opted for broader functions in non-pigmentary tissues. The differential stress responses of the two paralogs further provide new insights into tissue-specific genotoxic stress signaling and melanogenic regulation in teleosts. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

► Show Figures

Figure 1

13 pages, 1059 KB

Open AccessArticle

Genetic Traceability of European Sea Bass (Dicentrarchus labrax) and Gilthead Seabream (Sparus aurata) for Technological Advancements in Breeding Management

by Silvia Tumminia, Stefano Reale, Carlotta Piazza, Gianluca Sarà, Mar Bosch-Belmar, Federica Bruno, Germano Castelli, Eugenia Oliveri, Fabrizio Vitale, Marco Tolone and Silvia Scibetta

Fishes 2026, 11(6), 338; https://doi.org/10.3390/fishes11060338 - 4 Jun 2026

Viewed by 784

Abstract

This study evaluated the genetic variability and traceability potential of farmed European sea bass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) populations from a fish farm located in Petrosino (Marsala, Sicily) (FAO 37), using microsatellite markers. A total of 64 D. labrax and 63 S. aurata individuals were genotyped with species-specific multiplex panels (9 and 10 loci, respectively). High levels of polymorphism were observed in both species, with an average of 12 alleles per locus in D. labrax and 9.1 alleles per locus in S. aurata. Mean observed heterozygosity (Ho) was 0.530 in D. labrax and 0.459 in S. aurata, while expected heterozygosity (He) reached 0.762 and 0.702, respectively. The fixation index (F) indicated moderate heterozygote deficiency in both populations (0.320 in D. labrax and 0.352 in S. aurata). Significant deviations from Hardy–Weinberg equilibrium were detected at most loci in both species, suggesting non-random mating, genetic drift, or population substructure. The probability of identity (PI) values across loci confirmed the high discriminatory power of the microsatellite panels, supporting their suitability for individual identification and genetic traceability applications in aquaculture. Overall, the results highlight that, despite substantial genetic variability, the observed heterozygote deficiency and deviations from equilibrium may reflect suboptimal breeding management practices. These findings underline the importance of implementing regular genetic monitoring and integrating molecular tools into broodstock management to maintain genetic diversity, reduce inbreeding, and support sustainable aquaculture production. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

► Show Figures

Figure 1

17 pages, 2386 KB

Open AccessArticle

First Hybrid Genome Assembly of the Teleost Fish Red Cusk-Eel (Genypterus chilensis) from Oxford Nanopore and Illumina Reads: Comparative Genomic Analysis of Genypterus Species and Long Non-Coding RNA Tissue-Specific Expression

by Phillip Dettleff, Marcia Arriagada-Solimano, Vania Fuentealba, Karina Tobar, Millaray Sáez, Claudio Olave, Juan Manuel Estrada and Juan Antonio Valdés

Fishes 2026, 11(4), 244; https://doi.org/10.3390/fishes11040244 - 17 Apr 2026

Viewed by 1176

Abstract

The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly of G. chilensis using Nanopore long-reads and Illumina short-reads, integrated with structural and functional annotations from RNA-seq data of the intestine and head kidney. The resulting genome assembly was 439.89 Mb in size, with an N50 of 7.96 Mb, containing 35,029 coding genes. Comparative genomics with G. blacodes revealed high similarity in genome size and completeness. Additionally, 14,681 lncRNAs were annotated, with 641 lncRNAs and 7323 coding genes differentially expressed in a tissue-specific expression pattern. These findings provide a high-quality genomic resource that enhances the understanding of lncRNA regulation and genome structure in the Genypterus genus. This study establishes a foundation for future research on commercial traits, conservation, and the evolution of the Ophidiiformes order. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

► Show Figures

Figure 1

18 pages, 2825 KB

Open AccessArticle

Expression Profiles of Growth-Related Genes in CRISPR/Cas9-Mediated MRF4-Crispant Nile Tilapia

by Zahid Parvez Sukhan, Yusin Cho, Doohyun Cho, Cheol Young Choi and Kang Hee Kho

Fishes 2026, 11(1), 52; https://doi.org/10.3390/fishes11010052 - 14 Jan 2026

Viewed by 889

Abstract

Genome editing of late myogenic regulators provides a way to dissect the mechanisms through which transcriptional programs and growth-related signaling pathways shape muscle gene expression programs in farmed fish. This study disrupted myogenic regulatory factor 4 (MRF4) in Nile tilapia using CRISPR/Cas9 to examine downstream transcriptional changes in fast skeletal muscle across the trunk, belly, and head regions. Adult F0 crispants carried a frameshift mutation that truncated the basic helix–loop–helix domain and showed an approximate 80–85% reduction in MRF4 mRNA across the trunk, belly, and head muscles. The expression of 23 genes representing myogenic regulatory factors, MEF2 paralogs, structural and contractile components, non-myotomal regulators, cell adhesion and fusion-related transcripts, and growth-related genes within the GH–IGF–MSTN axis was quantified and compared between wild-type and MRF4-crispants. Expressions of major structural genes remained unchanged despite MRF4 depletion, whereas MyoG and MyoD were upregulated together with MEF2B and MEF2D, indicating strong transcriptional compensation. Twist1, ID1, PLAU, CDH15, CHRNG, NCAM1, MYMK, GHR, and FGF6 were also significantly elevated, while IGF1 was reduced, and MSTN remained stable. Together, these results show that MRF4 loss is associated with coordinated transcriptional changes in regulatory and growth-related pathways, while major fast-muscle structural and contractile transcript levels remain stable, thereby highlighting candidate transcriptional targets for future studies that will evaluate links to muscle phenotype and growth performance in Nile tilapia. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

► Show Figures

Figure 1

12 pages, 1045 KB

Open AccessArticle

Gene Expression and Antioxidant Characteristics of Rainbow Trout (Oncorhynchus mykiss) Eggs Used for Meiotic Gynogenesis

by Konrad Ocalewicz, Karolina Pałucha, Agata Błaszczyk, Marcin Kuciński, Stefan Dobosz, Ligia Panasiak and Rafał Rożyński

Fishes 2025, 10(11), 585; https://doi.org/10.3390/fishes10110585 - 13 Nov 2025

Viewed by 1077

Abstract

Gynogenesis is a reproductive mode where offspring inherit exclusively maternal chromosomes. Gynogenetic development in fish may be induced intentionally by activating eggs with the UV-irradiated, inactive spermatozoa. In the meiotic variant of gynogenesis, the resultant haploid gynogenetic zygote is then exposed to a physical shock to inhibit the release of the 2nd polar body and to reconstitute the diploid state of the embryo. Here, meiotic gynogenesis was induced in the rainbow trout eggs from different clutches to find any differences in terms of gene expression and antioxidant enzyme activity between eggs with high and low ability for gynogenetic development. The survival rates of the gynogenotes after hatching from the eggs originating from five females varied from 16.6 ± 4.3% to 53.8 ± 9.8%. Biochemical and molecular examination revealed that eggs with higher developmental potential for meiotic gynogenesis exhibited significantly greater glutathione peroxidase (GPx) activity than eggs with lower efficiency of gynogenesis. Moreover, eggs exhibiting the highest ability for gynogenetic development showed increased transcription of the keratin 8 gene and decreased abundance of keratin 18 and tubulin β mRNA transcripts. Since keratins protect oocytes from physical stress after ovulation, the high abundance of keratin 8 in the rainbow trout eggs may increase their resilience to the physical shock applied for the zygote diploidization during gynogenesis. On the other hand, a low level of tubulin-building microtubules may increase the efficiency of high hydrostatic pressure (HHP) shock used for diploidization of the gynogenetic zygotes. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

► Show Figures

Figure 1

12 pages, 3504 KB

Open AccessArticle

Full-Length Transcriptome Reveals Heterologous Sperm Fragments in Natural Gynogenetic Grass Carp

by Lang Qin, Yuxiang Wang, Ming Wen, Jinhui Huang, Xu Huang, Qian Chen, Dan Peng, Yang Wu, Qianye Wei, Fangzhou Hu, Kaijun Gong, Chun Zhang, Qinbo Qin, Chang Wu and Shaojun Liu

Fishes 2025, 10(11), 570; https://doi.org/10.3390/fishes10110570 - 7 Nov 2025

Viewed by 955

Abstract

Grass carp (Ctenopharyngodon idella) is one of the most economically important cyprinid species cultured in China. The diploid gynogenetic grass carp (2nGGC, 2n = 48) was generated from the hybrid of female grass carp (GC, 2n = 48) and male topmouth culter (TC, 2n = 48, Culter alburnus). This study obtained the full-length transcriptome of 2nGGC from five tissues using Pacific Biosciences (Pacbio) single-molecule real-time long-read isoform sequencing. Following the mapping of long reads to GC and TC reference genomes, a total of 1848 fusion isoforms were identified. Among them, 775 were distributed across different genomes, indicating that chimeric DNA fragments of TC were embedded in the 2nGGC genome. After removing the fusion genes and redundant isoforms, 107,721 full-length transcripts were obtained from 2nGGC, providing important full-length reference sequences for further research. Finally, comparative analysis of homologous gene variation identified 34 fragments in 2nGGC containing recombinant SNPs derived from both GC and TC. These results provide evidence that natural gynogenesis represents a form of “micro-hybridization” characterized by heterogeneous DNA fragments, distinct from traditional hybridization involving chromosome-level recombination. These findings offer valuable reference for fish genetic breeding. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

► Show Figures

Figure 1

19 pages, 9104 KB

Open AccessArticle

Integrated Analysis of Phenotypic and Hepatic Transcriptomic Profiles Reveals Enhanced Cold Tolerance in Triploid Crucian Carp

by Suifei Tao, Zexun Zhou, Shandong Chen, Jialin Cui, Yude Wang, Kaikun Luo, Wei Liu, Qingfeng Liu, Wuhui Li and Shaojun Liu

Fishes 2025, 10(10), 519; https://doi.org/10.3390/fishes10100519 - 12 Oct 2025

Viewed by 1168

Abstract

Cold stress poses a critical threat to fish survival by triggering metabolic dysfunction, oxidative damage, immune suppression, and apoptosis. However, hybrid polyploid fish triploid crucian carp (3nRCR, 3n = 150) demonstrate superior stress tolerance. In this study, we investigated the cold adaptation mechanisms in different ploidy cyprinid fishes: triploid crucian carp compared to its diploid improved red crucian carp (Carassius auratus red var., RCC, 2n = 100, ♀) and improved allotetraploid (4nAT, 4n = 200, ♂) progenitors. Under controlled cooling, 3nRCR lost equilibrium at a significantly lower temperature (3.2 °C) than RCC (4.0 °C) and 4nAT (4.5 °C), confirming its superior enhanced cold resistance. Histological examination revealed minimal tissue damage in 3nRCR, characterized by reduced gill inflammation and cellular apoptosis. Transcriptomics revealed triploid-specific molecular strategies: 3nRCR uniquely activated retinol metabolism and metabolic rewiring (arginine/proline metabolism, oxidative phosphorylation). Notably, in the immune-related NLR signaling pathway, both nlrp1 and nlrp3 (key inflammasome components) were significantly downregulated in 3nRCR (p < 0.01). In contrast, genes involved in endoplasmic reticulum (ER) stress response, including chop and nrf2, were markedly upregulated, indicating a reinforced cellular stress resolution mechanism absent in both RCC and 4nAT. Our results demonstrate that triploid cold adaptation is orchestrated through a balanced interaction among mitochondrial apoptosis, ER stress, and inflammasome pathways. These findings provide novel insights into hybrid polyploid adaptation mechanisms and targets for cold-resilient aquaculture breeding. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

► Show Figures

Journal Menu

Journal Browser

Genetics and Breeding of Fishes

Share This Special Issue

Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (7 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI