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
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