Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.3
3.5
Journals
Biology
Special Issues
Germplasm Resources and Molecular Breeding for Sustainable Aquatic Species Improvement
share announcement

Germplasm Resources and Molecular Breeding for Sustainable Aquatic Species Improvement

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biochemistry and Molecular Biology".

Deadline for manuscript submissions: 30 April 2027 | Viewed by 3133

Special Issue Editor

Dr. Falin Zhou

E-Mail Website
Guest Editor
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
Interests: marine; ship; germplasm resource evaluation; molecular marker; genomics; gene editing; selective breeding; environment adaptation

Special Issue Information

Dear Colleagues,

With the ongoing rapid development of global aquaculture, the conservation and utilization of aquatic germplasm resources have become critical for sustainable industry growth. Genetic diversity within aquatic species serves as the foundation for improving traits such as growth performance, disease resistance, environmental adaptability, and product quality. Advances in molecular breeding technologies—including genomic selection, marker-assisted breeding, and gene editing—have revolutionized the genetic improvement of aquatic organisms. However, challenges persist in efficiently evaluating germplasm resources, deciphering genetic mechanisms of key traits, and applying molecular tools to practical breeding programs.

Environmental stressors, habitat degradation, overexploitation, and emerging diseases further threaten the genetic integrity and diversity of aquatic species, underscoring the urgency to explore innovative strategies for germplasm preservation and genetic enhancement. This Special Issue aims to address these challenges by compiling cutting-edge research on the identification, conservation, and utilization of aquatic germplasm resources, as well as the development and application of molecular breeding technologies.

We warmly invite original research articles, reviews, and perspectives that address, but are not limited to, the following topics:

Germplasm resource evaluation: Genetic diversity assessment, population structure analysis, and conservation strategies.
Molecular marker development: Applications in trait mapping, pedigree analysis, and genetic resource management.
Genomic insights: Whole-genome sequencing, functional genomics, and epigenetic regulation of economically important traits.
Gene editing and biotechnology: CRISPR-Cas9, transgenesis, and their roles in trait improvement.
Selective breeding programs: Integration of traditional and molecular approaches for enhanced productivity and resilience.
Climate adaptation and sustainability: Breeding strategies to address environmental changes and aquaculture sustainability.

By advancing our understanding of aquatic germplasm resources and molecular breeding, this Special Issue seeks to foster innovation in aquaculture practices and contribute to global food security.

Dr. Falin Zhou
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-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology 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 2700 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 resource evaluation
  • molecular marker
  • genomics
  • gene editing
  • selective breeding
  • environment adaptation

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 (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

18 pages, 11051 KB  
Article
Population Genetic Structure and Regional Divergence of the Endangered Freshwater Fish Black Shinner Pseudopungtungia nigra Based on Mitochondrial DNA
by Kang-Rae Kim and In-Chul Bang
Biology 2026, 15(11), 833; https://doi.org/10.3390/biology15110833 - 26 May 2026
Viewed by 308
Abstract
Assessing genetic structure is important for conserving endangered freshwater fishes inhabiting fragmented river systems. Pseudopungtungia nigra, a Korean endemic species, occurs in several isolated drainages, but its mitochondrial population structure has not been fully evaluated. In this study, we analyzed mitochondrial cytochrome [...] Read more.
Assessing genetic structure is important for conserving endangered freshwater fishes inhabiting fragmented river systems. Pseudopungtungia nigra, a Korean endemic species, occurs in several isolated drainages, but its mitochondrial population structure has not been fully evaluated. In this study, we analyzed mitochondrial cytochrome b (cytb) sequences from 80 individuals across eight populations to examine genetic diversity, haplotype composition, and population differentiation. A total of 25 haplotypes were detected, indicating relatively high diversity at the species level. However, diversity was uneven among populations: the Mangyeonggang (MG) population contained only two haplotypes, both of which were not found in the other populations, and showed the lowest haplotype and nucleotide diversity among the sampled populations. Multiple analyses, including pairwise differentiation, haplotype network reconstruction, principal coordinates analysis, and AMOVA, consistently identified MG as the most divergent population. The mitochondrial pattern was also concordant with previously reported microsatellite-based structure, supporting a major division between MG and the remaining populations. These findings indicate that P. nigra preserves substantial diversity overall, whereas the MG population showed a restricted and population-specific cytb haplotype composition. This study provides a genetic basis for defining conservation units and for guiding restoration and management strategies in this endangered species. Full article
(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding for Sustainable Aquatic Species Improvement)
►▼ Show Figures

Graphical abstract

20 pages, 2987 KB  
Article
Lipidomic Profiling of Dechorionated Fertilized Eggs and Egg Chorion in Three Tropical Marine Fish Species: Insights into Reproductive Physiology and Nutrition
by Yi-Hong Liu, Hua-Yang Guo, Bao-Suo Liu, Teng-Fei Zhu, Lin Xian, Nan Zhang, Ke-Cheng Zhu, Jian-She Zhang and Dian-Chang Zhang
Biology 2026, 15(2), 172; https://doi.org/10.3390/biology15020172 - 17 Jan 2026
Viewed by 538
Abstract
Broodstock nutrition is a key determinant of reproductive output in marine fishes because lipids support yolk formation, embryonic development, and early larval viability. However, the allocation of lipid classes between fertilized eggs and the egg envelope (chorion) remains poorly characterized for many tropical [...] Read more.
Broodstock nutrition is a key determinant of reproductive output in marine fishes because lipids support yolk formation, embryonic development, and early larval viability. However, the allocation of lipid classes between fertilized eggs and the egg envelope (chorion) remains poorly characterized for many tropical species. In this study, we performed a comparative lipidomic analysis of dechorionated fertilized egg contents and isolated chorion from three tropical marine fishes (Trachinotus ovatus, Platax teira, and Plectropomus leopardus) using UHPLC–Q Exactive Orbitrap MS/MS. Multivariate analyses revealed clear tissue- and species-specific lipid patterns. Dechorionated eggs were enriched in energy-storage lipids, dominated by triacylglycerols and essential polyunsaturated fatty acids, whereas chorion tissues contained higher levels of structural and signaling lipids, including phosphatidylinositols and sphingolipids. Each species exhibited a distinct lipid signature, with T. ovatus characterized by higher secosteroids and free fatty acids, P. teira by glycerophosphoethanolamines and phosphoinositols, and P. leopardus by abundant triradylglycerols. Pathway enrichment highlighted glycerophospholipid metabolism and sphingolipid signaling as prominent processes during early development. These findings clarify lipid partitioning between dechorionated fertilized egg contents and the chorion and provide a biochemical rationale for optimizing species-specific broodstock diets to enhance egg quality in tropical marine aquaculture. Full article
(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding for Sustainable Aquatic Species Improvement)
►▼ Show Figures

Figure 1

15 pages, 2572 KB  
Article
Transcriptome Assembly and Comparative Analysis of the Superoxide Dismutase (SOD) Gene Family in Three Hyotissa Species
by Xiangjie Kong, Sheng Liu, Shan Zhang, Youli Liu, Zhihua Lin and Qinggang Xue
Biology 2026, 15(1), 4; https://doi.org/10.3390/biology15010004 - 19 Dec 2025
Viewed by 904
Abstract
The genus Hyotissa (family Gryphaeidae) comprises ecologically and economically important marine bivalves, yet their molecular biology remains poorly characterized. This study presents de novo transcriptome sequencing of three Hyotissa species—H. sinensis, H. inaequivalvis, and Hyotissa sp.—to systematically identify and characterize [...] Read more.
The genus Hyotissa (family Gryphaeidae) comprises ecologically and economically important marine bivalves, yet their molecular biology remains poorly characterized. This study presents de novo transcriptome sequencing of three Hyotissa species—H. sinensis, H. inaequivalvis, and Hyotissa sp.—to systematically identify and characterize the superoxide dismutase (SOD) gene family, a crucial component of the antioxidant defense system. We identified 46 SOD genes, including both Cu/Zn-SOD and Fe/Mn-SOD types, which exhibited considerable variation in molecular properties, domain architecture, and potential phosphorylation sites. Phylogenetic analysis revealed both evolutionary conservation and diversification of SODs across species. Notably, we identified homologs of two specialized SOD types: Dominin, which showed mutations in metal-binding sites suggestive of functional divergence, and copper-only SOD repeat proteins (CSRPs), which retained copper-binding residues but lost zinc-binding capacity. These findings suggest that the SOD family in Hyotissa has undergone significant functional diversification, potentially as an adaptive response to their high-oxygen, high-ultraviolet reef habitats. This study provides foundational transcriptomic resources for Hyotissa and offers new insights into the evolution and environmental adaptation of SOD genes in marine bivalves. Full article
(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding for Sustainable Aquatic Species Improvement)
►▼ Show Figures

Figure 1

19 pages, 4710 KB  
Article
Identification of SNP Markers in the Glutamate Dehydrogenase (GDH) and Aspartate Aminotransferase 2 (AST2) Associated with Ammonia Nitrogen Tolerance in Penaeus monodon
by Yangyang Ding, Jinsong Chen, Song Jiang, Qibin Yang, Yundong Li, Jianhua Huang, Lishi Yang, Jianzhi Shi, Yebing Yu, Shigui Jiang and Falin Zhou
Biology 2025, 14(11), 1532; https://doi.org/10.3390/biology14111532 - 31 Oct 2025
Viewed by 763
Abstract
Black tiger shrimp (Penaeus monodon) is the largest species of penaeid, being commercially cultured globally, ranking as the second most farmed species in the shrimp industry. However, with the transformation of shrimp aquaculture from semi-intensive to high-density farming, the concentration of [...] Read more.
Black tiger shrimp (Penaeus monodon) is the largest species of penaeid, being commercially cultured globally, ranking as the second most farmed species in the shrimp industry. However, with the transformation of shrimp aquaculture from semi-intensive to high-density farming, the concentration of ammonia nitrogen in the aquatic environment has increased, severely affecting the growth and survival of shrimps. To increase production efficiency, breeding new strains of shrimp with the trait of tolerance to high ammonia nitrogen is desired in the black tiger shrimp aquaculture. Previous studies have shown that glutamate dehydrogenase (GDH) and aspartate aminotransferase 2 (AST2) play important roles in the metabolism of ammonia nitrogen in crustaceans. In the present study, we conducted synteny analysis of PmGDH and PmAST2 in different species. The interactions of PmGDH with ammonium (NH4+) and PmAST2 with aspartate were analyzed by docking. To develop molecule markers associated with ammonia nitrogen tolerance, SNPs of PmGDH and PmAST2 were identified by direct sequencing, genotyped by the SNaPshot technique, and characterized through genotype-phenotype association analysis by PLINK software version 1.9 in the three geographical populations, two families with different ammonia tolerance, and 120 susceptible and resistant individuals of black tiger shrimp. The results indicate that the GDH and AST2 genes are evolutionarily conserved in vertebrates, except for the black tiger shrimp, which suggests divergence in selective pressure between invertebrates and vertebrates. Notably, PmGDH may interact with NH4+ via the residue Asp178 within loop 1 in the GdhA domain through a hydrogen bonding interaction, and PmAST2 may interact with aspartate via helix 1, sheet 1, loop 1, and loop 2, through both hydrogen bonding interactions and a salt bridge interaction. A total of 12 SNPs were detected in the exons of PmGDH and PmAST2. Among these candidate SNPs, the distributions of PmGDH-1227 and PmAST2-132 showed both significant differences in the genotype and allele association analysis between susceptible and resistant groups. Haplotype association analysis showed that three haplotypes exhibited significantly different distributions between susceptible and resistant groups. In conclusion, PmGDH-1227 and PmAST2-132 were associated with ammonia nitrogen tolerance, and these SNP markers are expected to contribute to marker-assisted selection (MAS) breeding programs to obtain new strains of Penaeus monodon. Full article
(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding for Sustainable Aquatic Species Improvement)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop