International Journal of Aquaculture, 2025, Vol.15, No.1, 21-28 http://www.aquapublisher.com/index.php/ija 23 to rapid changes in gene frequencies associated with economic traits, and insulin-like growth factor (IGF) genes associated with growth rate show significant selection signals in breeding populations (Cádiz et al., 2020). The breeding populations in different regions show obvious regional differences in genetic structure. Brazil’s tilapia farming populations exhibit unique haplotype distributions on disease resistance-related genes, which may be due to local disease stress-driven selection results. Mexican breeding populations exhibit higher allelic frequencies on low temperature-tolerant-associated genes (heat shock protein HSP70), which is in line with its high-altitude breeding environment. These cases show that genetic selection during domestication directly shapes the functional genetic structure of the population. 3.3 Genetic differentiation characteristics of domesticated strains in different continents As tilapia gradually expanded to all parts of the world, domesticated strains from different continents showed unique genetic characteristics. After long-term artificial breeding, tilapia in Asia has formed multiple strains that adapt to different breeding modes. For example, GIFT (Genetic Improvement of Farmed Tilapia) shows faster growth rate and higher survival rate. Countries in the Americas have set different breeding goals based on their own breeding environment and market needs. In Brazil, breeding efforts focus on the improvement of growth rate and feed conversion rate. Through whole-genome resequencing, the researchers found that Wnt signaling pathway, gonadotropin-releasing hormone receptor and integrin signaling pathways are positively selected in improved lines, indicating that these pathways are closely related to growth and reproductive performance. In order to improve the comprehensive performance of tilapia, some countries in the Americas have carried out hybridization tests between different strains. Comparison of salt tolerance performance of the positive and negative progeny of the orange Mozambique tilapia and the Honalong tilapia. The difference in salt tolerance of the positive and negative progeny of the orange Mozambique tilapia and the Honalong tilapia was compared through the acute salt tolerance experiment. The results showed that the 96 h semi-lethal salinity (MLS-96) of the orthogonal offspring (Mohalo) and the anti-progeny (Mohalo) were 29.80±3.03‰ and 29.38±4.48‰, respectively. There was no significant difference between the two. The two hybrid offspring had obvious hybrid advantages and their salt tolerance was higher than that of the two parents. 4 Effects of Domestication on the Tilapia Genome 4.1 Changes in functional genes of tilapia under artificial selection Artificial selection drives significant changes in tilapia functional genes. For example, growth rate-related genes show significant frequency increases in long-term breeding. Taking Nile tilapia as an example, through genome-wide association analysis (GWAS), researchers found that the expression levels of the growth hormone-related gene GH and the insulin-like growth factor IGF-1 are significantly improved (Khaw et al., 2008). The increase in these gene expression directly promotes the rapid growth of fish and greatly improves the breeding benefits. Disease resistance traits have also been widely concerned. By selecting streptococcal disease resistance genes, strains with strong disease resistance are selected. Actual cases show that immune-related genes such as TLR, MHC, and other genomic regions of certain lines are significantly enriched, indicating that these genes are significantly enhanced under the pressure of artificial selection. Changes in these functional gene frequency reflect the directional effects humans exerted on the tilapia genome during domestication (Figure 1) (Mwanja et al., 2010). 4.2 Analysis of genome structure variation during domestication During the domestication of tilapia, the genome structure showed obvious mutations. Changes at the chromosome level are the most representative, such as chromosome inversion, translocation and repeat sequence amplification. Taking the genome sequencing study of Asian farmed tilapia as an example, through high-throughput sequencing and comparative genomic analysis, it was found that artificial domesticated lines had a large number of structural mutations in specific chromosomal segments. These variant regions often contain important functional genes, which directly affect the economic traits of tilapia. Further research shows that structural variation plays a key role in improving the adaptability of tilapia to high-density farming environments. Inverted variation in specific chromosomal regions makes it easier for certain strains to adapt to hypoxic environments and improves overall
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