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,
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