Strategies and Approaches for Improvement of Aquaculture

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Animal Science".

Deadline for manuscript submissions: closed (29 July 2022) | Viewed by 29748

Special Issue Editors


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Guest Editor
Department of Aquaculture, College of Life Sciences, National Taiwan Ocean University, Keelung 20224, Taiwan
Interests: virology; immunology; biotechnology; bioinformatics; aquaculture
Special Issues, Collections and Topics in MDPI journals
Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
Interests: DNA, RNA or protein delivery in vivo; biochemistry; signal pathway

Special Issue Information

Dear colleagues,

At present, aquaculture is an extremely important industry worldwide. The production of farmed fish and shellfish from aquaculture has continuously increased, which could compensate for the declining and rapidly accelerating depletion of wild fisheries. However, there have many challenges in the aquaculture industry, including disease, immune response, breeding process and physiology problems, which are affected by biological, technical, environmental and economic factors. Therefore, the aquaculture industry has developed a lot of innovation and technology. Innovation in aquaculture means finding new solutions to integrate the use of various optimization criteria, which are crucial in the development of new means of production, and the possibility of a variable feeding path throughout the fattening process in fish and shellfish cultures.

In this Special Issue, we offer a broad spectrum of reviews and original research contributions in the topic of novel strategies and approaches to improve the quality and value of fish and shellfish in aquaculture, with a particular emphasis on the marine biotechnological dimensions. The scope of this issue includes a control strategy for disease, potential breeding techniques, fish physiology and behavior, multi-omics approaches, and technological advances in big data and artificial intelligence. This Special Issue aims to be useful to the novel and emerging technology in aquaculture to improve the health and quality of aquatic animals and price integration, and thus enhance competitiveness and sustainability.

Prof. Dr. Ming-Wei Lu
Dr. Mi Zhao
Guest Editors

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Keywords

  • aquaculture
  • novel control strategy for disease
  • potential breeding techniques
  • multi-omics approaches used in aquaculture
  • big data and artificial intelligence

Published Papers (11 papers)

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Research

Jump to: Review

14 pages, 712 KiB  
Article
Finding the Best Match: A Ranking Procedure of Fish Species Combinations for Polyculture Development
by Nellya Amoussou, Marielle Thomas, Alain Pasquet and Thomas Lecocq
Life 2022, 12(9), 1315; https://doi.org/10.3390/life12091315 - 26 Aug 2022
Cited by 3 | Viewed by 1334
Abstract
Polyculture is a potentially interesting rearing practice for future aquaculture developments. Nevertheless, it may result in beneficial as well as detrimental consequences for fish production. One way to maximize the benefits of polyculture is to combine species with high levels of compatibility and [...] Read more.
Polyculture is a potentially interesting rearing practice for future aquaculture developments. Nevertheless, it may result in beneficial as well as detrimental consequences for fish production. One way to maximize the benefits of polyculture is to combine species with high levels of compatibility and complementarity. This requires the development of a ranking procedure, based on a multi-trait assessment, that highlights the most suitable species combinations for polyculture. Moreover, in order to ensure the relevance of such a procedure, it is important to integrate the socio-economic expectations by assigning relative weights to each trait according to the stakeholder priorities. Here, we proposed a ranking procedure of candidate fish polycultures (i.e., species combinations that could be potentially interesting for aquaculture) based on a multi-trait assessment approach and the stakeholder priorities. This procedure aims at successively (i) weighting evaluation results obtained for each candidate polyculture according to stakeholder priorities; (ii) assessing differentiation between candidate species combinations based on these weighted results; and (iii) ranking differentiated candidate polycultures. We applied our procedure on three test cases of fish polycultures in recirculated aquaculture systems. These test cases each focused on a target species (two on Sander lucioperca and one on Carassius auratus), which were reared in two or three different alternative candidate fish polycultures. For each test case, our procedure aimed at ranking alternative combinations according to their benefits for production and/or welfare of the target species. These benefits were evaluated based on survival rate as well as morphology, behavioral, and physiological traits. Three scenarios of stakeholder priorities were considered for weighting evaluation results: placing a premium on production, welfare, or both for the target species. A comparison of our procedure results between these scenarios showed that the ranking changed for candidate polycultures in two test cases. This highlights the need to carefully consider stakeholder priorities when choosing fish polycultures. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
13 pages, 3357 KiB  
Article
The Advantages of Inorganic Fertilization for the Mass Production of Copepods as Food for Fish Larvae in Aquaculture
by Guo-Kai Hong and Kwee Siong Tew
Life 2022, 12(3), 441; https://doi.org/10.3390/life12030441 - 17 Mar 2022
Cited by 4 | Viewed by 2729
Abstract
Copepods are commonly used as live feed for cultured fish larvae, but the current mass production method using organic fertilizers cannot meet the market demand for copepods. We evaluated the feasibility of applying an inorganic fertilization method, which is currently in use in [...] Read more.
Copepods are commonly used as live feed for cultured fish larvae, but the current mass production method using organic fertilizers cannot meet the market demand for copepods. We evaluated the feasibility of applying an inorganic fertilization method, which is currently in use in freshwater and marine larviculture, to the mass production of copepods. For 30 days, and with five replicates of each treatment, we made comparative daily measurements of various parameters of (1) copepod cultures fertilized with commercially available condensed fish solubles (organic fertilization) and (2) other cultures in which the concentration of inorganic phosphorus was maintained at 100 μg P L−1 and that of inorganic nitrogen at 700 μg N L−1 (inorganic fertilization). With inorganic fertilization, pH fluctuated over a smaller range and much less filamentous algae grew in the tanks. The mean production of copepod nauplii over the course of the study was similar between the two treatments, but the combined density of copepodites and adult copepods was significantly higher with inorganic fertilization. Compared to commercial zooplankton products, copepods cultured with inorganic fertilization were smaller, were mixed with fewer (almost none) non-copepod contaminants, were also pathogen-free, and could be produced at the cheapest cost per unit output. Based on these results, we conclude that the inorganic fertilization method can profitably be adopted by commercial copepod producers to meet the demand from fish farmers, especially for small-sized copepods. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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12 pages, 2952 KiB  
Article
Combining Direct PCR Technology and Capillary Electrophoresis for an Easy-to-Operate and Highly Sensitive Infectious Disease Detection System for Shrimp
by Hung-Yun Lin, Shao-Chieh Yen, Shou-Kuan Tsai, Fan Shen, John Han-You Lin and Han-Jia Lin
Life 2022, 12(2), 276; https://doi.org/10.3390/life12020276 - 13 Feb 2022
Cited by 2 | Viewed by 2953
Abstract
Infectious diseases are considered the greatest threat to the modern high-density shrimp aquaculture industry. Specificity, rapidity, and sensitivity of molecular diagnostic methods for the detection of asymptomatic infected shrimp allows preventive measures to be taken before disease outbreaks. Routine molecular detection of pathogens [...] Read more.
Infectious diseases are considered the greatest threat to the modern high-density shrimp aquaculture industry. Specificity, rapidity, and sensitivity of molecular diagnostic methods for the detection of asymptomatic infected shrimp allows preventive measures to be taken before disease outbreaks. Routine molecular detection of pathogens in infected shrimp can be made easier with the use of a direct polymerase chain reaction (PCR). In this study, four direct PCR reagent brands were tested, and results showed that the detection signal of direct PCR in hepatopancreatic tissue was more severely affected. In addition, portable capillary electrophoresis was applied to improve sensitivity and specificity, resulting in a pathogen detection limit of 25 copies/PCR-reaction. Juvenile shrimp from five different aquaculture ponds were tested for white spot syndrome virus infection, and the results were consistent with the Organization for Animal Health’s certified standard method. Furthermore, this methodology could be used to examine single post larvae shrimp. The overall detection time was reduced by more than 58.2%. Therefore, the combination of direct PCR and capillary electrophoresis for on-site examination is valuable and has potential as a suitable tool for diagnostic, epidemiological, and pathological studies of shrimp aquaculture. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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11 pages, 2012 KiB  
Article
Effects of Hydrostatic Pressure Treatment of Newly Fertilized Eggs on the Ploidy Level and Karyotype of Pikeperch Sander lucioperca (Linnaeus, 1758)
by Jenő Káldy, Eszter Patakiné Várkonyi, Georgina Lea Fazekas, Zoltán Nagy, Zsuzsanna J. Sándor, Katalin Bogár, Gyula Kovács, Mariann Molnár, Bence Lázár, Katalin Goda, Zsuzsanna Gyöngy, Zsuzsanna Ritter, Péter Nánási, Jr., Ákos Horváth and Uroš Ljubobratović
Life 2021, 11(12), 1296; https://doi.org/10.3390/life11121296 - 26 Nov 2021
Cited by 2 | Viewed by 2138
Abstract
We studied the effect of different magnitudes (7000 PSI (48.26 MPa), 8000 PSI (55.16 MPa), and 9000 PSI (62.05 MPa)) of hydrostatic pressure on the ploidy of pikeperch larvae. Pressure shock was applied 5 min after the fertilization of eggs at a water [...] Read more.
We studied the effect of different magnitudes (7000 PSI (48.26 MPa), 8000 PSI (55.16 MPa), and 9000 PSI (62.05 MPa)) of hydrostatic pressure on the ploidy of pikeperch larvae. Pressure shock was applied 5 min after the fertilization of eggs at a water temperature of 14.8 ± 1 °C. A 7000 PSI pressure shock was applied for 10 or 20 min, while 8000 and 9000 PSI treatments lasted for 10 min. Each treatment with its respective control was completed in triplicate, where different females’ eggs served as a replicate. In the treatment groups exposed to 7000 PSI for 10 min, only diploid and triploid larvae were identified, while 2n/3n mosaic individuals were found after a 20-min exposure to a 7000 PSI pressure shock. The application of 8000 or 9000 PSI pressure shocks resulted in only triploid and mosaic individuals. Among larvae from eggs treated with 8000 PSI, three mosaic individuals with 2n/3n karyotype were identified (4.0 ± 6.9%), while a single (2.0 ± 3.5%) 1n/3n mosaic individual was found in the 9000 PSI-treated group. To our knowledge, this is the first report that demonstrates the induction of a haplo-triploid karyotype by hydrostatic pressure shock in teleost fish. The dominance of triploid individuals with a reasonable survival rate (36.8 ± 26.1%) after 8000 PSI shock supports the suitability of the hydrostatic pressure treatment of freshly fertilized eggs for triploid induction in pikeperch. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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14 pages, 2129 KiB  
Article
Examination of Physiological and Morphological Differences between Farm-Bred and Wild Black-Spotted Pond Frogs (Pelophylax nigromaculatus)
by Jun-Kyu Park, Jeong Bae Kim and Yuno Do
Life 2021, 11(10), 1089; https://doi.org/10.3390/life11101089 - 15 Oct 2021
Cited by 4 | Viewed by 2372
Abstract
Due to the decline in the population and the difficulty of in situ conservation, several anuran species are being reared in captivity. In this study, we identified physiological and morphological differences between farm-bred and wild frogs. Nine different serum components were used as [...] Read more.
Due to the decline in the population and the difficulty of in situ conservation, several anuran species are being reared in captivity. In this study, we identified physiological and morphological differences between farm-bred and wild frogs. Nine different serum components were used as indicators of osmotic pressure, homeostatic state, organ function, and nutritional status of farm-bred frogs and wild frogs, while radiographic techniques were used to visualize differences in bone mineral density and body composition ratio. Additionally, X-ray skeletal images were used for morphological analysis to estimate differences in locomotory performance between the two groups. Wild frogs harbor traits that aid in better locomotory performance than farm-bred frogs. They also have a relatively lower fat content ratio and higher calcium and phosphorus serum levels than farm-bred frogs, suggesting a difference in nutritional status. However, hepatic stress was higher in wild frogs than in farm-bred frogs. Veterinary clinical examinations allow for the identification of differences in nutritional and morphological conditions between farm-bred and wild frogs. Determining the health of animals can help improve their living conditions, eliminate conditions that can negatively affect them, and effectively manage them on farms, in zoos, and at ex situ conservation institutes. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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15 pages, 3876 KiB  
Article
Dietary Administration of Novel Multistrain Probiotics from Healthy Grouper Intestines Promotes the Intestinal Immune Response against NNV Infection
by Joan Tang Xiao Joe, Henry Tan Shi Sung, Jen-Leih Wu, Yu-Shen Lai and Ming-Wei Lu
Life 2021, 11(10), 1053; https://doi.org/10.3390/life11101053 - 07 Oct 2021
Cited by 2 | Viewed by 1944
Abstract
Epinephelus lanceolatus (giant grouper) is a high-value cultured species in the Asia-Pacific region. However, nervous necrosis virus (NNV) is an infectious viral disease that affects over 120 species of marine cultured species and causes high mortality, ranging from 90–100% in the grouper industry. [...] Read more.
Epinephelus lanceolatus (giant grouper) is a high-value cultured species in the Asia-Pacific region. However, nervous necrosis virus (NNV) is an infectious viral disease that affects over 120 species of marine cultured species and causes high mortality, ranging from 90–100% in the grouper industry. Probiotics isolated from the intestines of healthy individuals have provided insight into novel approaches involved in the defense against viral pathogens. In this study, we isolated three strains of bacteria as candidate probiotics from healthy grouper intestines and a 28-day feeding trial was performed. At day 21, the nervous necrosis virus (NNV) challenge test was conducted for 7 days to evaluate the antiviral effect of candidate probiotics. The results showed that candidate probiotics could improve growth conditions, such as weight gain (WG) and specific growth rate (SGR), and increase the utilization of feed. Furthermore, the candidate probiotic mixture had the ability to protect against NNV, which could decrease the mortality rate by 100% in giant grouper after NNV challenge. Subsequently, we analyzed the mechanism of the candidate probiotic mixture’s defense against NNV. A volcano plot revealed 203 (control vs. NNV), 126 (NNV vs. probiotics − NNV), and 5 (control vs. probiotics − NNV) differentially expressed transcripts in intestinal tissue. Moreover, principal components analysis (PCA) and cluster analysis heatmap showed large differences among the three groups. Functional pathway analysis showed that the candidate probiotic mixture could induce the innate and adaptive immunity of the host to defend against virus pathogens. Therefore, we hope that potential candidate probiotics could be successfully applied to the industry to achieve sustainable aquaculture. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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15 pages, 3331 KiB  
Article
Feasibility Study on the Use of Fly Maggots (Musca domestica) as Carriers to Inhibit Shrimp White Spot Syndrome
by Po-Yu Huang, Yi-Hsuan Huang, Jiann-Horng Leu and Li-Li Chen
Life 2021, 11(8), 818; https://doi.org/10.3390/life11080818 - 11 Aug 2021
Cited by 2 | Viewed by 2480
Abstract
The shrimp aquaculture industry has encountered many diseases that have caused significant losses, with the most serious being white spot syndrome (WSS). Until now, no cures, vaccines, or drugs have been found to counteract the WSS virus (WSSV). The purpose of this study [...] Read more.
The shrimp aquaculture industry has encountered many diseases that have caused significant losses, with the most serious being white spot syndrome (WSS). Until now, no cures, vaccines, or drugs have been found to counteract the WSS virus (WSSV). The purpose of this study was to develop an oral delivery system to transport recombinant proteinaceous antigens into shrimp. To evaluate the feasibility of the oral delivery system, we used white shrimp as the test species and maggots as protein carriers. The results indicated that the target protein was successfully preserved in the maggot, and the protein was detected in the gastrointestinal tract of the shrimp, showing that this oral delivery system could deliver the target protein to the shrimp intestine, where it was absorbed. In addition, the maggots were found to increase the total haemocyte count and phenoloxidase activity of the shrimp, and feeding shrimp rVP24-fed maggots significantly induced the expression of penaeidins 2. In the WSSV challenge, the survival rate of rVP24-fed maggots was approximately 43%. This study showed that maggots can be used as effective oral delivery systems for aquatic products and may provide a new method for aquatic vaccine delivery systems. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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15 pages, 6643 KiB  
Communication
De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens
by Huapu Chen, Xiaomeng Li, Yaorong Wang, Chunhua Zhu, Hai Huang, Wei Yang and Guangli Li
Life 2021, 11(8), 803; https://doi.org/10.3390/life11080803 - 09 Aug 2021
Cited by 4 | Viewed by 2092
Abstract
The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are [...] Read more.
The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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17 pages, 2505 KiB  
Article
Comparative Physiological and Transcriptomic Profiling Offers Insight into the Sexual Dimorphism of Hepatic Metabolism in Size-Dimorphic Spotted Scat (Scatophagus argus)
by Huapu Chen, Dongneng Jiang, Zhiyuan Li, Yaorong Wang, Xuewei Yang, Shuangfei Li, Shuisheng Li, Wei Yang and Guangli Li
Life 2021, 11(6), 589; https://doi.org/10.3390/life11060589 - 21 Jun 2021
Cited by 8 | Viewed by 2480
Abstract
The spotted scat (Scatophagus argus) is an economically important cultured marine fish that exhibits a typical sexual size dimorphism (SSD). SSD has captivated considerable curiosity for farmed fish production; however, up till now the exact underlying mechanism remains largely unclear. As [...] Read more.
The spotted scat (Scatophagus argus) is an economically important cultured marine fish that exhibits a typical sexual size dimorphism (SSD). SSD has captivated considerable curiosity for farmed fish production; however, up till now the exact underlying mechanism remains largely unclear. As an important digestive and metabolic organ, the liver plays key roles in the regulation of fish growth. It is necessary to elucidate its significance as a downstream component of the hypothalamic-pituitary-liver axis in the formation of SSD. In this study, the liver physiological differences between the sexes were evaluated in S. argus, and the activity of several digestive and metabolic enzymes were affected by sex. Females had higher amylase, protease, and glucose-6-phosphate dehydrogenase activities, while males exhibited markedly higher hepatic lipase and antioxidant enzymes activities. A comparative transcriptomics was then performed to characterize the responsive genes. Illumina sequencing generated 272.6 million clean reads, which were assembled into 79,115 unigenes. A total of 259 differentially expressed genes were identified and a few growth-controlling genes such as igf1 and igfbp1 exhibited female-biased expression. Further analyses showed that several GO terms and pathways associated with metabolic process, particularly lipid and energy metabolisms, were significantly enriched. The male liver showed a more active mitochondrial energy metabolism, implicating an increased energy expenditure associated with reproduction. Collectively, the female-biased growth dimorphism of S. argus may be partially attributed to sexually dimorphic metabolism in the liver. These findings would facilitate further understanding of the nature of SSD in teleost fish. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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Review

Jump to: Research

19 pages, 7972 KiB  
Review
Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow
by Rabiatul-Adawiah Zainal-Abidin, Nor Afiqah-Aleng, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun and Zeti-Azura Mohamed-Hussein
Life 2022, 12(5), 650; https://doi.org/10.3390/life12050650 - 27 Apr 2022
Cited by 3 | Viewed by 3190
Abstract
Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. [...] Read more.
Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. PPI network has been widely applied in biomedical research to understand the pathobiology of human diseases. It has also been used to understand the plant physiology that relates to crop improvement. However, the application of the PPI network in aquaculture is limited as compared to humans and plants. This review aims to demonstrate the workflow and step-by-step instructions for constructing a PPI network using bioinformatics tools and PPI databases that can help to predict potential interaction between proteins. We used zebrafish proteins, the oestrogen receptors (ERs) to build and analyse the PPI network. Thus, serving as a guide for future steps in exploring potential mechanisms on the organismal physiology of interest that ultimately benefit aquaculture research. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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15 pages, 736 KiB  
Review
The Roles of Neuropeptide Y (Npy) and Peptide YY (Pyy) in Teleost Food Intake: A Mini Review
by Daniel Assan, Umar Farouk Mustapha, Huapu Chen, Zhiyuan Li, Yuhao Peng and Guangli Li
Life 2021, 11(6), 547; https://doi.org/10.3390/life11060547 - 10 Jun 2021
Cited by 23 | Viewed by 4229
Abstract
Neuropeptide Y family (NPY) is a potent orexigenic peptide and pancreatic polypeptide family comprising neuropeptide Y (Npy), peptide YYa (Pyya), and peptide YYb (Pyyb), which was previously known as peptide Y (PY), and tetrapod pancreatic polypeptide (PP), but has not been exhaustively documented [...] Read more.
Neuropeptide Y family (NPY) is a potent orexigenic peptide and pancreatic polypeptide family comprising neuropeptide Y (Npy), peptide YYa (Pyya), and peptide YYb (Pyyb), which was previously known as peptide Y (PY), and tetrapod pancreatic polypeptide (PP), but has not been exhaustively documented in fish. Nonetheless, Npy and Pyy to date have been the key focus of countless research studies categorizing their copious characteristics in the body, which, among other things, include the mechanism of feeding behavior, cortical neural activity, heart activity, and the regulation of emotions in teleost. In this review, we focused on the role of neuropeptide Y gene (Npy) and peptide YY gene (Pyy) in teleost food intake. Feeding is essential in fish to ensure growth and perpetuation, being indispensable in the aquaculture settings where growth is prioritized. Therefore, a better understanding of the roles of these genes in food intake in teleost could help determine their feeding regime, regulation, growth, and development, which will possibly be fundamental in fish culture. Full article
(This article belongs to the Special Issue Strategies and Approaches for Improvement of Aquaculture)
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