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Molecular Genetics Applied to Aquaculture: From Breeding Stock Selection to...
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Molecular Genetics Applied to Aquaculture: From Breeding Stock Selection to Biotechnological Innovations

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (25 July 2025) | Viewed by 3116

Special Issue Editors

Dr. Cristiana Ramalho Maciel

E-Mail Website
Guest Editor
Instituto de Estudos Costeiros, Universidade Federal do Pará (UFPA), Bragança, PA, Brazil
Interests: comparative physiology; Macrobrachium; aquaculture; molecular; genetics; transcriptome
Prof. Dr. Fernando Araújo Abrunhosa

E-Mail Website
Guest Editor
Coastal Studies Institute (IECOS), Universidade Federal do Pará, Brazil
Interests: aquaculture; fish; molecular; genetics
Dr. Vanessa Paes da Cruz

E-Mail Website
Guest Editor Assistant
Instituto de Estudos Costeiros, Universidade Federal do Pará (UFPA), Bragança, PA, Brazil
Interests: cytogenetics; development of molecular markers, with emphasis on studies in population genetics for fish conservation
Dr. Ítalo Antônio de Freitas Lutz

E-Mail Website
Guest Editor Assistant
Instituto de Estudos Costeiros, Universidade Federal do Pará (UFPA), Bragança, PA, Brazil
Interests: conservation and biodiversity; bioecology of crustaceans; fish; artisanal and industrial fishing; dynamics of fish populations; assessment and management of fish stocks; genetics applied to fishing and aquaculture and forensic inspection

Special Issue Information

Dear Colleagues,

Sustainable aquaculture is crucial to increasing production efficiency, competitiveness, and product quality. To achieve these goals, improvements in feeding practices, breeding conditions, disease control, and genetics are essential. Genetic management of breeding stocks, supported by pedigree programs, can produce animals with higher growth rates, fertility, and disease resistance. Advances in molecular genetics now allow precise monitoring of genetic diversity using molecular markers, which aids in the selection of superior breeding stocks. Forensic tools also allow the detection of commercial fraud, safeguarding the integrity of aquaculture practices. Next-generation sequencing has revolutionized the field, providing vast data that fuels biotechnological innovations. Nutrigenomics, for example, guides nutritional testing, optimizing resources and time. In addition, genetic manipulation techniques, such as the production of monosex populations, have become practical solutions for many aquatic species. This Special Issue aims to present research on molecular genetic tools to advance aquaculture. Our aim is to discuss and develop strategies that not only improve production efficiency and competitiveness but also ensure that aquaculture is sustainable.

Dr. Cristiana Ramalho Maciel
Prof. Dr. Fernando Araújo Abrunhosa
Guest Editors

Dr. Vanessa Paes da Cruz
Dr. Ítalo Antônio de Freitas Lutz
Guest Editor Assistant

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 100 words) can be sent to the Editorial Office for announcement on this website.

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. Genes 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

  • genomic information
  • nutrigenomic
  • breeding programs
  • genetic structure
  • population structure
  • technological innovations in aquaculture
  • genetic improvement
  • marker-assisted selection (mas)
  • genetic diversity
  • application of omics in aquaculture

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Published Papers (4 papers)

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Research

13 pages, 280 KiB  
Article
Genotype-by-Environment Interaction in Red Tilapia (Oreochromis spp.): Implications for Genetic Parameters and Trait Performance
by Tran Huu Phuc, Pham Dang Khoa, Nguyen Thi Dang, Tran Thi Mai Huong, Huynh Thi Bich Lien, Vo Thi Hong Tham, Nguyen Huynh Duy and Nguyen Hong Nguyen
Genes 2025, 16(8), 966; https://doi.org/10.3390/genes16080966 - 18 Aug 2025
Viewed by 43
Abstract
The intensive farming of aquaculture species such as red tilapia (Oreochromis spp.) across diverse production systems can lead to changes in genetic parameters and responses of economically important traits in this species. This study represents the first attempt to understand these changes [...] Read more.
The intensive farming of aquaculture species such as red tilapia (Oreochromis spp.) across diverse production systems can lead to changes in genetic parameters and responses of economically important traits in this species. This study represents the first attempt to understand these changes in growth traits (body weight, total length), quality attributes (body colour), and survival rate in red tilapia. Data for these traits were collected from 75,950 individual fish, progeny of 970 full-sib families (comprising 970 dams and 486 sires); they were selected for high body weight and evaluated in two distinct culture environments: fresh- and saltwater ponds. A multi-trait mixed model was employed to estimate genetic parameters and selection responses. Genetic variance estimates for the quality and survival traits varied across the two environments. However, genetic correlations among the traits studied were similar between fresh and saline water. Furthermore, significant G × E interactions, particularly for the quality and survival traits, were evidenced by divergent genetic correlations (rg = 0.57–0.83) between homologous traits across different environments. The findings emphasise the importance of incorporating G × E interactions into the selection program for red tilapia, particularly when the breeding objectives extend to include quality and survival traits. Selection strategies should consider the prevailing culture system—for instance, favouring genotypes suited to the freshwater pond environment over those adapted to the saltwater environment. Continual assessment of full-sib groups across these environments is recommended to refine our understanding of G × E interactions and optimise future breeding programs for red tilapia. This may involve selecting genotypes capable of consistent performance across environments or developing environment-specific breeding programs. Full article
(This article belongs to the Special Issue Molecular Genetics Applied to Aquaculture: From Breeding Stock Selection to Biotechnological Innovations)
13 pages, 1149 KiB  
Article
Transcriptome Profiling Reveals Differences Between Rainbow Trout Eggs with High and Low Potential for Gynogenesis
by Konrad Ocalewicz, Artur Gurgul, Stefan Dobosz, Igor Jasielczuk, Tomasz Szmatoła, Ewelina Semik-Gurgul, Mirosław Kucharski and Rafał Rożyński
Genes 2025, 16(7), 803; https://doi.org/10.3390/genes16070803 - 8 Jul 2025
Viewed by 448
Abstract
Background/Objectives: Fish eggs activated with UV-irradiated spermatozoa and exposed to the High Hydrostatic Pressure (HHP) shock to inhibit first cell cleavage develop as gynogenetic Doubled Haploids (DHs) that are fully homozygous individuals. Due to the expression of the recessive genes and side effects [...] Read more.
Background/Objectives: Fish eggs activated with UV-irradiated spermatozoa and exposed to the High Hydrostatic Pressure (HHP) shock to inhibit first cell cleavage develop as gynogenetic Doubled Haploids (DHs) that are fully homozygous individuals. Due to the expression of the recessive genes and side effects of the gamete treatment, survival of fish DHs is rather low, and most of the mitotic gynogenotes die before hatching. Nevertheless, as maternal gene products provided during oogenesis control the initial steps of embryonic development in fish, a maternal effect on the survival of gynogenotes needs to be also considered to affect efficiency of gynogenesis. Thus, the objective of this research was to apply an RNA-seq approach to discriminate transcriptional differences between rainbow trout (Oncorhynchus mykiss) eggs with varied abilities to develop after gynogenetic activation. Methods: Gynogenetic development of rainbow trout was induced in eggs originated from eight females. Maternal RNA was isolated and sequenced using RNA-Seq approach. Survival rates of gynogenotes and transcriptome profiles of eggs from different females were compared. Results: RNA-seq analysis revealed substantial transcriptional differences between eggs originated from different females, and a significant correlation between the ability of the eggs for gynogenesis and their transcriptomic profiles was observed. Genes whose expression was altered in eggs with the increased survival of DHs were mostly associated (GO BP) with the following biological processes: development, cell differentiation, cell migration and protein transport. Some of the genes are involved in the oocyte maturation (RASL11b), apoptosis (CASPASE 6, PGAM5) and early embryogenesis, including maternal to zygotic transition (GATA2). Conclusions: Inter-individual variation of the transcription of maternal genes correlated with the competence of eggs for gynogenesis suggest that at least part of the mortality of the rainbow trout DHs appear before activation of zygotic genome and expression of the lethal recessive traits. Full article
(This article belongs to the Special Issue Molecular Genetics Applied to Aquaculture: From Breeding Stock Selection to Biotechnological Innovations)
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30 pages, 5615 KiB  
Article
Phylogenomic and Evolutionary Insights into Lipoprotein Lipase (LPL) Genes in Tambaqui: Gene Duplication, Tissue-Specific Expression and Physiological Implications
by Rômulo Veiga Paixão, Izabel Correa Bandeira, Vanessa Ribeiro Reis, Gilvan Ferreira da Silva, Fernanda Loureiro de Almeida O’Sullivan and Eduardo Sousa Varela
Genes 2025, 16(5), 548; https://doi.org/10.3390/genes16050548 - 30 Apr 2025
Viewed by 507
Abstract
Background/Objectives: Lipoprotein lipase (LPL) is a key enzyme in lipid metabolism, crucial for the hydrolysis of triglycerides in lipoproteins and maintaining lipid homeostasis in vertebrates. This study aims to characterize the lipoprotein lipase genes in the tambaqui (Colossoma macropomum) genome, investigating [...] Read more.
Background/Objectives: Lipoprotein lipase (LPL) is a key enzyme in lipid metabolism, crucial for the hydrolysis of triglycerides in lipoproteins and maintaining lipid homeostasis in vertebrates. This study aims to characterize the lipoprotein lipase genes in the tambaqui (Colossoma macropomum) genome, investigating their evolutionary history from a phylogenomic perspective. Methods: Phylogenetic and syntenic analyses were used to identify the lpl gene copies in the tambaqui genome and expression patterns were examined across different tissues. A comparative analysis with lpl genes from other vertebrates was also conducted to assess evolutionary relationships and functional diversification. Results: We identified three lpl gene copies in the tambaqui genome: lpl1a, lpl1b, and the lesser-known member of the lipoprotein lipase subfamily, lpl2a. These proteins possess conserved sites essential for lipoprotein lipase function, with variations that may affect their physicochemical properties and lipolytic activity. Key amino acid variations, such as in the lid region and glycosylation sites, were observed among orthologs. Gene expression analysis showed high lpl1a and lpl2a expression in the liver, and lpl1b expression in the gonads, suggesting tissue-specific roles. Comparative analysis revealed distinct expression patterns among teleost fish, with tambaqui exhibiting a unique profile consistent with its migratory lifestyle and varied diet. Conclusions: This study offers new insights into the evolution and functional diversification of lipoprotein lipases in vertebrates, highlighting the complexity of lipid metabolism in fish. These findings contribute to understanding the adaptability of teleost fish to diverse environments and lay the foundation for future research in lipid metabolism regulation, including Neotropical species, with potential applications in aquaculture and conservation. Full article
(This article belongs to the Special Issue Molecular Genetics Applied to Aquaculture: From Breeding Stock Selection to Biotechnological Innovations)
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16 pages, 10886 KiB  
Article
In Silico Identification of the Laccase-Encoding Gene in the Transcriptome of the Amazon River Prawn Macrobrachium amazonicum (Heller, 1862)
by Gabriel Monteiro de Lima, Fernando Araújo Abrunhosa, Bruna Ramalho Maciel, Ítalo Lutz, Janieli do Socorro Amorim da Luz Sousa, Carlos Murilo Tenório Maciel and Cristiana Ramalho Maciel
Genes 2024, 15(11), 1416; https://doi.org/10.3390/genes15111416 - 31 Oct 2024
Viewed by 1468
Abstract
Background: Macrobrachium amazonicum is an opportunistic and omnivorous species that primarily feeds on plant material. Recent studies have shown that Endo-β-1,4-glucanase and Endo-β-1,4-mannanase are expressed in the transcriptome of adult specimens, while juveniles are capable of digesting nutrients from purified cellulose in their [...] Read more.
Background: Macrobrachium amazonicum is an opportunistic and omnivorous species that primarily feeds on plant material. Recent studies have shown that Endo-β-1,4-glucanase and Endo-β-1,4-mannanase are expressed in the transcriptome of adult specimens, while juveniles are capable of digesting nutrients from purified cellulose in their diet. In organisms that degrade raw plant material, laccase plays a key role in oxidizing phenolic compounds found in lignin, leading to its depolymerization and increasing access to cellulose and hemicellulose microfibrils. Objective: In this study, we conducted an in silico identification and characterization of the laccase-encoding gene, as this enzyme is linked to lignin biodegradation in herbivorous crustaceans. Methods: We analyzed the transcriptomes of the hepatopancreas from adult M. amazonicum, sequenced using the Illumina HiSeq 2500 platform. Subsequently, bioinformatics analyses were conducted to predict the conserved regions and active sites associated with laccase activity. Results: A complete open reading frame (ORF) of the laccase protein was identified in all datasets, comprising 609 amino acids. The top 40 similarity hits corresponded exclusively to crustaceans such as prawns, crayfish, and crabs (86.3–51.4%), while the highest divergence was observed in relation to fungi, plants, and bacteria. Three conserved domains were detected, along with the complete set of copper-binding centers (T1Cu, T2Cu, and T3Cu). A notable variable residue was methionine, suggesting a reduced redox potential in M. amazonicum laccase. Conclusion: These findings, combined with recent reports on the nutritional requirements of M. amazonicum, contribute to a deeper understanding of the digestive physiology of this species and offer valuable insights into its ability to utilize plant fibers as energy sources. Full article
(This article belongs to the Special Issue Molecular Genetics Applied to Aquaculture: From Breeding Stock Selection to Biotechnological Innovations)
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