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Application of Germplasm Innovation Technology in Aquactic Genetic Breeding

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 30 April 2026 | Viewed by 1709

Special Issue Editor

Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
Interests: aquaculture; biotechnology; germplasm improvement; genetic breeding; gene function; genomics; gene editing; population genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recently, the aquaculture industry has expanded rapidly, and germplasm improvement has become an issue of growing public attention. With the rapid advancement of aquatic biotechnology, aquaculture breeding has evolved from traditional selective and hybrid breeding to advanced genetic approaches, including sex-control breeding, trait-related marker-assisted selection breeding (e.g., growth, disease resistance), genome-wide genotyping-based selection, genome editing, and surrogate broodstock breeding. As a result, an increasing number of new aquatic strains have been developed with improved performance in traits such as sex differentiation, fecundity, survival rate, growth, and disease resistance.

Although various biological methods—including transcriptomics, proteomics, and metabolomics—have been employed, the fundamental mechanisms underlying genetic changes remain unclear. This lack of theoretical understanding has significantly limited the progress of germplasm improvement.

This Special Issue aims to present recent and innovative studies in aquatic biotechnology, spanning from both fundamental and applied research. It seeks to provide a platform for researchers focusing on aquatic biotechnology and its applications in germplasm improvement and genetic breeding.

Potential topics include, but are not limited to, the molecular basis of economic traits, regulatory mechanisms of sex and reproduction, theories and methods for efficient breeding, gene function and molecular mechanisms of genomics and breeding, and genetic structure.

Dr. Hui Qiao
Guest Editor

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Keywords

  • aquaculture
  • biotechnology
  • germplasm improvement
  • genetic breeding
  • gene function
  • genomics
  • gene editing

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Published Papers (3 papers)

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Research

21 pages, 3930 KB  
Article
High Oleic Acid Diet Promotes Growth and Muscle Metabolic Remodeling in Eriocheir sinensis: Multi-Omics Insight into Lipid Deposition and Nutrient Quality
by Xiaowei Li, Pao Xu, Jianxiang Chen, Jiyan He, Miaomiao Xue, Changchang He, Qingyong Wang, Changxin Kong, Hang Wang, Changyou Song and Hongxia Li
Int. J. Mol. Sci. 2026, 27(4), 1694; https://doi.org/10.3390/ijms27041694 - 10 Feb 2026
Viewed by 415
Abstract
Dietary lipid sources critically influence growth, health, and muscle quality in Chinese mitten crab (Eriocheir sinensis), yet how high oleic acid diet (HOA) regulates intramuscular nutrient deposition remains unclear. Here, a 10-week feeding trial compared isonitrogenous and isoenergetic diets, in which [...] Read more.
Dietary lipid sources critically influence growth, health, and muscle quality in Chinese mitten crab (Eriocheir sinensis), yet how high oleic acid diet (HOA) regulates intramuscular nutrient deposition remains unclear. Here, a 10-week feeding trial compared isonitrogenous and isoenergetic diets, in which soybean oil was replaced with high-oleic peanut oil. HOA significantly improved weight gain, specific growth rate, and protein efficiency ratio, without affecting survival, hepatosomatic index (HSI), or gonadosomatic index (GSI). HOA enhanced antioxidant capacity by increasing catalase activity and reducing malondialdehyde, while key non-specific immune enzymes were unchanged. In muscle, HOA did not increase intramuscular oleic acid (OA) content but reduced linoleic acid and upregulated genes involved in fatty acid transport and β-oxidation. HOA also shifted free amino acids (higher glutamate and lysine; lower proline) without significant transcriptional upregulation of the mechanistic target of rapamycin (mTOR) pathway or changing total protein. Multi-omics analyses indicated altered nucleotide/purine pathways and pronounced glycerophospholipid remodeling, identifying discriminatory lipid species. Overall, oleic-acid-rich lipids promote growth and antioxidant defense while reprogramming muscle lipid metabolism, supporting their targeted use to optimize crab muscle quality. Full article
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18 pages, 6582 KB  
Article
First High-Density Linkage Map and Quantitative Trait Loci for Disease Resistance in Striped Catfish Pangasianodon hypophthalmus
by Nguyen Thanh Vu, Tran Huu Phuc, Tran Thi Mai Huong and Nguyen Hong Nguyen
Int. J. Mol. Sci. 2026, 27(2), 784; https://doi.org/10.3390/ijms27020784 - 13 Jan 2026
Cited by 1 | Viewed by 450
Abstract
While striped catfish (Pangasianodon hypophthalmus) is an economically important aquaculture species, its genomic resources remain limited. To date, linkage maps, QTL (quantitative trait loci) analyses, and the identification of candidate genes associated with disease resistance traits are very limited. Therefore, the [...] Read more.
While striped catfish (Pangasianodon hypophthalmus) is an economically important aquaculture species, its genomic resources remain limited. To date, linkage maps, QTL (quantitative trait loci) analyses, and the identification of candidate genes associated with disease resistance traits are very limited. Therefore, the present study aimed to construct a high-density linkage map and identify candidate genes for this species. Our analysis was conducted on a pedigree population consisting of 560 individuals (490 offspring and 70 parents for 40 families), whose genomes were analyzed using a genotyping-by-sequencing platform. After stringent filtering, 9882 high-quality SNPs were retained for linkage analysis. Linkage analysis placed 8786 markers onto 30 linkage groups (LGs), with an average density of 0.43 SNPs per cM. Recombination rates varied across the 30 linkage groups (LGs), averaging of 3.6 cM/Mb in males, 6.7 cM/Mb in females, and 5.1 cM/Mb when sex-averaged. Using the linkage map, our QTL analysis identified three significant QTLs for disease resistance to Edwardsiella ictaluri, the causative agent of Bacillary Necrosis of Pangasius (BNP). The QTLs were located on LG1, LG9 and LG29, and their peak markers explained 17.03% of the phenotypic variance. An LD-based interval of approximately ±25 kb surrounding the QTL peak was identified as the putative candidate region. However, subsequent genome-wide association analysis did not identify significant SNP effects within these regions, suggesting that the QTLs may represent polygenic or small-effect loci that are detectable only in linkage-based analyses. In summary, this study presents the first high-density SNP-based linkage map for striped catfish and reports significant QTL and associated candidate genes related to disease resistance and growth traits. These findings provide valuable insights into the genetic architecture of economically important traits in P. hypophthalmus. Nevertheless, further validation in independent populations is required before incorporating these markers into selective breeding programs. Full article
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20 pages, 2963 KB  
Article
A Distinct Defense Strategy: The Molecular Basis of WSSV Tolerance in Macrobrachium nipponense Revealed by Comparative Transcriptomics with Litopenaeus vannamei
by Yunpeng Niu, Sufei Jiang, Wenyi Zhang, Yiwei Xiong, Shubo Jin, Hui Qiao and Hongtuo Fu
Int. J. Mol. Sci. 2026, 27(2), 766; https://doi.org/10.3390/ijms27020766 - 12 Jan 2026
Viewed by 541
Abstract
White Spot Syndrome Virus (WSSV) remains one of the most devastating pathogens in global shrimp aquaculture, causing massive economic losses annually. This study employed comparative transcriptomics to elucidate the molecular basis of the differential resistance to WSSV between the highly susceptible Pacific white [...] Read more.
White Spot Syndrome Virus (WSSV) remains one of the most devastating pathogens in global shrimp aquaculture, causing massive economic losses annually. This study employed comparative transcriptomics to elucidate the molecular basis of the differential resistance to WSSV between the highly susceptible Pacific white shrimp (Litopenaeus vannamei) and the remarkably resistant oriental river prawn (Macrobrachium nipponense). Our analysis of gill, hepatopancreas, and muscle tissues at 24 h post-infection revealed fundamentally distinct defense strategies. The resistant M. nipponense employs a unique “proactive homeostatic reinforcement” strategy, characterized by significant enrichment of pathways central to cellular homeostasis, including signal transduction, cellular processes, and transport/catabolism. This approach, supported by coordinated up-regulation of heat shock proteins and structural genes, enables effective viral control without triggering excessive immune activation. In contrast, susceptible L. vannamei displays either widespread metabolic dysregulation leading to systemic collapse in moribund individuals or dependency on specific immune pathways (Toll-like receptor signaling and apoptosis) in survivors. Through comparative KEGG analysis, we identified heat shock protein 70 kDa (HSP70, K03283) as a key conserved gene and functionally validated its critical role in antiviral defense using RNA interference. Knockdown of HSP70 in M. nipponense significantly increased cumulative mortality and viral load, confirming its essential protective function. These findings provide novel insights into crustacean antiviral immunity and identify promising genetic targets for breeding WSSV-resistant shrimp strains, offering sustainable solutions for disease management in aquaculture. Full article
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