Animal Molecular Breeding, 2025, Vol.15, No.2, 82-90 http://animalscipublisher.com/index.php/amb 87 production efficiency and less reliance on hormone treatments, which enable the development of robust, high-performing strains for diverse aquaculture conditions. The effective application of MAS across different tilapia species and strains suggests that it has the promise to be applied on an industrial scale and significantly impact the world tilapia industry to promote sustainable and profitable tilapia aquaculture (Chen et al., 2018;2021; Wu et al., 2021; Vela-Avitúa et al., 2023). 6 Challenges and Future Prospects in Molecular Breeding 6.1 Stability of marker-trait associations and environmental interaction issues One of the central challenges of molecular breeding is to achieve marker-trait association stability across a number of environments. The utility of markers can be undermined by genotype-environment interactions that have the potential to change the expression of target traits and decrease the predictive power of markers in alternative environments. This is of utmost significance for multi-gene and polygenic complex traits, where marker-phenotype associations in the continuous validation of multi-location and multi-year tests become a prerequisite to guarantee valid selection gains (Luo et al., 2023; Chen, 2024). 6.2 Marker combination strategies for multi-trait selection Multi-trait selection involves the development and use of marker combination programs such as gene pyramiding and multiplexed marker panel application. The strategies simplify the breeding of favorable yield, quality, and stress tolerance alleles but also complicate the breeding programs. The combination of high-throughput genotyping and high-performance bioinformatics software has enabled handling of large-scale data and correct selection of individuals with the best multi-trait profiles, though it is not simple to balance trade-offs between traits without compromising genetic diversity (Luo et al., 2023; Chen, 2024). 6.3 Potential of integrating gene editing and omics technologies in future tilapia breeding The integration of gene editing technologies, such as CRISPR-Cas9, and omics technologies (genomics, transcriptomics, proteomics, and metabolomics) holds large potential to accelerate tilapia improvement for desired traits. With these technologies, it is possible to edit directly the target genes and investigate extensively the biological pathways of the complex traits. Gene editing integrated with omics decreases breeding cycles, improves the efficiency of introgression of qualities, and can create tilapia lines with augmented yield, disease resistance, and environmental tolerance. Ethical, regulative, and technical barriers must be addressed in an attempt to enjoy such gains (Singh et al., 2020; Chen, 2024). 6.4 Key directions for advancing MAS toward precision breeding systems In order to propel MAS towards precision breeding, the research work in the future needs to involve the development of cost-cutting high-throughput genotyping platforms, improving the predictability of quantitative traits, and the integration of multi-layer omics data for indirectly decomposing traits. The application of automatic genotyping technologies as well as artificial intelligence in predictive breeding will further enhance selection efficiency and enable the quick release of cultivars with desired traits. Further studies and collaboration are required to overcome the current challenges and facilitate the widespread and sustainable application of precision molecular breeding in tilapia and other aquaculture species (Singh et al., 2020; Chen, 2024). 7 Concluding Remarks There have been impressive recent achievements in the elucidation of the molecular foundation of tilapia high-yield and rapid-growth traits. Genome-wide association studies (GWAS) have identified major quantitative trait loci (QTLs) associated with body weight, growth rate, and fillet yield, which has a solid genetic foundation for trait enhancement. Polymorphisms in important genes, such as the myogenic regulatory factors (MRFs) gene family, have been highly associated with enhanced muscle growth and enhancement of growth. Meanwhile, gene editing technologies, including CRISPR/Cas9, have enabled functional verification of such candidate genes, with effective knockout of the myostatin (mstn) gene promoting enhanced muscle weight and growth performance enhancement in Nile tilapia. These findings collectively provide not only molecular insight into growth and yield traits, but also practicable targets for genetic improvement by marker-assisted selection (MAS).
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