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Animals
Special Issues
Genetics, Breeding, and Farming of Aquatic Animals
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Genetics, Breeding, and Farming of Aquatic Animals

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 7414

Special Issue Editors

Prof. Dr. Min Tao

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Guest Editor
State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, China
Interests: fish genetics and breeding; fish distant hybridization; reproductive development; reproductive endocrinology; growth and development; comparative transcriptomics; miRNA functional analysis
Prof. Dr. Chenghui Wang

E-Mail Website
Guest Editor
Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
Interests: aquaculture; selective breeding; comparative genomics; developmental biology; population genetics
Prof. Dr. Qizhi Liu

E-Mail Website
Guest Editor
College of Life Sciences, Hunan Normal University, 36 Lushan Rd, Building No. 3, Room 412, Yuelu District, Changsha 410081, China
Interests: fish distant hybridization; gynogenesis; coupling between transcription and splicing; innate immunity; breast cancer

Special Issue Information

Dear Colleagues,

The rapid advancement of biotechnology in recent years has expanded the frontiers of life sciences, particularly revolutionizing the technology utilized for breeding aquatic animals. Breeding biotechnology encompasses both classical and modern methods. Traditional breeding methods, including hybridization, family breeding, mass selection, and gynogenesis, have a longstanding history of use. Alongside these, modern breeding techniques such as genomic selection, marker-assisted selection, genetic modification, somatic cell cloning, and stem cell techniques have emerged, paving the way for genetic improvements in aquatic animals. These cutting-edge techniques offer novel opportunities regarding the development of breeding and farming in aquatic animals. Healthy aquaculture prioritizes practices that align with natural ecosystems, striving to minimize our environmental footprint and promote the well-being and health of aquatic species under cultivation. By focusing on disease management, optimized nutrition, and responsible resource use, it bolsters the conservation of biodiversity and promotes the resilience of aquatic ecosystems. Given this, it is crucial to thoroughly investigate advanced technologies and evolving trends in the breeding and farming of aquatic animals, to propel the ongoing advancement and growth of the aquaculture industry.

The Special Issue aims to compile papers presenting both fundamental and applied research in the genetics, physiology, breeding, and farming of aquatic animals. We invite you to submit original research articles and reviews on diverse aspects of genetics, physiology, breeding, and farming in aquatic organisms. We welcome the submission of both original research articles and reviews to this Special Issue. The scope of this Special Issue includes, but is not limited to, the following topics: breeding biotechnology, the protection and utilization of germplasm resources, growth and reproduction studies, healthy farming practices in aquatic animals, investigating disease resistance, exploring animal nutrition, and related topics.

We look forward to receiving your contributions.

Prof. Dr. Min Tao
Prof. Dr. Chenghui Wang
Prof. Dr. Qizhi Liu
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
  • genetics and breeding
  • breeding biotechnology
  • germplasm resource protection
  • germplasm utilization
  • growth and reproduction
  • healthy farming
  • disease resistance
  • animal nutrition

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Published Papers (7 papers)

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Research

15 pages, 2322 KB  
Article
Establishment and Biological Characteristics Analysis of a Hybrid Culter Lineage from Megalobrama amblycephala (♀) and Culter alburnus (♂)
by Jinhui Huang, Yingying Yang, Jiawang Huang, Xiaoyu Huang, Jiaxuan Zhu, Yanran Xiong, Lang Qin, Hongxuan Liang, Ming Wen, Yuxiang Wang, Xu Huang, Fangzhou Hu, Shi Wang, Chang Wu and Shaojun Liu
Animals 2025, 15(24), 3555; https://doi.org/10.3390/ani15243555 - 10 Dec 2025
Viewed by 280
Abstract
Culter alburnus (topmouth culter, TC) is extensively distributed in various rivers and lakes in China. As a widely adaptive fish species, they have significant economic value and special ecological roles. Intergeneric hybridization is a pivotal strategy for generating novel hybrid lineages and species. [...] Read more.
Culter alburnus (topmouth culter, TC) is extensively distributed in various rivers and lakes in China. As a widely adaptive fish species, they have significant economic value and special ecological roles. Intergeneric hybridization is a pivotal strategy for generating novel hybrid lineages and species. In a previous study, we obtained an improved bisexual hybrid culter, BTBTF1, derived from the hybrid lineage of Megalobrama amblycephala (blunt snout bream, BSB, 2n = 48, ♀) × Culter alburnus (2n = 48, ♂). In this study, we established an improved hybrid culter lineage by the self-crossing of BTBTF1 and evaluated the biological characteristics regarding cytology, morphology, and genetics. DNA content and chromosome analyses confirmed that BTBTF1-F2 was a diploid lineage (2n = 48), with morphological traits exhibiting intermediate values between parental species, except for significantly TC-biased full-length-to-body length (FL/BL) and body length-to-head length (BL/HL) ratios (p < 0.05). ITS sequencing analysis revealed that BTBTF1-F2 inherited ITS1 sequences from BSB and TC. The global methylation level in BTBTF1-F2 was substantially reduced compared to progenitors, characterized by elevated full and diminished hemimethylation states. Transcriptomic analysis identified 7877 differentially expressed genes (DEGs), displaying 9.05%/8.30% maternal (BSB)-dominant and 17.01%/18.95% paternal (TC)-dominant expression patterns in BTBTF1 and F2. Remarkable intergenerational similarity in phenotypic and molecular profiles, coupled with bidirectional inheritance of progenitor characteristics, confirmed BTBTF1-F2 as a genetically stable allodiploid lineage. Remarkably, methylation patterns, and DEG expression collectively demonstrated significant TC-oriented bias (p < 0.05). This study reports a novel stabilized allodiploid culter lineage after a comprehensive assessment at cytology, morphology, and genetic levels, and provides new insights into genetic bias in hybrid progeny. Full article
(This article belongs to the Special Issue Genetics, Breeding, and Farming of Aquatic Animals)
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21 pages, 4270 KB  
Article
The Formation of a Novel Intergeneric Hybrid Fish Derived from Megalobrama amblycephala (♀) × Culter dabryi (♂)
by Zhifeng Zhou, Xinge Ouyang, Chang Wu, Siyu Fan, Faxian Yu, Liran Zhang, Xinxin Yu, Zhong Tang, Lang Qin, Yi Zhou, Shengnan Li, Ming Wen, Yuequn Wang, Min Tao and Shaojun Liu
Animals 2025, 15(22), 3302; https://doi.org/10.3390/ani15223302 - 15 Nov 2025
Viewed by 562
Abstract
Distant hybridization in fish serves to integrate the genetic material from two distinct, distantly related species. In this study, we successfully produced a new hybrid fish (BG) through the intergeneric hybridization of blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48, [...] Read more.
Distant hybridization in fish serves to integrate the genetic material from two distinct, distantly related species. In this study, we successfully produced a new hybrid fish (BG) through the intergeneric hybridization of blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48, ♀) and green tip culter (Culter dabryi, GTC, 2n = 48, ♂). The objective of this research was to characterize the genetic, morphological, reproductive, and nutritional features of the hybrid compared with its parents. The DNA content and chromosomal number analysis revealed that BG was a diploid hybrid fish with 48 chromosomes. Integrated analysis of 5S rDNA, mitochondrial DNA, and Sox9 gene sequences revealed that BG predominantly inherited its genetic traits from BSB. Notably, certain gene fragments (376 bp segment of 5S rDNA class II and 718 bp segment of BG Sox9-II) originated from the paternal GTC, demonstrating biparental genomic integration. The growth performance analysis revealed that BG exhibited enhanced growth, achieving a body weight significantly greater than that of BSB and 1.81-fold that of GTC (both p < 0.05). The reproductive analysis indicated that BG possessed bisexual fertility, with testicular histology revealing accelerated spermatogenesis relative to BSB. Additionally, the nutritional analysis of BG muscle revealed elevated levels of crude protein (18.13%) and umami amino acids (5.45%) compared to those in its parents. BG showed higher growth, bisexual fertility, and improved muscle nutritional composition. This hybrid represents a promising resource for cyprinid breeding and aquaculture diversification. Full article
(This article belongs to the Special Issue Genetics, Breeding, and Farming of Aquatic Animals)
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20 pages, 2049 KB  
Article
First Observation of Embryonic Development and Paralarvae of Amphioctopus kagoshimensis
by Jinchao Zhu, Juanwen Yu, Siqing Chen, Tianshi Zhang, Qing Chang and Li Bian
Animals 2025, 15(22), 3249; https://doi.org/10.3390/ani15223249 - 10 Nov 2025
Viewed by 420
Abstract
To evaluate the aquaculture potential of Amphioctopus kagoshimensis, we investigated the reproductive biology, embryonic development, and early paralarval morphology of Amphioctopus kagoshimensis under controlled laboratory conditions. Each adult specimen collected from the coastal waters of Fujian Province spawned approximately 4000–5000 eggs (mean [...] Read more.
To evaluate the aquaculture potential of Amphioctopus kagoshimensis, we investigated the reproductive biology, embryonic development, and early paralarval morphology of Amphioctopus kagoshimensis under controlled laboratory conditions. Each adult specimen collected from the coastal waters of Fujian Province spawned approximately 4000–5000 eggs (mean ± SD: 4375 ± 478 eggs), with an overall hatching rate of 75% ± 10% (n = 2). Embryonic development lasted approximately 30 days at 22.0–24.5 °C and followed a classical 20-stage pattern. Hatchlings measured an average mantle length of 1.4 ± 0.1 mm and exhibited a merobenthic strategy, characterized by planktonic paralarvae with progressive morphological differentiation. The chromatophores appeared progressively on the head, mantle, arms, and funnel, with numbers increasing from 5 to 23 per arm by 30 days post-hatching. Paralarvae demonstrated active swimming, feeding behavior, and arm sucker development during rearing. By day 30, mantle length reached 2.5 mm, with significant growth in arm length and behavioral complexity. Its relatively small adult size (mantle length 8 cm), a moderate egg size (2.6 mm), fecundity and successful artificial incubation and 30-day paralarvae seedling suggested it may be a suitable model species for developmental studies and potential candidate for merobenthic octopod aquaculture in East Asia. Full article
(This article belongs to the Special Issue Genetics, Breeding, and Farming of Aquatic Animals)
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15 pages, 1109 KB  
Article
Genetic Diversity and Core Germplasm Identification in Penaeus japonicus Using Whole-Genome Resequencing
by Dingyuan Zhang, Jikang Shentu, Weijian Liu, Yanxia Wang, Minjun Zhu, Zhiming Yang and Liegang Si
Animals 2025, 15(18), 2759; https://doi.org/10.3390/ani15182759 - 22 Sep 2025
Viewed by 576
Abstract
The kuruma shrimp (Penaeus japonicus), a globally high-value aquaculture species, faces critical challenges in sustainable development due to genetic diversity degradation and declining disease resistance. This study employed whole-genome resequencing (WGRS) to systematically assess genetic diversity, population structure, and core germplasm [...] Read more.
The kuruma shrimp (Penaeus japonicus), a globally high-value aquaculture species, faces critical challenges in sustainable development due to genetic diversity degradation and declining disease resistance. This study employed whole-genome resequencing (WGRS) to systematically assess genetic diversity, population structure, and core germplasm characteristics across 20 geographically distinct populations from Zhejiang, Fujian (China), and introduced Japanese stocks. Using 343.40 Gb of high-quality sequencing data (average depth: 12.44×), we identified 9,146,248 single nucleotide polymorphisms (SNPs), with 6.32% located in exon regions, while intergenic (56.75%) and intronic regions (30.99%) showed the highest polymorphism density. Principal component analysis (PCA) and phylogenetic tree construction revealed two major clades: Fujian (FJ) and Japan-introduced (RB) populations clustered closely due to shared artificial breeding backgrounds, whereas Zhejiang (XS) and Fujian (LS) populations displayed genetic heterogeneity driven by adaptive divergence. Core germplasm screening via the CoreHunter algorithm selected four representative individuals (FJ4-M, LS1-M, XS1-M, XS6-M), with the modified Rogers’ distance (0.34) and allele coverage (0.93) confirming effective preservation of original genetic diversity. This study provides genomic insights and technical frameworks for germplasm conservation, precision breeding, and genetic improvement in P. japonicus. Full article
(This article belongs to the Special Issue Genetics, Breeding, and Farming of Aquatic Animals)
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12 pages, 1739 KB  
Article
Identification of Hybrid Sturgeon (Acipenser baerii × Acipenser schrenckii) from Their Parents Using Germplasm
by Shiyong Yang, Zhongmeng Zhao, Zihan Xu, Ya Liu, Menghao Jiang, Lin Fu, Jin Zhang, Zhaoxin Jing, Xiaojian Pang, Wuyuntana Shao, Chaoyang Zhang, Yunkun Li, Xiaogang Du and Jiayun Wu
Animals 2025, 15(7), 907; https://doi.org/10.3390/ani15070907 - 21 Mar 2025
Cited by 2 | Viewed by 1278
Abstract
The hybrid sturgeon Acipenser baerii × A. schrenckii is the most widely cultured commercial sturgeon in China. However, its morphological similarity to the parental species frequently leads to misuse of germplasm in the breeding process, resulting in a decline in the quality of [...] Read more.
The hybrid sturgeon Acipenser baerii × A. schrenckii is the most widely cultured commercial sturgeon in China. However, its morphological similarity to the parental species frequently leads to misuse of germplasm in the breeding process, resulting in a decline in the quality of the sturgeon production. In this study, we have developed a protocol by using mitochondrial DNA barcoding and microsatellite locus analysis for the accurate identification of sturgeon species. Genetic distance and phylogenetic analysis based on the mitochondrial COI segment showed that A. baerii exhibited the closest genetic relationship with orthogonal individuals A. baerii (♀) × A. schrenckii (♂). Conversely, A. schrenckii displayed the highest genetic similarity with reciprocal individuals A. schrenckii (♀) × A. baerii (♂). Additionally, genetic structure analysis and factor correlation analysis (FCA) were conducted using six microsatellite loci among 100 samples, including eight species and two hybrid sturgeon. The results showed that all samples, encompassing both hybrid sturgeon (A. baerii × A. schrenckii) and their parental species, were accurately grouped into ten clusters, thereby validating the precision of this species assignment method. Full article
(This article belongs to the Special Issue Genetics, Breeding, and Farming of Aquatic Animals)
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14 pages, 3391 KB  
Article
Growth Superiority and Genetic Characterization of the Hybrid from Female Ussuri Catfish (Pseudobagrus ussuriensis) and Male Longsnout Catfish (Leiocassis longirostris)
by Minghua Xie, Yulin Zhou, Yi Gong, Min Liu, Peng Zhen, Zhi Li, Li Zhou, Jianfang Gui and Zhongwei Wang
Animals 2024, 14(24), 3617; https://doi.org/10.3390/ani14243617 - 15 Dec 2024
Cited by 3 | Viewed by 1434
Abstract
Crossbreeding is a traditional breeding technique and has been performed successfully in many fish species. However, distant hybridization between different genera is hard to be successful because of reproductive isolation. In this study, diploid hybrids (PL) were successfully derived from the hybridization of [...] Read more.
Crossbreeding is a traditional breeding technique and has been performed successfully in many fish species. However, distant hybridization between different genera is hard to be successful because of reproductive isolation. In this study, diploid hybrids (PL) were successfully derived from the hybridization of Ussuri catfish (Pseudobagrus ussuriensis, PU, ♀, 2n = 52) and longsnout catfish (Leiocassis longirostris, LL, ♂, 2n = 52). And the morphological data, external frame parameters, chromosomal karyotypes, DNA content measurement, mitochondrial DNA control region, and species-specific marker identification were applied to investigate the traits and genetic characterization of the PL hybrid offspring and their parents. Both quantifiable traits and shape frame parameters of the PL hybrid offspring were revealed to be intermediate between those of their parents; however, cluster analysis showed that their external morphology was more in favor of the maternal PU. The growth comparisons showed that the hybrids had significant growth advantages over maternal PU. Based on karyotype patterns, DNA contents and mitochondrial DNA, the hybrid origin and maternal inheritance of hybrid offspring were further confirmed. According to the sequence variations identified from the genome sequences of the two catfish species, one species-specific marker was developed to distinguish the PL hybrid offspring and their parents. Therefore, this study provides a successful case for intergeneric hybridization and hybrid superiority, and the PL hybrid shows promise for commercial application, pending further studies into its husbandry, health, and welfare with larger populations of fish. Full article
(This article belongs to the Special Issue Genetics, Breeding, and Farming of Aquatic Animals)
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12 pages, 2598 KB  
Article
Single-Nucleus RNA Sequencing Reveals the Transcriptome Profiling of Ovarian Cells in Adolescent Cyprinus carpio
by Mingxi Hou, Jin Zhang, Qi Wang, Ran Zhao, Yiming Cao, Yingjie Chen, Kaikuo Wang, Ning Ding, Yingjie Qi, Xiaoqing Sun, Yan Zhang and Jiongtang Li
Animals 2024, 14(22), 3263; https://doi.org/10.3390/ani14223263 - 13 Nov 2024
Cited by 2 | Viewed by 1901
Abstract
The common carp (Cyprinus carpio) is a crucial freshwater species cultivated worldwide for food consumption. Female carp have better growth performance than males, which fascinates scholars to uncover the mechanism of gonadal differentiation and produce mono-sex populations. However, the mechanism of [...] Read more.
The common carp (Cyprinus carpio) is a crucial freshwater species cultivated worldwide for food consumption. Female carp have better growth performance than males, which fascinates scholars to uncover the mechanism of gonadal differentiation and produce mono-sex populations. However, the mechanism of ovarian development at single-cell resolution is limited. Here, we conducted single-nucleus RNA sequencing in adolescent common carp ovaries. Our study obtained transcriptional profiles of 13,155 nuclei and revealed 13 distinct cell clusters in the ovaries, including three subtypes of germ cells and four subtypes of granulosa cells. We subsequently performed pseudotime trajectory analysis to delineate potential mechanisms underlying the development of germ cells and granulosa cells. We identified 1250 dynamic expression genes in germ cells and 1815 in granulosa cells (q-value < 0.01), including zp3, eif4a2 and aspm in germ cells and fshr and esr1 in granulosa cells. The functional annotation showed that dynamic expression genes in germ cells were involved in sperm–egg recognition and some terms related to meiosis, such as sister chromatid segregation and homologous recombination. Genes expressed dynamically in granulosa cells were related to the TGF-β signaling pathway, response to gonadotropin, and development of primary female sexual characteristics. In addition, the dynamic genes expressed in granulosa cells might relate to the complex communication between different cell types. In summary, our study provided a transcriptome profile of common carp ovaries at single-nucleus resolution, and we further revealed the potential cell type-specific mechanisms underlying oogenesis and the differentiation of granulosa cells, which will facilitate breeding all-female common carp populations. Full article
(This article belongs to the Special Issue Genetics, Breeding, and Farming of Aquatic Animals)
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