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
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