International Journal of Aquaculture 2024, Vol.14, No.2 http://www.aquapublisher.com/index.php/ija © 2024 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
International Journal of Aquaculture 2024, Vol.14, No.2 http://www.aquapublisher.com/index.php/ija © 2024 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, aquaculture product quality and traceability, as well as socio-economics of aquaculture and impacts. 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), 2024, Vol. 14 ISSN 1927-6648 http://aquapublisher.com/index.php/ija © 2024 AquaPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content 2024, Vol. 14, No.2 【Research Perspective】 Molecular Breeding Techniques for Disease Resistance in Common Carp: Current Advances and Future Prospects 51-61 Yanhong Liu, Lingfei Jin DOI: 10.5376/ija.2024.14.0006 【Research Insight】 Unraveling the Genetic Mechanisms of Algal Adaptation: Insights from Genomics and Transcriptomics 62-72 ManmanLi DOI: 10.5376/ija.2024.14.0007 【Research Report】 Nutritional Improvements in Tilapia Fillets: Increasing Omega-3 Fatty Acid Content through Dietary Manipulations 73-80 Yue Zhu, Xianming Li DOI: 10.5376/ija.2024.14.0008 【Feature Review】 Genomic and Developmental Mechanisms Underlying Growth and Environmental Adaptation in Largemouth Bass (Micropterus salmoides) 81-90 Guilin Wang, Chenmin Sun, Liqing Chen DOI: 10.5376/ija.2024.14.0009 【Review and Progress】 Phytochemical Properties and Nutritional Benefits of Lotus Rhizome (Nelumbo nucifera): A Comprehensive Review 91-100 Fan Wang, Fei Zhao DOI: 10.5376/ija.2024.14.0010 Advances in Monitoring and Managing Aquatic Ecosystem Health: Integrating Technology and Policy 101-111 Liting Wang DOI: 10.5376/ija.2024.14.0011
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 51 Research Perspective Open Access Molecular Breeding Techniques for Disease Resistance in Common Carp: Current Advances and Future Prospects Lingfei Jin , Yanhong Liu Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: lingfei.jin@jicat.org International Journal of Aquaculture, 2024, Vol.14, No.2 doi: 10.5376/ija.2024.14.0007 Received: 11 Jan., 2024 Accepted: 20 Feb., 2024 Published: 12 Mar., 2024 Copyright © 2024 Jin and Liu, 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: Jin L.F., and Liu Y.H., 2024, Molecular breeding techniques for disease resistance in common carp: current advances and future prospects, International Journal of Aquaculture, 14(2): 51-61 (doi: 10.5376/ija.2024.14.0007) Abstract The fatty acid composition of aquaculture fish is of great importance in enhancing their nutritional value and human health. With the development of the aquaculture industry, researchers are increasingly focusing on how to optimize the fatty acid composition of fish through genetic and biochemical strategies. This study aims to explore the correlation between the fatty acid composition of aquaculture fish and human health. The study found that the fatty acid profiles of different fish are influenced by their diets, with marine fish generally having higher levels of n-3 polyunsaturated fatty acids such as EPA and DHA, compared to freshwater fish. The type of feed used significantly affects the nutritional value of the fish, with sustainable feeds often resulting in lower levels of EPA and DHA. Selective breeding has shown potential to increase the levels of beneficial fatty acids in fish muscle, and alternative lipid sources such as microalgae and genetically modified crops may serve as future sources of essential fatty acids. The study indicates that both genetic and biochemical strategies can effectively enhance the fatty acid composition of aquaculture fish, thereby improving their nutritional value, which is significant for the prevention of cardiovascular diseases. This research aims to provide theoretical basis and practical guidance for future studies and practical applications. Keywords Aquaculture fish; Fatty acid composition; Human health; Genetic strategies; Biochemical strategies 1 Introduction Common carp (Cyprinus carpio L.) is one of the most widely cultivated fish species globally, valued for its adaptability to diverse environmental conditions and its significant role in aquaculture. Originating from Asia, common carp has been introduced to various parts of the world, becoming a staple in both commercial and subsistence fisheries. The species is known for its robust growth rates and ability to thrive in a range of aquatic habitats, making it a crucial component of freshwater aquaculture systems (Jeney et al., 2011). Disease resistance in common carp is of paramount importance due to the substantial economic losses caused by infectious diseases (Verma et al., 2021). Among the most significant pathogens affecting common carp are Cyprinid herpesvirus-3 (CyHV-3), also known as koi herpesvirus (KHV), and Aeromonas hydrophila. CyHV-3 is notorious for causing high mortality rates in both ornamental and food production carp, with outbreaks leading to severe economic impacts on the aquaculture industry (Rakus et al., 2012). Similarly, Aeromonas hydrophila is a bacterial pathogen that can cause significant morbidity and mortality in carp populations, further underscoring the need for disease-resistant strains (Jeney et al., 2011). Recent studies have highlighted the genetic basis of disease resistance in common carp, identifying specific genes and alleles associated with increased resistance to these pathogens. For instance, polymorphisms in the major histocompatibility (MH) class II B genes have been linked to varying levels of resistance to CyHV-3, suggesting that these genetic markers could be utilized in selective breeding programs to enhance disease resistance (Rakus et al., 2009). Additionally, differential gene expression analyses have provided insights into the immune responses of carp lines with varying susceptibility to CyHV-3, revealing potential targets for genetic improvement (Rakus et al., 2012). This study aims to integrate the latest advancements in molecular breeding techniques to enhance disease resistance in carp. By synthesizing recent research findings, it summarizes genetic markers and molecular
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 52 pathways associated with disease resistance in carp and evaluates the effectiveness of different breeding strategies. The study also discusses future prospects and challenges. By providing a comprehensive review of the current state of molecular breeding for disease resistance in carp, this study aims to inform future studies and guide the development of more resilient aquaculture systems. 2 Overview of Disease Resistance in Common Carp 2.1 Major diseases affecting common carp Common carp (Cyprinus carpio L.) are susceptible to a variety of diseases that can significantly impact aquaculture productivity. Among the most notable diseases are those caused by bacterial pathogens such as Aeromonas hydrophila, which leads to motile aeromonad septicaemia (MAS) (Jeney et al., 2011; Liu et al., 2014), and viral infections like Cyprinid herpesvirus-3 (CyHV-3), also known as koi herpesvirus(KHV) (Palaiokostas et al., 2018a; Palaiokostas et al., 2019). Additionally, carp are affected by various parasites, mainly including Dactylogyrus, Trichodina, and copepod parasites (Obaid et al., 2021). These diseases can lead to high mortality rates and cause substantial economic losses in carp farming. 2.2 Traditional breeding approaches Traditional breeding approaches for disease resistance in common carp have primarily involved selective breeding, crossbreeding, and hybridization. Selective breeding has been used to enhance resistance to specific diseases, such as dropsy, through long-term selection programs. Crossbreeding and hybridization have also been employed to combine desirable traits from different strains, leading to improved growth rates and disease resistance (Vandeputte et al., 2003). For instance, the Krasnodar common ca. 2.3 Limitations of conventional methods Despite the successes of traditional breeding methods, there are several limitations. Conventional breeding approaches often require long timeframes to achieve significant genetic improvements and may not always result in the desired level of disease resistance. Additionally, the genetic basis of disease resistance is complex and influenced by multiple genes, making it challenging to achieve consistent results through traditional methods alone (Vandeputte et al., 2003). Furthermore, environmental factors can introduce biases in heritability estimates, complicating the selection process (Vandeputte et al., 2003). The need for more precise and efficient breeding techniques has led to the exploration of molecular breeding methods, which offer the potential to overcome these limitations and accelerate the development of disease-resistant common carp. 3 Marker-Assisted Selection (MAS) 3.1 Principles and applications of MAS Marker-Assisted Selection (MAS) is a molecular breeding technique that utilizes DNA markers to select for desirable traits in organisms, such as disease resistance in common carp. The primary principle of MAS is to identify and use molecular markers that are closely linked to genes of interest, thereby enabling the selection of individuals carrying these genes without the need for phenotypic screening. This approach significantly accelerates the breeding process by allowing early and accurate selection of desirable traits (Banu et al., 2017; Eze, 2019). MAS has been successfully applied in various breeding programs, particularly for traits with simple inheritance patterns. For instance, in crop plants, MAS has been used to introgress resistance genes into elite cultivars, thereby enhancing disease resistance and improving overall crop performance (Eze, 2019). Similarly, in nematode resistance breeding, MAS has facilitated the rapid and objective identification of resistant plant accessions, streamlining the breeding process (Banu et al., 2017). 3.2 Advantages over traditional methods MAS offers several advantages over traditional breeding methods. Firstly, it reduces the time and resources required for breeding by enabling early selection of desirable traits. Traditional breeding often involves lengthy and labor-intensive processes of phenotypic screening, which can be bypassed using MAS (Eze, 2019; Banu et al., 2017).
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 53 MAS enhances the precision of breeding programs. By using molecular markers, breeders can accurately select for specific genes, reducing the risk of losing desirable traits during the breeding process. This precision is particularly beneficial for traits with simple inheritance patterns, where the linkage between markers and genes is strong (Eze, 2019). Moreover, MAS can be integrated with high-throughput genotyping platforms, further accelerating the breeding process and enabling the handling of large populations. This integration opens new avenues for molecular-based resistance breeding, making it more efficient and effective (Banu et al., 2017). 3.3 Case studies Eze (2019) discussed how MAS (Marker-Assisted Selection) can use molecular genetic markers as criteria for selecting desirable traits, thereby accelerating the breeding process and improving accuracy and efficiency. MAS is particularly suitable for selecting traits that are difficult to measure, have low heritability, or are recessive. Through MAS, traits such as growth rate, disease resistance, and meat quality can be improved more quickly. The study conducted a cohabitation model experiment to compare the survival rates and virus transmission abilities of different types of carp when faced with CyHV-3 virus infection. The results showed that disease-resistant fish not only had higher survival rates after virus infection but also had a lower capacity to transmit the virus. This implies that disease-resistant fish have a significant advantage in reducing virus spread and infection. These findings are of great importance for disease control and fish breeding in aquaculture. 4. Quantitative Trait Loci (QTL) Mapping 4.1 Identification of QTLs linked to disease resistance Quantitative Trait Loci (QTL) mapping is a powerful tool for identifying genetic regions associated with disease resistance. In common carp, significant progress has been made in identifying QTLs linked to resistance against various pathogens. For instance, a genome-wide significant QTL affecting resistance to Koi Herpesvirus (KHV) was identified on linkage group 44, explaining approximately 7% of the additive genetic variance. This QTL region includes the TRIM25 gene, which was identified as a promising candidate gene for resistance due to a putative premature stop mutation (Palaiokostas et al., 2018a). Additionally, QTL mapping has been extensively used in plants to study complex disease resistance, providing insights into the number of resistance loci involved, their interactions, and their race-specificity. 4.2 Use of QTLs in breeding programs The identification of QTLs linked to disease resistance has significant implications for breeding programs. Marker-assisted selection (MAS) can be employed to incorporate these valuable traits into breeding lines, enhancing disease resistance in future generations. For example, DNA markers tightly linked to quantitative resistance loci (QRLs) controlling quantitative disease resistance (QDR) can be used for MAS to incorporate these traits into crops such as wheat, barley, common bean, tomato, and pepper (Clair et al., 2010). In the context of common carp, incorporating QTLs linked to KHV resistance into breeding programs could reduce morbidity and economic losses in carp farming (Palaiokostas et al., 2018a). 4.3 Case studies The study by Jia et al. (2021) provides valuable insights into the use of Quantitative Trait Loci (QTL) mapping for identifying genetic markers associated with disease resistance. By integrating transcriptome data and focusing on immune-related pathways and genes, the study elucidates how QTL mapping can precisely locate key genetic loci that contribute to resistance against CyHV-3 (Figure 1). This approach enables selective breeding of carp strains with enhanced disease resistance, thereby improving the efficiency of aquaculture. Figure 1 illustrates the application of QTL (Quantitative Trait Loci) mapping technology in breeding disease-resistant carp. The experiment compared the daily mortality rates and pathological changes between disease-resistant and non-resistant carp strains after infection with the CyHV-3 virus, verifying the effectiveness of resistance genes in reducing viral infection and transmission. The experimental results indicated that the disease-resistant strains had significantly lower mortality rates and pathological damage compared to the
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 54 non-resistant strains, demonstrating the presence and function of resistance genes. This figure shows that QTL mapping technology can effectively identify and select resistance genes, thereby enhancing the disease resistance of carp. This provides empirical support for the application of molecular breeding techniques in aquaculture. Figure 1 Differential appearance of general mortality and pathology between fish from the breeding and non-breeding strains. (Adopted from Jia et al., 2021) Image caption: (A) The PCR validation of the CyHV-3 virus genes TK and Sph. Lane 1-2 represents the negative control, and afterwards, lane 3-22 represents the result for tested 10 virus infected fish. (B) Comparison of daily mortality between the breeding and non-breeding strains. (C) The degree of swelling trunk kidney was limited in the survivors from the breeding strain (a) compared with the markedly enlarged trunk kidney observed in fish from the non-breeding strain (b). The arrow indicates the trunk kidney region. “**” means the very significant difference (p < 0.01) between current compared two groups (Adapted from Jia et al., 2021) 5 Genomic Selection (GS) 5.1 Overview of genomic selection Genomic Selection (GS) is a modern breeding technique that utilizes genome-wide genetic information to predict the breeding values of individuals. This method has gained attention in aquaculture due to its potential to enhance the accuracy of selection and accelerate genetic gains compared to traditional pedigree-based selection methods. GS involves the use of dense genetic markers spread across the genome to capture the genetic architecture of traits of interest, allowing for more precise selection of breeding candidates (Palaiokostas et al., 2018b; Palaiokostas et al., 2019).
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 55 5.2 Benefits in improving disease resistance The application of GS in aquaculture, particularly in common carp, has shown significant promise in improving disease resistance. One of the primary benefits of GS is its ability to increase the accuracy of selecting individuals with desirable traits, such as resistance to diseases like Koi Herpesvirus (KHV). Studies have demonstrated that GS can enhance prediction accuracy by 8%-18% over traditional methods, thereby improving the efficiency of breeding programs aimed at disease resistance (Palaiokostas et al., 2019). Additionally, GS allows for the simultaneous improvement of multiple traits, such as disease resistance and growth rate, which is crucial for maintaining overall productivity in aquaculture (Palaiokostas et al., 2018b; Lin et al., 2020). 5.3 Case studies Several case studies highlight the successful application of GS in improving disease resistance in common carp and other aquaculture species: 1) Koi Herpesvirus Resistance in Common Carp: A study involving 1,425 common carp juveniles challenged with KHV utilized Restriction Site-Associated DNA sequencing (RAD-seq) to genotype the population. The study identified a significant Quantitative Trait Locus (QTL) on linkage group 44, explaining approximately 7% of the additive genetic variance for KHV resistance. The TRIM25 gene was identified as a promising candidate within this QTL region, suggesting its potential role in enhancing disease resistance through GS (Palaiokostas et al., 2018a). 2) Juvenile Growth Rate in Common Carp: Another study on common carp focused on juvenile growth rate as a polygenic production trait. Using RAD sequencing, the study constructed a medium-density genetic map and tested GS, resulting in an 18% improvement in prediction accuracy over pedigree-based methods. This case illustrates the broader applicability of GS beyond disease resistance, highlighting its potential to enhance economically important traits in common carp breeding programs (Palaiokostas et al., 2018b). These case studies collectively demonstrate the efficacy of GS in improving disease resistance and other key traits in aquaculture, paving the way for more resilient and productive breeding programs. 6 CRISPR/Cas9 and Gene Editing 6.1 Mechanism of CRISPR/Cas9 The CRISPR/Cas9 system, derived from the adaptive immune system of bacteria, has emerged as a powerful tool for genome editing. The mechanism involves two key components: the Cas9 protein, which acts as a molecular scissor, and a guide RNA (gRNA) that directs Cas9 to a specific location in the genome. The gRNA binds to a complementary DNA sequence, and the Cas9 protein induces a double-strand break at this site. The cell's natural repair mechanisms then take over, either through non-homologous end joining (NHEJ) or homology-directed repair (HDR), allowing for targeted insertions, deletions, or modifications of genes (Mushtaq et al., 2019; Islam et al., 2020; Ahmad at al., 2020). 6.2 Applications in developing disease-resistant strains CRISPR/Cas9 has been extensively utilized in developing disease-resistant strains across various species, including plants, livestock, and aquaculture species like common carp. In plants, CRISPR/Cas9 has been used to knock out susceptibility genes or to introduce resistance genes, thereby enhancing resistance to bacterial, viral, and fungal pathogens (Mushtaq et al., 2019; Ahmad at al., 2020). In livestock, CRISPR/Cas9 has facilitated the insertion of disease resistance genes such as NRAMP1 in cattle for tuberculosis resistance and the deletion of the CD163 gene in pigs for resistance to porcine reproductive and respiratory syndrome (PRRS) (Islam et al., 2020). In common carp, CRISPR/Cas9 has been employed to target genes related to bone development and muscle growth, demonstrating its potential for genetic improvement in aquaculture (Zhong et al., 2016). 6.3 Case studies CRISPR/Cas9 has many successful applications in developing disease-resistant strains. For example, the study by Dorfman et al. (2024) conducted a detailed analysis of different strains of carp exposed to the CyHV-3 virus. It was found that disease-resistant strains not only had higher survival rates but also significantly reduced the viral
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 56 load in the water (Figure 2). In common carp, CRISPR/Cas9 has been used to disrupt the sp7 and myostatin genes, leading to severe skeletal defects and increased muscle cell growth, respectively, demonstrating the efficiency of this system in modifying the genome of common carp and its potential in aquaculture genetic research and breeding (Zhong et al., 2016). Figure 2 Cumulative mortality of experimental groups (Adopted from Dorfman et al., 2024) Image caption: (A) Mean cumulative mortality by days (adjusted to start day) for shedders (full lines) and cohabitants (dashed lines). (B) Final mean cumulative mortalities and standard errors for resistant (left bars) and susceptible (right bars) categories. (C) shedders, right censored to day 12 and (D) cohabitants, right censored to day 16. Note that survival analyses results are similar to mortality analyses presented in (A) (Adapted from Dorfman et al., 2024) Figure 2 from Dorfman et al. (2024) shows the cumulative mortality rates during the experiment for different treatment groups (resistant and susceptible shedders and their cohabitants), averaged over four replicates. The results demonstrate that improving disease resistance in common carp through molecular breeding techniques, such as CRISPR/Cas9, is not only feasible but also effective. The final cumulative mortality rate of resistant shedders was significantly lower than that of susceptible shedders, confirming the presence and effect of resistance genes. Specifically, the cumulative mortality rate for susceptible shedders was 83%, while for resistant shedders it was only 20%. This outcome validates that resistant carp have a higher survival rate when facing CyHV-3 virus. By selecting and introducing resistance genes through molecular breeding techniques like CRISPR/Cas9, the survival rate and overall disease resistance of carp against viral infections are significantly enhanced. These findings provide strong support and scientific evidence for the application of molecular breeding in aquaculture. 7 Transcriptomics and Proteomics 7.1 Role of transcriptomics in understanding disease response Transcriptomics has played a pivotal role in elucidating the molecular mechanisms underlying disease resistance in common carp. By analyzing the transcriptome of CyHV-3-resistant strains, researchers have identified key immune-related genes and pathways that contribute to the fish's ability to combat infections. For instance,
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 57 integrative transcriptomic analysis has revealed that the resistance to CyHV-3 in common carp involves specific innate immune mechanisms, including autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and mucin 3 (MUC3) (Jia et al., 2020; Jia et al., 2021). Additionally, transcriptome analysis of common carp infected with Aphanomyces invadans has highlighted the importance of efficient antigen processing, enhanced phagocytosis, and increased leukocyte recruitment in disease resistance (Verma et al., 2020). These findings underscore the significance of transcriptomics in identifying immune pathways and potential genetic markers for breeding disease-resistant carp. 7.2 Proteomic approaches to identify disease resistance markers Proteomics complements transcriptomics by providing insights into the protein-level changes associated with disease resistance. Proteomic studies have identified several proteins and pathways that are crucial for the immune response in common carp. For example, the identification of single nucleotide polymorphisms (SNPs) in immune response genes, such as TLRs and MyD88, has facilitated the development of genetic markers for mapping innate immune response genes (Kongchum et al., 2010). Moreover, the characterization of proteins involved in the immune response, such as CD40 and CD154, has revealed their significant roles in resistance to viral infections like grass carp reovirus (GCRV) (Lu et al., 2018). These proteomic approaches are essential for identifying disease resistance markers that can be used in selective breeding programs to enhance the resilience of common carp to various pathogens. 7.3 Case studies Transcriptomics and proteomics have extensive applications in understanding and enhancing disease resistance in common carp. Resistance to Aphanomyces invadans: Transcriptome analysis of common carp infected with A. invadans revealed that efficient antigen processing, enhanced phagocytosis, and increased leukocyte recruitment contribute to the fish's resistance to this pathogen (Verma et al., 2020). The study identified 5,288 differentially expressed genes (DEGs) and 731 genes involved in 21 immune pathways through RNA sequencing of head kidney samples from infected and uninfected carp (Figure 1). The findings highlight the carp's ability to efficiently process and present antigens, enhance phagocytosis, recognize pathogen-associated molecular patterns, and recruit leukocytes to the infection site. This systematic understanding of disease resistance mechanisms at the molecular level is of great value for developing disease management strategies. Figure 3 in the study by Verma et al. (2021) shows that 12 days post-infection (dpi), no gross lesions were observed in both the experimental and control groups of common carp. However, histopathological examination revealed mild degeneration of muscle fibers and the presence of hyphae at the injection site in the infected fish. By 12 dpi, granulomas had formed around the hyphae, indicating that the immune response helped to combat the infection. This figure emphasizes the effectiveness of the carp's immune response in controlling the pathogen and preventing extensive tissue damage, highlighting the role of granuloma formation in disease resistance. Transcriptomics and proteomics are powerful tools for understanding the molecular basis of disease resistance in common carp. By identifying key immune pathways and genetic markers, these approaches pave the way for the development of disease-resistant carp strains through selective breeding programs. 8 Challenges and Future Directions 8.1 Genetic diversity and inbreeding One of the primary challenges in molecular breeding for disease resistance in common carp is maintaining genetic diversity while avoiding inbreeding. Inbreeding can lead to a reduction in genetic variability, which is crucial for the adaptability and long-term survival of the species. Studies have shown that different strains of common carp exhibit varying levels of resistance to diseases such as Aeromonas hydrophila and Cyprinid herpesvirus-3 (CyHV-3) (Jeney et al., 2011). The use of genetically diverse strains, such as the Tata and Szarvas 15 domesticated strains, has been effective in producing families with higher resistance to diseases (Jeney et al., 2011). However,
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 58 continuous monitoring and management of genetic diversity are essential to prevent inbreeding depression and ensure the sustainability of breeding programs. Figure 3 Common carp injected with zoospores of A. invadans (Adopted from Peng et al., 2016) Image caption: (A) No gross lesions observed 12 days post-infection (dpi); (B) Section of muscle from experimentally infected common carp showing granuloma (arrow) around the oomycete hyphae (arrowheads) at 12 dpi; (C) Section of muscle tissue from the control common carp injected with autoclaved pond water, showing normal muscle fibers; (D) Head kidney of experimentally infected common carp at 12 dpi showing normal architecture, i.e., haematopoietic tissue (arrowhead) and renal tubules (arrows), similar to the control group (Adapted from Peng et al., 2016) 8.2 Ethical and regulatory issues The application of molecular breeding techniques raises several ethical and regulatory concerns. The use of genetic markers and selective breeding for disease resistance must comply with national and international regulations to ensure the welfare of the fish and the safety of the environment. For instance, the World Organization for Animal Health has listed Koi herpesvirus as a notifiable disease, necessitating strict regulatory measures for its control (Palaiokostas et al., 2018a; Jia et al., 2020). Ethical considerations also include the potential impact of genetically modified organisms (GMOs) on natural ecosystems and the need for transparent communication with stakeholders, including consumers and environmental groups. 8.3 Technical limitations and costs The implementation of molecular breeding techniques involves significant technical challenges and costs. High-throughput sequencing technologies, such as Restriction Site-Associated DNA sequencing (RADseq), and genome-wide association studies (GWAS) are essential for identifying quantitative trait loci (QTL) and genetic markers associated with disease resistance (Palaiokostas et al., 2018a; Jia et al., 2020). However, these technologies require substantial financial investment and technical expertise. Additionally, the development and validation of single nucleotide polymorphism (SNP) markers for immune response genes are time-consuming and resource-intensive (Kongchum et al., 2010). The cost-effectiveness of these techniques must be evaluated to ensure their feasibility for large-scale breeding programs.
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 59 8.4 Environmental and ecological considerations The release of genetically selected or modified common carp into natural water bodies poses potential environmental and ecological risks. The introduction of disease-resistant strains could disrupt local ecosystems and affect the genetic makeup of wild populations. Studies have highlighted the importance of understanding the ecological impact of breeding programs and the need for comprehensive risk assessments (Palaiokostas et al., 2019). Moreover, the potential for horizontal gene transfer and the spread of resistance genes to other species must be carefully monitored. Sustainable breeding practices should aim to balance the benefits of disease resistance with the preservation of natural biodiversity and ecosystem health. 9 Concluding Remarks Molecular breeding techniques have shown significant promise in enhancing disease resistance in common carp (Cyprinus carpio). Key findings from recent studies highlight the role of major histocompatibility complex (MHC) genes, particularly MHC class IIα and IIβ alleles, in conferring resistance to pathogens such as Aeromonas hydrophila and Cyprinid herpesvirus-3 (CyHV-3). Integrative transcriptomic analyses have revealed that specific immune mechanisms, including autophagy, phagocytosis, and virus blockage by lectins and mucin 3, are crucial for resistance to CyHV-3. Additionally, genomic selection and quantitative trait locus (QTL) mapping have identified significant genetic markers and candidate genes, such as TRIM25 and various toll-like receptors (TLRs), that are associated with enhanced disease resistance. Molecular breeding is pivotal in aquaculture for several reasons. Firstly, it offers a sustainable alternative to antibiotics and vaccines, which can have environmental and health repercussions. By selecting for disease-resistant traits, molecular breeding reduces the incidence of infectious diseases, thereby improving fish health and survival rates. This is particularly important for economically significant species like common carp, which are susceptible to devastating diseases such as CyHV-3 and Aeromonas hydrophila infections. Moreover, molecular breeding techniques, including genomic selection and QTL mapping, enable precise and efficient identification of desirable traits, accelerating the breeding process and enhancing genetic gain. Future research should focus on expanding the genetic databases and refining molecular tools to further enhance the accuracy and efficiency of breeding programs. Key recommendations include: 1) Expanding Genetic Studies: Conduct comprehensive genome-wide association studies (GWAS) and QTL mapping to identify additional genetic markers and candidate genes associated with disease resistance 2) Integrative Approaches: Utilize integrative transcriptomic and proteomic analyses to uncover the complex immune mechanisms underlying disease resistance and to identify novel targets for genetic selection. 3 Genomic Selection: Implement and optimize genomic selection techniques across diverse carp populations to ensure broad applicability and to maximize genetic gain. 4) Cross-Breeding Programs: Develop cross-breeding programs that combine resistant strains from different genetic backgrounds to enhance overall disease resistance and genetic diversity. 5) Environmental Considerations: Investigate the interaction between genetic resistance and environmental factors to develop holistic breeding strategies that consider both genetic and ecological aspects. By following these recommendations, the aquaculture industry can significantly improve the resilience and productivity of common carp, ensuring sustainable and profitable fish farming practices. Acknowledgments The authors acknowledge the two anonymous peer reviewers for their careful evaluation and valuable feedback on the initial draft of this manuscript. Conflict of Interest Disclosure The publisher thanks the peer reviewers for their careful consideration and valuable recommendations on the manuscript.
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 60 Reference Ahmad S., Wei X., Sheng Z., Hu P., and Tang S., 2020, CRISPR/Cas9 for development of disease resistance in plants: recent progress limitations and future prospects, Briefings in Functional Genomics, 19(1): 26-39. https://doi.org/10.1093/bfgp/elz041 Banu J., Meena K., Selvi C., and Manickam S., 2017, Molecular marker-assisted selection for nematode resistance in crop plants, Journal of Entomology and Zoology Studies, 5: 1307-1311. Clair D., 2010, Quantitative disease resistance and quantitative resistance Loci in breeding, Annual Review of Phytopathology, 48: 247-68. https://doi.org/10.1146/annurev-phyto-080508-081904 Eze F., 2019, “Marker-assisted selection in fish: a review”, Asian Journal of Fisheries and Aquatic Research, 3(4): 1-11. https://doi.org/10.9734/ajfar/2019/v3i430038 Islam M., Rony S., Rahman M., Çınar M., Villena J., Uddin M., and Kitazawa H., 2020, Improvement of disease resistance in livestock: application of immunogenomics and CRISPR/Cas9 technology, Animals : an Open Access Journal from MDPI, 10(12): 2236. https://doi.org/10.3390/ani10122236 Jeney G., Ardó L., Rónyai A., Bercsényi M., and Jeney Z., 2011, Resistance of genetically different common carp Cyprinus carpio L., families against experimental bacterial challenge with Aeromonas hydrophila, Journal of Fish Diseases, 34(1): 65-70. https://doi.org/10.1111/j.1365-2761.2010.01211.x Jia Z., Chen L., Yanlong G., Shengwen L., Peng W., Li C., Zhang Y., Hu X., Zhou Z., Shi L., and Xu P., 2020, Genetic mapping of Koi herpesvirus resistance (KHVR) in Mirror carp (Cyprinus carpio) revealed genes and molecular mechanisms of disease resistance, Aquaculture, 519: 734850. https://doi.org/10.1016/j.aquaculture.2019.734850 Jia Z., Wu N., Jiang X., Li H., Sun J., Shi M., Li C., Ge Y., Hu X., Ye W., Tang Y., Shan J., Cheng Y., Xia X., and Shi L., 2020, Integrative transcriptomic analysis reveals the immune mechanism for a cyhv-3-resistant common carp strain, Frontiers in Immunology, 12: 687151. https://doi.org/10.3389/fimmu.2021.687151 Jia Z., Wu N., Jiang X., Li H., Sun J., Shi M., Li C., Ge Y., Hu X., Ye W., Tang Y., Shan J., Cheng Y., Xia X., and Shi L., 2021, Integrative transcriptomic analysis reveals the immune mechanism for a CyHV-3-resistant common carp strain, Frontiers in Immunology, 12: 687151. https://doi.org/10.3389/fimmu.2021.687151 Kongchum P., Palti Y., Hallerman E., Hulata G., and David L., 2010, SNP discovery and development of genetic markers for mapping innate immune response genes in common carp (Cyprinus carpio)., Fish and Shellfish Immunology, 29(2): 356-361. https://doi.org/10.1016/j.fsi.2010.04.013 Lin Z., Hosoya S., Sato M., Mizuno N., Kobayashi Y., Itou T., and Kikuchi K., 2020, Genomic selection for heterobothriosis resistance concurrent with body size in the tiger pufferfish Takifugu rubripes, Scientific Reports, 10(1): 19976. https://doi.org/10.1038/s41598-020-77069-z Liu J., Liu Z., Zhao X., and Wang C., 2014, MHC class IIα alleles associated with resistance to Aeromonas hydrophila in purse red common carp Cyprinus carpio Linnaeus, Journal of fish diseases, 37(6): 571-575. https://doi.org/10.1111/jfd.12131 Lu X., Chen Y., Cui Z., Zhang X., Lu L., Li S., Xia X., Nie P., and Zhang Y., 2018, Characterization of grass carp CD40 and CD154 genes and the association between their polymorphisms and resistance to grass carp reovirus, Fish and Shellfish Immunology, 81: 304-308. https://doi.org/10.1016/j.fsi.2018.07.037 Mushtaq M., Sakina A., Wani S., Shikari A., Tripathi P., Zaid A., Galla A., Abdelrahman M., Sharma M., Singh A., and Salgotra R., 2019, Harnessing genome editing techniques to engineer disease resistance in plants, Frontiers in Plant Science, 10: 550. https://doi.org/10.3389/fpls.2019.00550 Ortega F., and Lopez-Vizcon C., 2012, Application of molecular marker-assisted selection (MAS) for disease resistance in a practical potato breeding programme, Potato Research, 55: 1-13. https://doi.org/10.1007/s11540-011-9202-5 Obaid H., Hussein N., Obed T., and Boundenga L., 2021, Common Carp ( Cyprinus carpio) parasites diversity and prevalence in Erbil aquacultures: gills, skin and intestinal infections, The Iranian Journal of Veterinary Science and Technology, 13: 34-41. https://doi.org/10.22067/IJVST.2021.64304.0 Palaiokostas C., Kocour M., Prchal M., and Houston R., 2018b, Accuracy of genomic evaluations of juvenile growth rate in common carp (Cyprinus carpio) using genotyping by sequencing, Frontiers in Genetics, 9: 350926. https://doi.org/10.3389/fgene.2018.00082 Palaiokostas C., Robledo D., Veselý T., Prchal M., Pokorová D., Piačková V., Pojezdal Ľ., Kocour M., and Houston R., 2018a, Mapping and sequencing of a significant quantitative trait locus affecting resistance to koi herpesvirus in Common Carp, G3: Genes|Genomes|Genetics, 8: 3507-3513. https://doi.org/10.1534/g3.118.200593 Palaiokostas C., Veselý T., Kocour M., Prchal M., Pokorová D., Piačková V., Pojezdal Ľ., and Houston R., 2019, Optimizing genomic prediction of host resistance to koi herpesvirus disease in carp, Frontiers in Genetics, 10: 543. https://doi.org/10.3389/fgene.2019.00543
International Journal of Aquaculture, 2024, Vol.14, No.2, 51-61 http://www.aquapublisher.com/index.php/ija 61 Rakus K., Irnazarow I., Adamek M., Palmeira L., Kawana Y., Hirono I., Kondo H., Matras M., Steinhagen D., Flasz B., Brogden G., Vanderplasschen A., and Aoki T., 2012, Gene expression analysis of common carp (Cyprinus carpio L.) lines during Cyprinid herpesvirus 3 infection yields insights into differential immune responses, Developmental and Mparative Immunology, 37(1): 65-76. https://doi.org/10.1016/j.dci.2011.12.006 Rakus K., Wiegertjes G., Adamek M., S`i A., Lepa A., and Irnazarow I., 2009, Resistance of common carp (Cyprinus carpio L.) to Cyprinid herpesvirus-3 is influenced8 by major histocompatibility (MH) class II B gene polymorphism, Fish and Shellfish Immunology, 26(5): 737-743. https://doi.org/10.1016/j.fsi.2009.03.001 Vandeputte M., 2003, Selective breeding of quantitative traits in the common carp (Cyprinus carpio): a review, Aquatic Living Resources, 16: 399-407. https://doi.org/10.1016/S0990-7440(03)00056-1 Verma D., Peruzza L., Peruzza L., Trusch F., Trusch F., Yadav M., R., Shubin S., Morgan K., Mohindra V., Hauton C., West P., Pradhan P., and Sood N., 2020, Transcriptome analysis reveals immune pathways underlying resistance in the common carp Cyprinus carpio against the oomycete Aphanomyces invadans, Genomics, 113(1): 944-956. https://doi.org/10.1016/j.ygeno.2020.10.028 Zhong Z., Niu P., Wang M., Huang G., Xu S., Sun Y., Xu X., Hou Y., Sun X., Yan Y., and Wang H., 2016, Targeted disruption of sp7 and myostatin with CRISPR-Cas9 results in severe bone defects and more muscular cells in common carp, Scientific Reports, 6(1): 22953. https://doi.org/10.1038/srep22953
International Journal of Aquaculture, 2024, Vol.14, No.2, 62-72 http://www.aquapublisher.com/index.php/ija 62 Research Insight Open Access Unraveling the Genetic Mechanisms of Algal Adaptation: Insights from Genomics and Transcriptomics ManmanLi Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: manman.li@hitar.org International Journal of Aquaculture, 2024, Vol.14, No.2 doi: 10.5376/ija.2024.14.0008 Received: 10 Feb., 2024 Accepted: 15 Mar., 2024 Published: 31 Mar., 2024 Copyright © 2024 Li, 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: Li M.M., 2024, Unraveling the genetic mechanisms of algal adaptation: insights from genomics and transcriptomics, International Journal of Aquaculture, 14(2): 62-72 (doi: 10.5376/ija.2024.14.0008) Abstract Algal adaptability is a key factor in global ecological balance, and studying its adaptation mechanisms provides significant biological insights. This study aims to reveal the genetic mechanisms behind algae's adaptation to various environmental stresses through genomics and transcriptomics. It specifically describes the structure of algal genomes and transcriptomic features, and through case studies, shows how algae adjust gene expression to cope with environmental stresses, particularly focusing on stress response genes, regulatory networks, and evolutionary adaptations. Moreover, by integrating genomic and transcriptomic data analysis, the study enhances the overall understanding of algal adaptation mechanisms. The results not only deepen the understanding of algal genetic adaptability but also advance algal biotechnology, providing new strategies for environmental protection and sustainable utilization of biological resources. Keywords Algae; Genomics; Transcriptomics; Adaptability; Bioinformatics 1 Introduction Algae, a diverse group of photosynthetic eukaryotes, play a crucial role in global carbon fixation and primary production in aquatic ecosystems. They exhibit a wide range of adaptations to various environmental conditions, from the harsh tidal zones inhabited by brown algae to the nutrient-poor waters where marine cyanobacteria thrive (Cock et al., 2010; Teng et al., 2017; Chen et al., 2020). The evolutionary history of algae is marked by multiple endosymbiotic events, leading to the acquisition of plastids and the diversification of algal lineages. These adaptations are not only morphological but also genetic, involving complex regulatory mechanisms that enable algae to respond to environmental stresses such as light intensity, salinity, and temperature fluctuations (Raven et al., 2003). Algal species provides insights into the evolutionary processes that have shaped the diversity and complexity of itselfs (Blaby-Haas and Merchant, 2019). It helps in identifying key genes and pathways that contribute to the resilience and productivity of algae in various habitats. This knowledge is particularly important in the context of climate change, as it can inform strategies for conserving and managing algal populations that are critical for ecosystem stability and carbon cycling. Additionally, the study of algal genomics and transcriptomics can lead to biotechnological applications, such as the development of biofuels and the improvement of algal strains for aquaculture and bioremediation (Matsuzaki et al., 2004). This study unravel the genetic mechanisms underlying algal adaptation by synthesizing findings from recent genomics and transcriptomics studies. The objectives are to: elucidate the genetic strategies employed by different algal groups to adapt to their environments, highlight the role of horizontal gene transfer and gene regulation in these adaptive processes, and explore the implications of these genetic mechanisms for ecological and biotechnological applications. Integrating data from multiple studies, this study seeks to provide a comprehensive understanding of how genetic diversity and evolutionary pressures shape the adaptability of algae, thereby contributing to the broader field of evolutionary biology and environmental science.
International Journal of Aquaculture, 2024, Vol.14, No.2, 62-72 http://www.aquapublisher.com/index.php/ija 63 2 Overview of Algal Genomics Algal genomics is a rapidly advancing field that provides critical insights into the genetic mechanisms underlying the adaptation, evolution, and functional capabilities of algae. With the increasing biotechnological, environmental, and nutraceutical importance of algae, understanding their genomic structure, the techniques used in their study, and key genomic findings is essential. 2.1 Algal genome structure The structure of algal genomes varies significantly across different species, reflecting their diverse evolutionary histories and ecological niches. For instance, the genome of the polar eukaryotic microalga Coccomyxa subellipsoidea exhibits significant synteny conservation with its relatives, yet shows extensive intra-chromosomal rearrangements, which may contribute to its adaptation to cold environments (Blanc et al., 2012). Similarly, the genomic analysis of Picochlorum species reveals substantial heterozygosity and allelic diversity, which are crucial for their adaptation to variable environments such as salt plains and brackish waters (Foflonker et al., 2018). These structural variations highlight the complex genomic architecture that supports the ecological versatility of algae. 2.2 Techniques in algal genomics Advancements in sequencing technologies and bioinformatics have revolutionized the study of algal genomics. Whole-genome sequencing, transcriptomics, and comparative genomics are among the key techniques employed. For example, RNA-Seq analysis has been used to assess gene expression patterns in Alexandrium minutumunder nutrient-deficient conditions, providing insights into its physiological adaptations and stress responses (Meng et al., 2019). Additionally, the use of population genomics approaches, such as genome-wide association studies (GWAS) and selection scans, has enabled the identification of loci associated with adaptation and speciation in various algal species (Bamba et al., 2018). These techniques facilitate a comprehensive understanding of the genetic basis of algal adaptation and evolution. 2.3 Key genomic findings in algal research Several key findings have emerged from genomic studies of algae, shedding light on their adaptive strategies and evolutionary processes. The genomic analysis of Picochlorum species has revealed that gene gain, loss, and horizontal gene transfer (HGT) play significant roles in their adaptation to salinity stress. In Coccomyxa subellipsoidea, the presence of unique gene clusters and the loss of certain proteins suggest specific adaptations to low temperatures. Furthermore, the study of Galdieria sulphuraria under continuous cold stress has identified numerous genetic variants and candidate genes involved in thermal adaptation, highlighting the complexity of the adaptive response at the genetic level (Rossoni and Weber, 2019). These findings underscore the dynamic nature of algal genomes and their capacity for rapid adaptation to changing environmental conditions. 3 Transcriptomics in Algal Research 3.1 Principles of transcriptomics Transcriptomics is the study of the complete set of RNA transcripts produced by the genome under specific circumstances or in a specific cell. This field provides insights into gene expression patterns and regulatory mechanisms, which are crucial for understanding the functional elements of the genome and the molecular constituents of cells and tissues. In algal research, transcriptomics helps elucidate how algae respond to environmental changes, stress conditions, and nutrient availability, thereby revealing the underlying genetic mechanisms of adaptation and survival. 3.2 Techniques in transcriptome analysis Several advanced techniques are employed in transcriptome analysis, including RNA sequencing (RNA-Seq), quantitative real-time PCR (qRT-PCR), and microarray analysis. RNA-Seq is a powerful and widely used method that allows for the comprehensive analysis of the transcriptome, providing both qualitative and quantitative data on RNA expression levels (Morse et al., 2018). This technique involves the conversion of RNA into complementary DNA (cDNA), which is then sequenced using high-throughput sequencing technologies. qRT-PCR is often used to validate RNA-Seq results by quantifying the expression levels of specific genes.
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