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International Journal of Aquaculture 2025, Vol.15, No.5 http://www.aquapublisher.com/index.php/ija © 2025 AquaPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher Aqua Publisher Editedby Editorial Team of International Journal of Aquaculture Email: edit@ija.aquapublisher.com Website: http://www.aquapublisher.com/index.php/ija Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada International Journal of Aquaculture (ISSN 1927-5773) is an open access, peer reviewed journal published online by AquaPublisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all working and studying within varied areas of aquaculture, containing the latest developments and techniques for practice in aquaculture; information about the entire area of applied aquaculture, including breeding and genetics, physiology, aquaculture-environment, hatchery design and management, utilization of primary and secondary resources in aquaculture, production and harvest, the biology and culture of aquaculturally important and emerging species. All the articles published in International Journal of Aquaculture are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. AquaPublisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors' copyrights. Aqua Publisher is an international Open Access publisher specializing in the field of marine science and aquaculture registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada.
International Journal of Aquaculture (online), 2025, Vol. 15, No. 5 ISSN 1927-6648 http://aquapublisher.com/index.php/ija © 2025 AquaPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Towards Sustainable Aquaculture: A Review on The Use of Microalgae as Functional Feed Ingredients Costa D.S., Pereira-Júnior J.A., Martins M.L. International Journal of Aquaculture, 2025, Vol. 15, No. 5, 221-228 Genetic Basis of Growth Traits in Shrimp Based on QTL and GWAS Studies Linhua Zhang, Shiying Yu International Journal of Aquaculture, 2025, Vol. 15, No. 5, 229-239 Mitochondrial DNA Analysis for Resolving the Phylogenetic Relationships of Tilapia Species Xian Li, Xiaoli Chen, Rudi Mai International Journal of Aquaculture, 2025, Vol. 15, No. 5, 240-247 Nutritional and Antioxidant Properties of Porphyra spp.: Implications for Human Health Qiong Wang, Liting Wang International Journal of Aquaculture, 2025, Vol. 15, No. 5, 248-254 Evolutionary Pathways of Fishes: Insights from Fossil Records and Molecular Phylogenetics Xianming Li, Lingfei Jin International Journal of Aquaculture, 2025, Vol. 15, No. 5, 255-265
International Journal of Aquaculture, 2025, Vol.15, No.5, 221-228 http://www.aquapublisher.com/index.php/ija 221 Feature Review Open Access Towards Sustainable Aquaculture: A Review on The Use of Microalgae as Functional Feed Ingredients CostaD.S. 1 , Pereira-Júnior J.A. 2, Martins M.L. 3 1 LMM-Marine Mollusc Laboratory, Aquaculture Department, UFSC, Florianópolis, SC, Brazil 2 LCM-Marine Shrimp Laboratory, Aquaculture Department, UFSC, Florianópolis, SC, Brazil. 3 AQUOS-Aquatic Organisms Health Laboratory, Aquaculture Department, UFSC, Florianópolis, SC, Brazil Corresponding authors: domicksonsc@hotmail.com International Journal of Aquaculture, 2025, Vol.15, No.5 doi: 10.5376/ija.2025.15.0021 Received: 19 Jul., 2025 Accepted: 03 Sep., 2025 Published: 18 Sep., 2025 Copyright © 2025 Costa et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Costa D.S., Pereira-Júnior J.A., and Martins M.L., 2025, Towards sustainable aquaculture: a review on the use of microalgae as functional feed ingredients, International Journal of Aquaculture, 15(5): 221-228 (doi: 10.5376/ija.2025.15.0021) Abstract Population growth is intensifying the demand for sustainable protein sources, positioning aquaculture as a strategic sector for global food security. However, the industry faces nutritional, economic, and environmental challenges, particularly due to the high cost and ecological impact of fishmeal (FM) and fish oil (FO), which are widely used in commercial feeds. These inputs are rich in essential fatty acids, such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), whose production relies on intensive harvesting of marine species, thereby compromising the sustainability of the supply chain. In this context, microalgae have emerged as promising alternatives due to their high nutritional and functional value, including proteins, long-chain polyunsaturated fatty acids (LC-PUFAs), antioxidants, and bioactive compounds. This review compiles scientific evidence demonstrating that the inclusion of microalgae in fish and shrimp diets can maintain or enhance lipid composition, immunocompetence, pathogen resistance, antioxidant activity, and gut health in cultured organisms. Species such as Schizochytriumsp., Nannochloropsis sp., Chlorella sp., and Spirulina sp. have shown promising results. Although further studies are needed to determine optimal inclusion levels and potential synergies among species, current data support the potential of microalgae to contribute to a more efficient and sustainable aquaculture. Keywords Fishmeal; Fish oil; Antioxidants; Bioactive compounds 1 Introduction The development and growth of the human population have driven a continuous search for alternatives to meet the increasing demand for resources, especially food (Gil et al., 2024). In this context, expanding the production of proteins for human consumption in a safe and sustainable way represents a significant challenge for various sectors, including aquaculture. Aquaculture is an activity focused on the production of aquatic organisms such as fish, crustaceans, mollusks, and algae. This practice plays a strategic role in global food security, since, according to data from the Food and Agriculture Organization of the United Nations (FAO, 2024), aquaculture production has reached 223.2 million tons. Of this total, 185.4 million tons corresponded to the production of aquatic animals, while 37.8 million tons referred to algae production. Furthermore, approximately 89% of aquatic animal production was intended for human consumption. Despite the significant figures achieved by aquaculture, challenges still persist regarding the nutrition of farmed organisms, especially fish and shrimp (Evrendilek, 2024). These issues go beyond technical aspects such as diets formulation, balanced and nutritionally adequate feed, and also encompass economic and environmental concerns, including high production costs and the sustainability of the production system. In this context, it is worth noting that feed accounts for a large portion of the total production costs (Baki and Yücel, 2017) making it one of the main obstacles to the economic viability of aquaculture, especially for small and medium-sized producers. The high cost of aquaculture feed is largely associated with the use of ingredients such as fishmeal (FM) and fish oil (FO), which are valued for their high concentration of polyunsaturated fatty acids (PUFAs), especially docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) (Zhang et al. 2024) which play essential roles in
International Journal of Aquaculture, 2025, Vol.15, No.5, 221-228 http://www.aquapublisher.com/index.php/ija 222 the growth and reproduction processes of aquatic organisms (Thiruvasagam et al., 2024). However, the intensive use of these inputs raises important concerns related to the sustainability of their production. According to FAO (2024), approximately 19% of fish aquaculture production is directed toward the manufacture of these ingredients, which raises significant environmental concerns, as this practice is closely linked to overfishing (Satyakumar et al., 2024) of species such as anchoveta (Engraulis ringens), the main raw material used. This fishing pressure has led to a progressive reduction in natural stocks of the species, compromising the long-term sustainability of the production chain. Given the concerns regarding the sustainability of FM and FO production, initiatives have emerged aimed at replacing these ingredients in aquaculture diets. However, such replacement presents a considerable challenge, as alternative ingredients must not only be safe for farmed organisms but also possess a nutritional composition compatible with that of traditional inputs, particularly regarding the PUFA profile, with emphasis on long-chain polyunsaturated fatty acids (LC-PUFAs), such as DHA and EPA (Zhang et al., 2024). A deficiency of these compounds in the diet can significantly impair the zootechnical performance of fish and shrimp, affecting their growth, reducing their immunocompetence, and decreasing their final nutritional value, which may negatively impact their commercial acceptance. In this context, microalgae have emerged as a promising alternative due to their high nutritional and functional value. These microorganisms are important sources of essential amino acids, carbohydrates, carotenoids, polysaccharides, and long-chain polyunsaturated fatty acids (LC-PUFAs) (Bergmann et al., 2024), in addition to containing bioactive compounds with antioxidant potential, such as flavonoids, alkaloids, glycosides, β-carotene, and phenolic compounds (Salem et al., 2022). Given this multifunctional potential, the present work aims to compile updated scientific evidence on the feasibility of using microalgae as partial or total replacements for fishmeal and fish oil in diets formulated for fish and shrimp, with a focus on nutritional and immunological aspects. 2 Effects of Microalgae Inclusion on The Nutritional Quality of Fish and Shrimp The wide diversity of microalgae species, combined with their high nutritional value, has sparked growing interest in research aimed at developing sustainable solutions. These investigations primarily seek to mitigate the environmental impacts associated with conventional aquaculture practices, particularly the intensive production and use of fishmeal (FM) and fish oil (FO) in commercial feed formulations. In this context, Sarker et al. (2020) investigated the total replacement of FO and the gradual replacement of FM using whole cells of Schizochytriumsp. and defatted biomass of Nannochloropsis oculata in the feeding of Nile tilapia (Oreochromis niloticus) over a period of 183 days. The authors observed that the fillets of fish fed with the total replacement diet (100NS) of FM and FO had a significantly higher lipid content (1.8%) compared to the control diet (commercial feed with FM and FO). Regarding amino acid composition, methionine and histidine levels were lower in the 33% replacement diet (33NS) and numerically higher in the 66% replacement diet (66NS), when compared to both the control and 100NS diets. Additionally, the levels of polyunsaturated fatty acids (PUFAs) were significantly higher in the microalgae-based diets, regardless of the replacement level, especially docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). DHA deposition in the fillet was highest in the 100NS diet (5.15 mg/g), contrasting with the lowest value observed in the control diet (2.47 mg/g). Supporting the potential of microalgae as alternative nutrient sources in aquafeeds, Karapanagiotidis et al. (2022) evaluated the replacement of FM with Chlorella vulgaris and FO with a blend of Schizochytrium sp. and Microchloropsis gaditana (SM) in the diet of Sparus aurata over 12 weeks. The results indicated that fish fed with 100% FO replacement (SM100) showed increased levels of muscle PUFAs, including linoleic acid (18 : 2n-6), γ-linolenic acid (18 : 3n-6), arachidonic acid (20 : 4n-6), adrenic acid (22 : 4n-6), and docosapentaenoic acid (DPA, 22 : 5n-6). On the other hand, SM diets with 50% and 100% replacement led to lower concentrations of n-3 PUFAs such as stearidonic acid (18 : 4n-3), eicosatetraenoic acid (ETA, 20 : 4n-3), and DPA (22 : 5n-3), compared to the control group.
International Journal of Aquaculture, 2025, Vol.15, No.5, 221-228 http://www.aquapublisher.com/index.php/ija 223 Complementary results were presented by Seong et al. (2021), who evaluated the lipid profile of Pagrus major fed for 75 days with FO-free diets containing meals of Nannochloropsis sp. (NAN: 22.8 ± 1.0%) and Schizochytrium sp. (SCH: 25.0 ± 0.0%). Both treatments resulted in higher n-6 PUFA levels in the whole fish body compared to the control diet. However, the n-3 PUFA levels were lower in these groups. In contrast, supplementation with combinations of Nannochloropsis sp., Schizochytriumsp., and Chlorella sp. (NSC), or only Nannochloropsis sp. and Schizochytrium sp. (NS), led to increases in total n-3 PUFA contents (13.3 ± 2.6% and 13.1 ± 0.6%, respectively) and long-chain n-3 PUFA (LC-PUFA n-3) levels of 9.4 ± 1.5% and 10.1 ± 0.6%, respectively. The feasibility of similar replacements was also explored in shrimp feeding by Pakravan et al. (2017), who analyzed the effects of replacing FM with Spirulina platensis at different levels in the diet of Litopenaeus vannamei over eight weeks. Shrimp receiving 100% FM replacement with S. platensis showed higher whole-body concentrations of fatty acids such as linoleic acid (16.10 ± 0.08%) and α-linolenic acid (2.40 ± 0.05%). Meanwhile, arachidonic acid (4.24 ± 0.03%), DHA (10.70 ± 0.23%), and EPA (9.86 ± 0.02%) levels were higher in the group with 25% FM replacement, suggesting that intermediate replacement levels may favor the accumulation of nutritionally relevant fatty acids. Additional studies with L. vannamei reinforce these findings. Allen et al. (2019) reported that diets containing high levels of fermented Schizochytriumsp. meal led to reduced EPA levels in the muscle compared to the control diet (4.94 ± 0.04%). On the other hand, FO-free diets with 62% and 75% of Schizochytriumsp. meal resulted in higher DHA levels (5.58 ± 0.19% and 5.46 ± 0.15%, respectively). Additionally, Li et al. (2022) demonstrated that total replacement of FM with Chlorella sorokiniana (C-100) negatively affected the amino acid profile of shrimp, reducing total amino acid content (877.9 ± 13.1 g/kg), essential amino acids (425.7 ± 11.4 g/kg), tyrosine (35.9 ± 0.5 g/kg), and proline (54.8 ± 4.2 g/kg). Moreover, methionine levels decreased in all microalgae-included groups, while lysine levels dropped in the 80% and 100% replacement groups (66.4 ± 3.3 g/kg and 64.1 ± 0.7 g/kg, respectively) (Figure 1). Figure 1 Illustrates the main findings reported in the cited literature
International Journal of Aquaculture, 2025, Vol.15, No.5, 221-228 http://www.aquapublisher.com/index.php/ija 224 Based on the studies presented, there is a clear convergence regarding the potential of microalgae as viable and sustainable alternatives to traditional sources of fishmeal (FM) and fish oil (FO) in aquafeeds. This substitution has gained prominence not only due to its ecological appeal but also because of the ability of microalgae to provide key nutrients, such as polyunsaturated fatty acids (PUFAs) and essential amino acids, although some nutritional limitations remain. In the study by Sarker et al. (2020), for example, the total replacement of FM and FO with Schizochytriumsp. and Nannochloropsis oculata resulted in a significant increase in DHA levels in tilapia fillets, demonstrating the efficiency of these microalgae in supplying beneficial lipids. However, variations in amino acid composition particularly the reduction in methionine and histidine levels in certain diets point to a specific nutritional limitation of these sources, suggesting the need for targeted supplementation. In the investigations conducted by Karapanagiotidis et al. (2022), although an increase in n-6 PUFA levels was observed following FO replacement, there was also a reduction in n-3 fatty acids such as ETA and DPA. This raises concerns regarding the nutritional value of the fish flesh from a human consumption perspective. These results suggest that the lipid composition of microalgae must be carefully balanced to avoid imbalances between omega-3 and omega-6 fatty acids an essential factor in determining the nutritional quality of farmed fish. In this context, the study by Seong et al. (2021) adds an important dimension to the discussion by demonstrating that combining different species of microalgae (Nannochloropsis, Schizochytrium, and Chlorella) was more effective in promoting adequate levels of n-3 PUFAs, including long-chain PUFAs (LC-PUFAs), in Pagrus major. These findings suggest that synergistic interactions between microalgal species may compensate for individual nutritional deficiencies, representing a promising strategy for developing more complete feed formulations. In the case of shrimp, the findings of Pakravan et al. (2017) and Allen et al. (2019) reveal a dose-dependent response to substitution: intermediate inclusion levels (25%) of Spirulina platensis, for example, were the most effective in increasing concentrations of beneficial fatty acids. Furthermore, replacement with Schizochytriumsp. led to an increase in DHA content but also a reduction in EPA levels, again reinforcing the importance of lipid balance in diet formulation. Finally, the study by Li et al. (2022) reveals a critical limitation: the total replacement of FM with Chlorella sorokiniana significantly impaired the essential amino acid profile in shrimp, resulting in a considerable reduction in their nutritional value. This finding underscores the need for a careful assessment of the protein quality of microalgae, with particular attention to the amino acid profile in formulations with high inclusion levels of these biomasses. In addition to the nutritional assessment, it is essential to analyze the impact of partial or total replacement of fishmeal (FM) and fish oil (FO) on the immunological parameters of fish and shrimp, as well as to investigate the potential antimicrobial activity that microalgae may exert against organisms with pathogenic potential. 3 Microalgae in Aquaculture: Ommunomodulation, Antimicrobial Activity, and Antioxidant Effects Studies have shown that the inclusion of microalgae such as Spirulina platensis, Chlorella vulgaris, Nannochloropsis spp., and Haematococcus pluvialis in diets with reduced fishmeal (FM) and fish oil (FO) promotes positive effects on immune parameters. For example, in experiments with Clarias gariepinus and Carassius auratus, the partial replacement of FM by Spirulina sp. and Chlorella sp. resulted in significant increases in red and white blood cell levels, hematocrit, hemoglobin, and expression of the genes TLR2, IL-1β, and TNF-α, as well as improved survival rate after challenge with Aeromonas hydrophila (Raji et al., 2018; Cao et al., 2018). Similarly, in Nile tilapia (Oreochromis niloticus), the replacement of 15% to 20% of fishmeal by Nannochloropsis oculata led to increased lysozyme activity, higher IgM (immunoglobulin) concentration, greater protection against infection byA. hydrophila, and preservation of intestinal integrity (Salem et al., 2022).
International Journal of Aquaculture, 2025, Vol.15, No.5, 221-228 http://www.aquapublisher.com/index.php/ija 225 These findings are consistent with those observed in salmonids, in which the combination of Schizochytriumspp. and Nannochloropsis gaditana in diets formulated for Salmo salar promoted activation of innate immunity, evidenced by increased expression of the genes C3 and NK-lysin, as well as elevation in the number of monocytes and immature erythrocytes (Sánchez et al., 2023). Similarly, the inclusion of Haematococcus sp. in diets for trout (Oncorhynchus mykiss) resulted in higher myeloperoxidase activity and increased survival rate after challenge with Vibrio anguillarum, reinforcing the immunomodulatory potential of microalgae (Aulia et al., 2024). Furthermore, a study with Oncorhynchus mykiss evaluated six diets containing progressive FO replacements by Schizochytrium sp. The best zootechnical performance was observed in the T20 diet (20% FO replacement), which resulted in weight gain, specific growth rate, and feed efficiency significantly higher (p < 0.05). This same diet showed the highest lysozyme activity level among treatments and provided greater survival rate of fish after challenge with Lactococcus garvieae, compared to the CON (control, 100% FO), T80 (80% replacement), and T100 (100% replacement) groups, indicating a relevant immunoprotective effect of the microalga even with partial FO replacement (Lee et al., 2022). Immune system modulation is considered one of the main benefits associated with the use of microalgae, which are rich in polyunsaturated fatty acids (PUFAs), β-glucans, and natural antioxidants (Bahi et al., 2023). Regarding the antimicrobial aspect, both extracts from Microchloropsis gaditana and Tetraselmis suecica demonstrate effective activity (Parra-Riofrio et al., 2023; Díaz et al., 2025). Specifically, M. gaditana can increase the antibacterial activity of Salmo salar serum against Piscirickettsia salmonis by more than 85% (Díaz et al., 2025). Additionally, extracellular polysaccharides fromT. suecica and Porphyridium cruentumshowed antiviral action against VHSV (Viral Hemorrhagic Septicemia Virus) in cell cultures, interfering at different stages of the viral cycle (Parra-Riofrio et al., 2023). In general, microalgae are rich sources of compounds with antimicrobial potential, including peptides, long-chain fatty acids, pigments (such as carotenoids and astaxanthin), phenols, and sulfated polysaccharides (Ahmed et al., 2022; Ilieva et al., 2024). These compounds may act directly or indirectly in reducing bacterial load and inhibiting common aquaculture pathogens. Antimicrobial activity related to the content of sulfated polysaccharides, for example, may be associated with alteration of bacterial cell wall integrity and inhibition of pathogen adhesion to the host (Rajasekar et al., 2019). Regarding antioxidant effects, several microalgae have demonstrated the ability to reduce oxidative stress and improve antioxidant enzyme activity. In Scophthalmus maximus, inclusion of Nannochloropsis sp. in the diet significantly increased the activities of the enzymes SOD (superoxide dismutase), GSH-Px (glutathione peroxidase), and total antioxidant capacity, while reducing hepatic levels of MDA (malondialdehyde) (Qiao et al., 2019). Similarly, in tilapia fed with different microalgae strains, an increase in T-AOC (total antioxidant capacity) in muscle tissue was observed, reduction in reactive oxygen species production, and positive regulation of the expression of the genes GSH-Px, CAT(catalase), and SOD, as well as higher resistance to infection by Aeromonas hydrophila (Ibrahim et al., 2022). Similar results were observed in mullet (Mugil liza) subjected to partial replacement of oil and FM by flaxseed oil and Spirulina sp. In this study, the 50% replacement treatment resulted in increased antioxidant capacity and improved zootechnical performance, without compromising the fatty acid profile of the fillet. These findings suggest that the combination of plant-based and microalgal ingredients can positively modulate the antioxidant response and contribute to maintaining product quality (Rosas et al., 2019). Modulation of intestinal microbiota is also a recurring effect associated with microalgae use. In Sparus aurata, for example, diets containing microalgae altered the bacterial profile of the intestine, promoting growth of the genera Pseudomonas and Bacillus (Katsoulis-Dimitriou et al., 2024). These effects may be related to the presence of complex polysaccharides, such as fucose, which act as selective substrates for probiotic bacteria.
International Journal of Aquaculture, 2025, Vol.15, No.5, 221-228 http://www.aquapublisher.com/index.php/ija 226 Besides fish, partial replacement of FM by microalgae has shown positive effects in other groups of aquatic organisms. In shrimp Litopenaeus vannamei, for example, inclusion of Chlorella sorokiniana as a partial FM substitute was effective at levels up to 28%, maintaining zootechnical performance, fillet quality, and antioxidant parameters (Li et al., 2022). The results obtained in multiple species and different experimental contexts reinforce the multifunctional potential of microalgae as promising ingredients in aquaculture. Their application contributes not only to reducing dependence on traditional marine resources but also to strengthening biosafety and sustainability in aquaculture production systems. Although further research is needed to standardize ideal concentrations, evaluate synergistic combinations among microalgal species, and elucidate the mechanisms of action involved, the data available so far are promising and point to a more sustainable and resilient aquaculture (Figure 2). Figure 2 Graphical representation of the information compiled from different literature sources 4 Final Considerations In summary, this review highlights the high potential of microalgae as dietary additives for fish and shrimp, contributing to improvements in lipid composition, strengthening of the immune system, antioxidant and antimicrobial activity, and modulation of the microbiota. Several studies have demonstrated that microalgae can partially replace fish oil and fishmeal, establishing themselves as a promising alternative to traditional, non-sustainable ingredients. Notably, Spirulina sp., Nannochloropsis sp., Schizochytriumsp., and Haematococcus pluvialis stand out for their nutritional, immunological, and antimicrobial potential. However, further research is needed to determine the optimal inclusion level of microalgae in diets, evaluate combinations of different species to fully meet the physiological and nutritional requirements of fish and shrimp, and investigate the effects of biomass processing prior to inclusion, particularly in relation to the complete replacement of fish oil and fishmeal. Authors’ Contributions Costa, D.S. was primarily responsible for the conceptualization and methodological design of the study, as well as for validation, investigation, and data curation. In addition, he contributed to the drafting of the original manuscript and the preparation of visualizations. Pereira-Júnior J.A. also participated in the conceptualization and methodological design, played an important role in the investigation, and assisted in drafting the original manuscript and creating visualizations. Martins M.L. supervised the overall research process. Acknowledgments The authors thank the National Council for Scientific and Technological Development (CNPq) Martins, M.L. (CNPq 306635/2018-6, 409821/2021-7). References Ahmed E.A., El-Sayed A.M., El-Sayed M.A., and El-Sayed M.A., 2022, In vitro antimicrobial activity of astaxanthin crude extract from Haematococcus pluvialis, Eur J Aquat Anim Health, 26: 95-106. https://doi.org/10.21608/ejabf.2022.224854
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International Journal of Aquaculture, 2025, Vol.15, No.5, 229-239 http://www.aquapublisher.com/index.php/ija 229 Meta Analysis Open Access Genetic Basis of Growth Traits in Shrimp Based on QTL and GWAS Studies Linhua Zhang1, Shiying Yu2 1 Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China 2 Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China Corresponding author: shiying.yu@cuixi.org International Journal of Aquaculture, 2025, Vol.15, No.5 doi: 10.5376/ija.2025.15.0022 Received: 30 Jul., 2025 Accepted: 09 Sep., 2025 Published: 20 Sep., 2025 Copyright © 2025 Zhang and Yu, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhang L.H., and Yu S.Y., 2025, Genetic basis of growth traits in shrimp based on QTL and GWAS studies, International Journal of Aquaculture, 15(5): 229-239 (doi: 10.5376/ija.2025.15.0022) Abstract Shrimps are an important part of global aquaculture, especially South American white shrimp and other varieties dominate the global aquatic supply, and their output accounts for more than half of the world's total crustacean production. Growth traits (such as body length, weight, etc.) are directly related to breeding yield and economic benefits, and are one of the core goals of aquatic breeding. In recent years, molecular genetic technologies such as quantitative trait locus (QTL) localization and genome-wide association analysis (GWAS) have made progress in the field of aquatic products and have been gradually applied to shrimp genetic breeding research. This study reviews the main growth traits of shrimp and their biological mechanisms, reviews the current application status of QTL localization and GWAS in the study of growth traits of shrimp, summarizes the research progress of key molecular markers and candidate genes, and discusses the combination of traditional breeding and molecular assistive means using Chinese shrimp as an example. Finally, future strategies and international cooperation in shrimp molecular breeding are expected. Keywords Shrimp; growth traits; Quantitative trait loci (QTL); Genome-wide association analysis (GWAS); Molecular marker-assisted breeding 1 Introduction Shrimp plays an important role in the global aquaculture industry. In particular, due to its fast growth and strong adaptability, Litopenaeus vannamei has become the world's highest-growing crustacean variety, accounting for more than 50% of the total global aquaculture crustacean production. Asia is the main production area, and the shrimp farming industry in China, Southeast Asia and India is booming, providing the world with a large amount of high-quality animal protein. Prawns are cultivated along the coast and inland China, and are one of the important industries for increasing fishery income and farmers to get rich. However, the development of different shrimp species is not balanced. For example, Chinese shrimps in China have plummeted due to disease outbreaks in the 1990s, while foreign vannabinoid shrimps have occupied the mainstream of breeding with higher survival and growth advantages (Ma et al., 2024; Wang et al., 2024). Growth rate and final yield are one of the most concerned economic traits of aquaculture. For shrimp farming, individual weight and specifications directly determine market value. Faster-growing shrimps can shorten the breeding cycle, reduce feed and management costs. Studies have shown that shrimp growth traits have moderate to high heritability and can be significantly improved through breeding. In traditional breeding, breeders mostly use fast growth and large individual parent shrimp as the selection criteria. After continuous generations of family breeding, the growth rate of some shrimp varieties has been significantly improved. For example, the growth rate of new varieties such as vannabinoid shrimp "Kohai 1" and "Zhongxing 2" cultivated in China has significantly improved compared with the unbreeding groups (Huang et al., 2019). With the development of molecular biology and genomics, breeders have begun to apply technologies such as QTL localization and GWAS to the genetic analysis of quantitative traits of aquatic animals. These methods have been successful in fish, such as Atlantic salmon, raw fish, etc., the growth, meat quality, disease resistance and other traits have been identified. QTL studies have constructed high-density genetic linkage maps to locate gene segments that control quantitative traits and provide molecular markers for important traits (Andriantahina et al.,
International Journal of Aquaculture, 2025, Vol.15, No.5, 229-239 http://www.aquapublisher.com/index.php/ija 230 2013; Chen et al., 2022). GWAS uses a large number of markers across the genome-wide range to find trait-related alleles at the population level, with higher resolution and application range than traditional QTLs. In shrimp, early QTL studies were able to roughly localize regions containing thousands of genes due to their limited marker density. With the development of high-throughput sequencing, tens of thousands of SNP markers have been developed and applied to map construction and association analysis, improving positioning accuracy and efficiency. 2 Biological Basis of Shrimp Growth Traits 2.1 Main growth trait indicators: body length, weight, shell thickness, survival rate Shrimp growth traits are usually characterized by several indicators that are phenotypically measurable, among which the most commonly used are body length and weight. Body length includes the full length and body length, etc., which can reflect the individual's morphological development. In genetic assessment, the average weight of a specific day age, daily weight gain or weight gain rate for a specific period is often used as a measure of growth rate. Shell thickness (shell hardness) is also a related trait. Although it does not directly represent growth rate, the thickness and weight of the shell will affect the net meat output ratio of shrimp, which has also been paid attention to in some breeding programs. In addition, survival rates are often regarded as important breeding traits and are closely related to growth (Yuan et al., 2018): Only under the premise of similar survival can it be practical to improve growth. Therefore, survival rate is sometimes used as an auxiliary indicator of growth tests. At the same time, there have been researches to include bait conversion rate, plumpness, etc. into the evaluation system of shrimp growth traits to more comprehensively measure growth performance. In QTL and GWAS analysis, these traits can be analyzed individually, or the overall growth phenotype can be extracted by comprehensive analysis methods such as principal components. 2.2 Physiological and metabolic regulation mechanisms The growth of shrimp is regulated by a variety of endocrine and metabolic factors. From an endocrine point of view, shrimp lack growth hormones similar to vertebrates, but have hormone-like molecules such as insulin-like peptides (ILPs). The ILP1 gene of vannabinoid shrimp was cloned and found that it is widely expressed in various tissues of the shrimp body, especially the highest among neuroendocrine organs (eye stems, etc.) (Su et al., 2024). This is similar to the role of insulin-like growth factors in regulating the growth and development of vertebrates, suggesting that ILP1 has an important function in the growth and development of shrimps. In addition, ecdysterone (20E) and ecdysterone (MIH) in shrimps indirectly affect growth rate by regulating the molting cycle: shrimps only increase in volume and weight after molting, and shortening molting intervals can improve growth rate (Naidu et al., 2013). In terms of metabolism, growth speed is often related to nutritional metabolism and energy distribution. Studies have compared the molecular differences of fast-growing and slow-growing shrimps, and found that the genome-wide DNA methylation level of slow-growing individuals has significantly increased and is accompanied by upregulation of metabolic-related gene expression. These differential genes are enriched in carbohydrate and fatty acid metabolism pathways, and it is speculated that slow-growing shrimp will use more nutrients to maintain basal metabolism and stress rather than somatic growth. This finding suggests that epigenetic modifications (such as DNA methylation) participate in the regulation of shrimp growth phenotype by affecting the expression of metabolic genes. 2.3 Effect of environmental factors on growth traits Environmental conditions largely determine the development of shrimp growth potential. Among them, water temperature is the most direct environmental factor affecting shrimp growth. The optimal growth temperature of vannabinoid prawns is about 28 °C~32 °C. Too low will reduce feeding and metabolic rates, and growth will slow down significantly, while too high may trigger a stress response and also inhibit growth (Heriyati et al., 2024). Studies have shown that under low temperature stress, the antioxidant enzyme activity and energy metabolism in shrimps change, and long-term low temperatures will lead to growth stagnation and even death. Dissolved oxygen levels are also crucial. Adequate dissolved oxygen keeps shrimps high intake and high metabolism. Conversely, hypoxia causes anorexia, growth stagnation, and weak shrimps are more susceptible to disease (Akbarurrasyid et
International Journal of Aquaculture, 2025, Vol.15, No.5, 229-239 http://www.aquapublisher.com/index.php/ija 231 al., 2023). Water quality factors such as ammonia nitrogen and nitrite have a recessive effect on growth: chronic low-concentration ammonia nitrogen stress can reduce the feeding rate and digestive enzyme activity of shrimps, and the growth rate is significantly reduced (Li et al., 2024). A study of vannabinoid shrimp found that under the dual stress of sub-chronic ammonia nitrogen and salinity, the specific growth rate and intake of shrimp were inhibited and induced changes in stress-related gene expression. In addition, stocking density and nutritional level can also affect growth traits. High-density farming often leads to slow growth and small individuals, which is due to crowded stress and intra-species competition. In terms of bait nutrition, insufficient protein content will limit growth, and adding an appropriate amount of immune enhancer (such as astaxanthin) can improve digestive enzyme activity and growth-promoting gene expression, thereby improving growth performance. 3 Application of QTL Study in Shrimp 3.1 Basic principles and methods of QTL research Quantitative trait loci (QTL) localization is a classic method to discover quantitative trait genes through genetic linkage analysis. The basic principle is to detect the linkage association between phenotypic traits and molecular markers on the constructed genetic linkage map. If the marker typing of a region is significantly correlated with the trait value, it is inferred that the region contains genolo points that affect the trait. Traditional QTL mapping usually uses two-parent hybrid families, such as crossing parents with different growth traits, obtaining F2 or backcrossing populations, and then phenotyping and genotyping of population individuals. According to different mapping models, statistical methods such as interval mapping and composite interval mapping can be used to scan the map to locate the significance QTL. The accuracy of QTL positioning depends on the spectrum density and population size. The QTL map of early shrimps used microsatellite markers (SSRs), etc., and the number of markers was limited, resulting in a wide QTL interval. In recent years, second-generation sequencing technology has promoted the construction of high-density maps, each map can contain thousands to tens of thousands of marks, improving mapping accuracy (Huang et al., 2019). 3.2 Research progress on localization of QTL related to shrimp growth traits In shrimp, the study of growth-related QTL has made some progress in recent years. The earliest attempt can be traced back to the QTL positioning study of the Chinese shrimp "Huanghai No. 1". Although those studies were published more than a decade ago, they demonstrated the possibility of genetic localization of shrimp growth traits for the first time. In the past five years, with the emergence of vannerbine shrimp genome sequencing and high-density maps, new achievements have been made in QTL localization for growth traits. Experts used a 268-individual shrimp family to detect 11 QTLs with significantly associated growth rates (Ma et al., 2024). These QTLs are distributed in multiple linkage groups of shrimp genomes. Each QTL can explain about phenotypic variations of about 5%~10%, with the sum of contribution rates exceeding 50%, indicating that growth traits are regulated by multiple genes and there are several main-effect sites. Some of these QTLs show colocalization among different traits, suggesting that there may be core genes that affect overall growth ability. 3.3 Comparison of QTLs in different population and genetic background It should be emphasized that the QTL effect is often population-specific, and the same trait may be controlled by different sites in different genetic backgrounds. This is particularly evident among shrimps. The sites found in early single-line-based QTL studies were not necessarily significant in other strains or wild populations. This is due to the differences in allelic frequencies, linkage imbalance structures of different groups, and the growth traits themselves are affected by environmental and gene interactions. For example, Wang et al. (2019) found a candidate gene in different groups is the scavenger receptor Class C on the 13th linkage group. These results suggest that growth regulation in different breeding populations may be mediated by different gene pathways (Wang et al., 2019). Therefore, when applying QTL to molecular breeding, its population applicability needs to be taken into account, and it is best to be able to re-verify the QTL effect in the target breeding population. One way to improve the universality of QTL is to use multi-population joint maps or genome-wide associations to directly analyze natural populations or breeding populations, thereby localizing "shared sites" associated with traits. In fact, GWAS makes up for the limitations of single-family QTL to some extent and can be used for cross-validation of results in different contexts (Rio et al., 2020).
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