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Fishes
Special Issues
Genetic Breeding and Developmental Biology of Aquaculture Animals
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Genetic Breeding and Developmental Biology of Aquaculture Animals

A special issue of Fishes (ISSN 2410-3888).

Deadline for manuscript submissions: closed (15 November 2024) | Viewed by 5232

Special Issue Editors

Dr. Zhi Ye

E-Mail Website
Guest Editor
College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
Interests: genetic breeding; developmental biology; gene editing; fish biology; epigenetics; economic traits
Dr. Baofeng Su

E-Mail Website
Guest Editor
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
Interests: fish breeding and physiology; genome editing; transgenics; applied bioinformatics and genomics; gene function and characterization; mucosal immunity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The strategic cultivation of high-quality varieties is critically important for the sustainable and efficient progression of the aquaculture sector. A thorough understanding of the developmental processes associated with the economic characteristics of aquaculture organisms is essential. Such knowledge enhances our grasp of the molecular mechanisms governing these traits, providing a solid scientific basis for their genetic enhancement. The rapid evolution of molecular biology techniques, notably advanced transgenic and gene editing methodologies, coupled with high-throughput sequencing, has substantially enriched our understanding of the genetic underpinnings of aquaculture species. Concurrently, this has streamlined and optimized the investigation of genes implicated in the development of economically significant traits.

While traditional breeding techniques, including individual selection, family selection, and hybrid breeding, retain their value due to their simplicity and operational feasibility, novel and emergent breeding technologies such as genome-wide selection, precision molecular-assisted breeding, and modular breeding approaches offer more precise and efficient avenues for genetic improvement. These cutting-edge techniques signify a forward-moving trend in the development of new, high-yield aquaculture breeds. This Special Issue is dedicated to exploring the molecular mechanisms involved in the formation of economic traits in aquaculture animals and delves into the latest research on efficient genetic breeding strategies.

Dr. Zhi Ye
Dr. Baofeng Su
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 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. Fishes 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

  • breeding
  • genetic enhancement
  • molecular mechanisms
  • gene editing
  • economic traits
  • aquaculture animals

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Published Papers (3 papers)

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Research

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20 pages, 5114 KiB  
Article
Genetic Parameter Estimates for Growth of Hāpuku (Groper, Polyprion oxygeneios) in Land-Based Aquaculture Using Random Regression Models
by Mark D. Camara, Jane E. Symonds, Seumas P. Walker, Dave McQueen, Yann Gublin, Glen Irvine, Steve M. Pether, Andrew Forsythe and Alvin N. Setiawan
Fishes 2024, 9(10), 376; https://doi.org/10.3390/fishes9100376 - 25 Sep 2024
Viewed by 518
Abstract
Hāpuku (Polyprion oxygeneios) is a promising candidate for aquaculture production in New Zealand. Methods for spawning, juvenile production, and growout to harvest entirely on land, where water quality, pathogens, environmental impacts, and genetic “pollution” can be tightly controlled, have been developed, [...] Read more.
Hāpuku (Polyprion oxygeneios) is a promising candidate for aquaculture production in New Zealand. Methods for spawning, juvenile production, and growout to harvest entirely on land, where water quality, pathogens, environmental impacts, and genetic “pollution” can be tightly controlled, have been developed, and genetic improvement to optimise land-based production is the obvious next step. However, estimates of genetic parameters are required to design a rigorous, disciplined, and effective selective breeding program. By using existing data consisting of irregularly spaced repeated measurements of fork length and live body weight collected on wild-collected founders and two generations of captively reared progeny, we evaluated the species’ genetic potential for improvement in growth. We first tested a range of univariate random regression models to identify the best-fitting models for these data. Subsequently, using a bivariate model, we estimated variance components for growth trajectories of fork length and whole body weight. With one to six records available per fish, the best-fitting univariate models included only a fixed effect for contemporary groups and fixed and random genetic third-order Legendre polynomials. More complex models that included full-sib family and/or permanent environmental effects produced unacceptable constrained and/or non-positive-definite solutions. Both traits are moderately heritable at all stages of the growout phase (~0.4–0.5), and the genetic correlation patterns between daily breeding values estimated via the covariance function are different for length and weight. Genetic correlations for length between all pairs of age-specific breeding values are positive and strong (>0.7) and change gradually and smoothly with increasing temporal separation. For weight, these correlations deteriorate more rapidly with increasing time lags between measurements and become negative for some age pairings. We conclude that random regression analyses are a valuable tool for extracting genetic information from irregularly spaced repeated measurements of fish size, speculate that emerging technologies for high-throughput genotyping and phenotyping will add to the value of this approach in the near future, and reason that a breeding strategy that rigorously takes into account the potentially unfavourable genetic correlations between breeding values for weight at some ages will further adapt hāpuku to land-based systems and enhance the profitability commercial-scale production. Full article
(This article belongs to the Special Issue Genetic Breeding and Developmental Biology of Aquaculture Animals)
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15 pages, 4928 KiB  
Article
The Identification of a Cell Cycle Regulation Gene Cyclin E from Hong Kong Oysters (Crassostrea hongkongensis) and Its Protein Expression in Response to Salinity Stress
by Hengtong Qiu, Huan Wang, Xiaomin Yan, Lin Hu, Yonglin Huang and Yanni Ye
Fishes 2024, 9(3), 102; https://doi.org/10.3390/fishes9030102 - 6 Mar 2024
Viewed by 1804
Abstract
Hong Kong oysters (Crassostrea hongkongensis) are an important marine bivalve with nutritional and commercial value. The expanded off-bottom farming scale in recent years makes the oysters more susceptible to exposure to abiotic stresses, such as salinity stress, an important environmental factor [...] Read more.
Hong Kong oysters (Crassostrea hongkongensis) are an important marine bivalve with nutritional and commercial value. The expanded off-bottom farming scale in recent years makes the oysters more susceptible to exposure to abiotic stresses, such as salinity stress, an important environmental factor that has been proven to have significant effects on oyster growth and development. However, the molecular mechanism is still unclear. Cyclin E is an important protein in the process of cell cycle regulation that is indispensable for propelling G1/S phase transition in a dose-dependent manner. In order to investigate whether the salinity stress affects cyclin E expression in oysters, the cDNA sequence of C. hongkongensis cyclin E (Ch-CCNE) was isolated from a gill cDNA library, and the 2.8 kbp length cDNA fragment contained a complete open reading frame (ORF) encoding 440 amino acid residues. Ch-CCNE mRNA was highly expressed in the gonad and low in the adductor mussel, mantle, gill, labial palp, and digestive gland. The recombinant CCNE protein was expressed and purified in a pET32a(+)-CCNE/Escherichia coli BL21(DE3) system via IPTG induction and was used for generating mice anti-Ch-CCNE antiserums. Western blot analysis showed that the CCNE protein in the gill was maintained at low expression levels under either hypo- (5 ppt) or hyper- (35 ppt) salinity, and could be produced at high levels under appropriate salinity during a 10-day exposure period. The immuno-localization indicated that the Ch-CCNE protein was distributed in the nucleus. These results suggested that either hypo- or hyper-salinity stress could inhibit the CCNE expression of Hong Kong oysters and their negative impact on cell division and proliferation. Full article
(This article belongs to the Special Issue Genetic Breeding and Developmental Biology of Aquaculture Animals)
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Review

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22 pages, 1542 KiB  
Review
Harnessing Hue: Advances and Applications of Fish Skin Pigmentation Genetics in Aquaculture
by Jialong Liu, Miaomiao Yin, Zhi Ye, Jingjie Hu and Zhenmin Bao
Fishes 2024, 9(6), 220; https://doi.org/10.3390/fishes9060220 - 10 Jun 2024
Viewed by 2239
Abstract
Fish exhibit a broad spectrum of colors and patterns facilitated by specialized cells known as chromatophores. The vibrant coloration of fish, controlled by complex genetic and environmental interactions, serves critical roles in ecological functions such as mating, predation, and camouflage. This diversity not [...] Read more.
Fish exhibit a broad spectrum of colors and patterns facilitated by specialized cells known as chromatophores. The vibrant coloration of fish, controlled by complex genetic and environmental interactions, serves critical roles in ecological functions such as mating, predation, and camouflage. This diversity not only makes fish an invaluable model for exploring the molecular mechanisms of pigmentation but also significantly impacts their economic value within the aquaculture industry, where color traits can drive marketability and breeding choices. This review delves into the sophisticated biological processes governing fish pigmentation and discusses their applications in enhancing aquaculture practices. By exploring the intersection of genetic regulation, environmental influences, and advanced breeding techniques, this review highlights both the scientific understanding and practical applications of fish coloration, providing a bridge between basic biological research and its application in commercial aquaculture. Full article
(This article belongs to the Special Issue Genetic Breeding and Developmental Biology of Aquaculture Animals)
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