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Animals
Special Issues
Genetic Selection and Breeding for Improved Traits in Aquaculture Animals
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Genetic Selection and Breeding for Improved Traits in Aquaculture Animals

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 20 October 2026 | Viewed by 5809

Special Issue Editors

Dr. Guodong Zheng

E-Mail Website
Guest Editor
1. Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
2. Genetics and Breeding Center for Blunt Snout Bream, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
Interests: fish; genetic; breeding
Dr. Wenzhi Guan

E-Mail
Guest Editor
Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
Interests: fish; genetic; breeding

Special Issue Information

Dear Colleagues,

This Special Issue is an important platform to promote the development of world aquatic science research, strengthen international academic exchanges, and showcase the latest scientific research achievements and progress in the field of aquatic science in different countries.

It will mainly publish papers and reviews on aquatic animal breeding research, aquaculture and breeding, aquaculture breeding technology development, fishery resources, fishery water environment protection, etc.

This Special Issue accepts theoretical and empirical research papers, particularly encouraging the combination of theory and empirical research. The published research results can represent the academic level and development trends in relation to aquaculture, reflecting new achievements and ideas in the research of aquaculture breeding technology worldwide.

Dr. Guodong Zheng
Dr. Wenzhi Guan
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. Animals 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 2400 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

  • aquatic animals
  • genetic improvement
  • molecular breeding
  • whole genome selection breeding
  • polyploidy and hybrid breeding

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Published Papers (6 papers)

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Research

16 pages, 1484 KB  
Article
Primary Culture and Characterization of a Crucian Carp (Carassius carassius) Osteoblast Cell Line (COBC) and the Effects of Hypoxia on Its Differentiation
by Zaozao Guo, Jiamin Liu, Songlin Chen, Guodong Zheng and Shuming Zou
Animals 2026, 16(5), 833; https://doi.org/10.3390/ani16050833 - 6 Mar 2026
Viewed by 518
Abstract
In the present study, vertebral bone tissues derived from Chongming crucian carp (Carassius carassius), a dominant species during the summer and autumn seasons on Chongming Island in the lower Yangtze River, were used to establish and characterize a Carassius carassius osteoblast [...] Read more.
In the present study, vertebral bone tissues derived from Chongming crucian carp (Carassius carassius), a dominant species during the summer and autumn seasons on Chongming Island in the lower Yangtze River, were used to establish and characterize a Carassius carassius osteoblast cell line (COBC). The established COBCs were assessed using chromosome analysis, osteocalcin enzyme-linked immunosorbent assay (ELISA), and osteogenesis-related gene expression analysis. Additionally, cellular responses to environmental stress were assessed. The results showed that COBC exhibited optimal proliferation in L-15 medium supplemented with 20% fetal bovine serum at 28 °C. The histochemical staining assay results were all positive, thereby confirming that the isolated cells display typical osteoblast characteristics. Quantitative PCR analysis revealed that osteogenic marker genes, including runx2a and runx2b, were expressed at significantly higher levels in COBCs than in fish tissues. Under hypoxic stress, COBCs exhibited morphological changes, an increase in cell death, significant alterations in gene expression, and variations in antioxidant enzyme activity. These responses facilitate adaptation to hypoxic stress. This study established the first osteoblast cell line of the Chongming crucian carp and characterized its biological properties and response to hypoxic stress. These findings offer a valuable in vitro cell model and technical support for research on fish bone tissue biology and the assessment of environmental stress effects. Full article
(This article belongs to the Special Issue Genetic Selection and Breeding for Improved Traits in Aquaculture Animals)
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17 pages, 2989 KB  
Article
Genetic Parameter Estimates for Growth, Meat Yield and Foot Color Traits of Pacific Abalone Haliotis discus hannai
by Shoudu Zhang, Tianyi Xu, Ming Li, Longwei Dai, Zhenlin Hao and Fucun Wu
Animals 2026, 16(5), 782; https://doi.org/10.3390/ani16050782 - 2 Mar 2026
Viewed by 447
Abstract
This study was designed to evaluate the genetic parameters of growth, meat yield and foot color in Pacific abalone (Haliotis discus hannai) to support the development of a quality-oriented breeding program. Using data from 141 pedigreed full-sib families, heritabilities and genetic [...] Read more.
This study was designed to evaluate the genetic parameters of growth, meat yield and foot color in Pacific abalone (Haliotis discus hannai) to support the development of a quality-oriented breeding program. Using data from 141 pedigreed full-sib families, heritabilities and genetic correlations among these traits were estimated. The results indicated that shell length at varying ages (0.45–0.71) and total wet weight (0.48) exhibited moderate-to-high heritabilities, suggesting substantial potential for genetic improvement in growth traits. The heritabilities for foot color (0.26) and meat weight (0.31) were moderate and statistically significant (p < 0.05), whereas the heritability for meat yield (0.14) was low and not statistically significant (p > 0.05). Strong positive genetic correlations were observed between shell length and total wet weight at harvest (0.90), as well as between total wet weight and meat weight at harvest (0.92). In contrast, the genetic correlations between total wet weight and foot color, and between total wet weight and meat yield, were low and not statistically significant (p > 0.05). These findings suggest that direct selection can effectively improve the growth and meat weight of Pacific abalone. However, improving foot color and meat yield may require independent or multi-trait selection approaches. Overall, this study provides crucial data for formulating a comprehensive breeding strategy that integrates both production efficiency and product quality in Pacific abalone aquaculture. Full article
(This article belongs to the Special Issue Genetic Selection and Breeding for Improved Traits in Aquaculture Animals)
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16 pages, 3861 KB  
Article
Integrated Gut Microbiome and Metabolome Analysis in Largemouth Bass (Micropterus salmoides) Following Viral Infection
by Hongyan Yu, Shaojian Dong, Lixia Wang and Shili Liu
Animals 2026, 16(5), 752; https://doi.org/10.3390/ani16050752 - 28 Feb 2026
Viewed by 535
Abstract
Largemouth bass (Micropterus salmoides) is an important aquaculture species increasingly threatened by viral diseases, particularly largemouth bass virus (LMBV), which can cause significant mortality. However, integrative analyses linking LMBV-induced gut microbiota dysbiosis to metabolomic dysfunction are limited. In this study, we [...] Read more.
Largemouth bass (Micropterus salmoides) is an important aquaculture species increasingly threatened by viral diseases, particularly largemouth bass virus (LMBV), which can cause significant mortality. However, integrative analyses linking LMBV-induced gut microbiota dysbiosis to metabolomic dysfunction are limited. In this study, we profiled the intestinal microbiome and metabolome alterations in largemouth bass following LMBV infection and conducted an integrated analysis. Infected fish showed reduced alpha diversity and significant shifts in community structure, including increased relative abundances of Bacteroidota and Fusobacteriota and a decrease in Proteobacteria. Opportunistic taxa, such as Pseudomonas and Mycobacterium, were enriched after infection. Metabolomic profiling revealed differential metabolites primarily involved in amino acid and carbohydrate metabolism. Integrative correlation analyses further identified significant associations between opportunistic bacteria and putative harmful metabolites, suggesting that LMBV-induced dysbiosis disrupts host metabolic homeostasis and contributes to immune dysfunction. These findings may clarify the microbiota–metabolite landscape during LMBV infection. Full article
(This article belongs to the Special Issue Genetic Selection and Breeding for Improved Traits in Aquaculture Animals)
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14 pages, 926 KB  
Article
Genetic Structures of Crassostrea ariakensis Generations Based on Partial Mitochondrial cox1 and rrnL Indicated a High Breeding Potential After Four-Years Successive Selections
by Ming Yan, Peizhen Ma, Zhihong Liu, Zhuanzhuan Li, Xianglun Li, Tao Yu, Weijun Wang, Chengwu Wang, Xiujun Sun, Liqing Zhou and Biao Wu
Animals 2026, 16(3), 451; https://doi.org/10.3390/ani16030451 - 1 Feb 2026
Viewed by 509
Abstract
With the rapid development of oyster farming and the emergence of new varieties, the identification and evaluation of genetic resources have become fundamental to the effective utilization of oyster germplasm resources. To evaluate the impact of selective breeding on the germplasm of Crassostrea [...] Read more.
With the rapid development of oyster farming and the emergence of new varieties, the identification and evaluation of genetic resources have become fundamental to the effective utilization of oyster germplasm resources. To evaluate the impact of selective breeding on the germplasm of Crassostrea ariakensis, this study conducted genetic structure analysis on five successive generations including four generations selected (F1 to F4) focusing on both fast growth and high glycogen content and one base population (F0) based on partial mitochondrial cox1 and rrnL gene sequences. Results showed that the 649 bp cox1 and 488 bp rrnL sequences exhibited (A+T)-biased composition and showed positive AT skew. A total of 12 haplotypes were found for the cox1 sequences, while only three haplotypes were detected for the rrnL sequences. However, among the F1 to F4 populations, only three cox1 haplotypes and two rrnL haplotypes were observed. Based on cox1 sequences, the values of the haplotype diversity index, average number of nucleotide differences, and nucleotide diversity index all decreased progressively from F1 to F4, indicating a reduction in genetic variation due to selective breeding. All populations exhibited a low level of nucleotide diversity (<0.05). In addition, the intra-population genetic distance declined from F0 to F4, with significant genetic differentiation between F0 and F1, as well as between F0 and F4 (p < 0.05). In contrast, only the F0 and F4 population had multiple rrnL haplotypes, and no statistically significant genetic differentiations were observed based on rrnL fragments (p > 0.05). The AMOVA results showed that intra-population genetic variation exceeded inter-population variation, regardless of whether it was assessed using the cox1 gene or the rrnL gene, indicating that substantial genetic diversity persists within populations despite multiple generations of selection, and complete genetic differentiation across generations has not been achieved. These findings indicate that the selectively bred lines retain considerable genetic potential and can serve as a valuable resource for future breeding programs. Full article
(This article belongs to the Special Issue Genetic Selection and Breeding for Improved Traits in Aquaculture Animals)
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15 pages, 1572 KB  
Article
Morphometric Traits as Predictors of Body Mass in the Marine Gastropod Semicassis bisulcatum: Insights for Aquaculture and Selective Breeding
by Dewei Cheng, Yun Chen, Xin Liu, Shiyuan Bao, Xuyang Chen, Ying Qiao and Ersha Dang
Animals 2025, 15(20), 3027; https://doi.org/10.3390/ani15203027 - 18 Oct 2025
Viewed by 1057
Abstract
The marine gastropod Semicassis bisulcatum, valued for its ornamental shell and edible soft tissue, lacks essential biological data for selective breeding. This study was conducted on 100 wild individuals collected from the Beibu Gulf to identify key morphological traits influencing body mass [...] Read more.
The marine gastropod Semicassis bisulcatum, valued for its ornamental shell and edible soft tissue, lacks essential biological data for selective breeding. This study was conducted on 100 wild individuals collected from the Beibu Gulf to identify key morphological traits influencing body mass (BM) and soft body mass (SBM). Both mass traits showed high variability (SBM CV = 41.04%; BM CV = 23.88%), indicating strong breeding potential. Path analysis revealed that shell thickness (ST) exhibited the strongest direct association with body mass (path coefficient = 0.509), while shell width (SW) was most closely linked to soft body mass (path coefficient = 0.482). The combined coefficient of determination confirmed that shell thickness (ST) and shell height (SH) together were the strongest predictors for body mass. Similarly, Shell width (SW) and aperture height (AH) together had the strongest combined effect on soft body mass. These findings provide a critical morphological basis for future selective breeding programs. Full article
(This article belongs to the Special Issue Genetic Selection and Breeding for Improved Traits in Aquaculture Animals)
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12 pages, 4682 KB  
Article
Artificial Induction of Meiotic Gynogenesis in Koi Carp Using Blunt Snout Bream Sperm and Identification of Gynogenetic Offspring
by Xiaoyu Chen, Xiulan Shi, Jun Guo, Kai Lin, Mingkun Luo and Zaijie Dong
Animals 2025, 15(10), 1411; https://doi.org/10.3390/ani15101411 - 13 May 2025
Cited by 1 | Viewed by 1588
Abstract
Artificial gynogenesis is an effective means of producing pure lines and is widely used for genetic analysis of fish and for sex control. In this study, inactivated sperm from heterogenous blunt snout bream (Megalobrama amblycephala, MA) were used to activate Kohaku koi [...] Read more.
Artificial gynogenesis is an effective means of producing pure lines and is widely used for genetic analysis of fish and for sex control. In this study, inactivated sperm from heterogenous blunt snout bream (Megalobrama amblycephala, MA) were used to activate Kohaku koi (Cyprinus carpio var. koi, CK) and produce high-quality female offspring. To determine whether the offspring were gynogenetic fish, the karyotype and DNA content of the CK, MA and the induced offspring (IO) were first compared and it was found that the IO were diploid with 100 chromosomes and their karyotype was 22m + 34sm + 22st + 22t. The DNA content of the IO was not significantly different from that of the CK. Subsequently, the amplified band profiles of CK, MA and IO were analyzed with species-specific microsatellite markers. The results showed that there were no amplified MA microsatellite bands in IO. The size of the amplified bands and the sequence of the 5S rDNA in CK, MA and IO were also analyzed. It was found that the amplified 5S rDNA gene fragments in IO contained two fragments that were both the same size as those of CK and matched more than 90% with those of CK. Finally, the sex of IO was verified using gonadal tissue sections. The result showed that IO was not an all-female population; males were also present (36.7%). In summary, a series of validation methods confirmed that the induced offspring were gynogenetic fish, which is the basis for the subsequent genetic improvement of pure lines of high-quality koi. Full article
(This article belongs to the Special Issue Genetic Selection and Breeding for Improved Traits in Aquaculture Animals)
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