Animal Molecular Breeding, 2025, Vol.15, No.2, 82-90 http://animalscipublisher.com/index.php/amb 83 Application of conventional selective breeding methods, though effective, is time-consuming and could be non-specific in improving quantitative traits that are regulated by multiple genes. Marker-Assisted Selection (MAS) has been an effective method in fish genetic breeding through which animals bearing desirable quality genetic markers for traits such as rapid growth and high yield can be identified and selected. With the utilization of molecular markers, the breeders can accelerate the selection, increase accuracy, along with achieving earlier genetic gains. In tilapia breeding, MAS enables the early detection of superior alleles and thereby makes it possible for the broodstock with greater genetic potential to be selectable. The method not only accelerates the development of improved strains but also assists in understanding the genetic architecture of economically important traits. The application of MAS in breeding programs is the single largest aquaculture genetics input that holds the promise of increased aquaculture productivity and sustainability. 2 Genetic Basis and Breeding Progress of Tilapia 2.1 Current status of genetic resources and breeding history of tilapia Nile tilapia (Oreochromis niloticus) is among the world aquaculture highs; there are massive genes pools within the African Continent but its large-scale production within Asia and elsewhere. The species is genetically diverse in the region although the farmed populations tend to be narrower in genetic base (Figure 1) (Geletu and Zhao, 2022). Selective breeding schemes, such as the Genetically Improved Farmed Tilapia (GIFT) scheme, have played a crucial role in developing high-performing lines by cross-mating genetic material between different populations along with relative species (Etherington et al., 2022; Barría et al., 2023). Some of the newer advancements include chromosome-scale genome assemblies, molecular markers for determining ancestry and monitoring genetic diversity in breeding programs, for example, those of Avallone et al. (2020), Etherington et al. (2022), and Barría et al. (2023). Nonetheless, threat from habitat loss, introgressive hybridization, and human activities has caused genetic deterioration in wild populations that needs conservation and use of genetic resources in an appropriate manner (Geletu and Zhao, 2022; Tibihika et al., 2024; Kwikiriza et al., 2025). Figure 1 Genetic distance construction of different populations of Nile tilapia (Adopted from Kwikiriza et al., 2025) Image caption: Red: Cages; Blue: Hatcheries; Green: Wild and black: Ponds (Adopted from Kwikiriza et al., 2025) 2.2 Limitations and bottlenecks of existing breeding strategies for rapid growth and high yield Notwithstanding progress, the current breeding schemes are faced with various challenges. Domestic tilapia has a relatively narrow genetic base, therefore increasing the possibility of inbreeding and reducing the ability to adapt (Geletu and Zhao, 2022; Kwikiriza et al., 2025). Irreplaceable loss of genetic variation is also at risk due to focus on some performing lines and less application of wild genetic bases (Lind et al., 2019; Geletu and Zhao, 2022). In addition, introgressive hybridization and translocation admixture are able to compromise the genetic integrity of wild and domesticated populations (Tibihika et al., 2024). Gene tracking and regulation of gene flow and maintenance of genetic diversity still pose high challenges to sustainable breeding (Avallone et al., 2020; Tibihika et al., 2024).
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