International Journal of Molecular Zoology, 2025, Vol.15, No.1, 38-47 http://animalscipublisher.com/index.php/ijmz 45 such as giant grouper and brown grouper, but incomplete annotations and limited identification of functional variant sites still hinder the in-depth application of GS in actual breeding (Zhou et al., 2019; Yang et al., 2022). In addition, many grouper breeding programs still rely on low-density genotyping platforms, which limits the detection accuracy of key trait loci and the accuracy of genomic prediction. Although a variety of high-throughput SNP typing technologies have been developed, they have not yet been widely promoted in the industry, especially in commercial hatcheries, and cost issues are still one of the obstacles to large-scale application (Shan et al., 2021; 2023). 7.2 Multi-trait selection and trade-off management Breeding groupers is not as simple as just looking at who grows faster. In reality, if you blindly pursue growth rate, you may ignore equally critical traits such as fertility and disease resistance. The problem is that there is often a kind of "one rises while the other falls" relationship between these traits. If not handled properly, you may lose one while focusing on the other. Studies have shown that the immune-related gene family of some grouper species has expanded, which to some extent shows that while improving growth performance, health traits actually have room for improvement (Zhou et al., 2019; Yang et al., 2022). But, whether both ends can be taken into account ultimately depends on whether the genetic correlation between these traits can be scientifically managed and precisely regulated. In addition to growth rate and disease resistance, traits directly linked to benefits, such as meat quality and feed conversion efficiency, must also be taken into account during breeding, especially consumer preferences, which are increasingly valued by the industry. The problem is that, the genomic tools for these economic traits are not mature enough at this stage, and many are still in the initial stage. If we want to really advance, we must continue to work hard on the identification of molecular markers and the construction of trait prediction models so that these key traits can also be included in the main channel of improvement (Wu et al., 2024). 8 Concluding Remarks Current research has identified a number of key genes and molecular markers that are closely related to the rapid growth of grouper. Most of these genes are related to physiological processes such as energy metabolism, cell cycle regulation, and bone development. Give an example, in high-density QTL positioning and RNA-seq analysis, a number of potential candidate genes such as kalrn, ypel1, supt7l, lacs5, ccnd2, mybpc2, and bmp2k were identified. At the same time, a number of SNP sites and QTL regions closely related to growth traits were found. These achievements provide very practical basic resources for the subsequent marker-assisted selection and genetic improvement. Genomic selection (GS) has shown good results in predicting breeding values and accelerating genetic progress in growth traits, ammonia tolerance, etc. Combining GWAS informative sites with advanced statistical models has not only improved prediction accuracy but also cost-effectiveness, making GS a viable tool in grouper breeding practice. However, most current studies focus on gene associations and expression patterns, and direct functional validation experiments and systematic annotation of reference genomes are still relatively lacking. The growth traits of grouper are also relatively complex and are affected by multiple genes and environmental factors. The interaction between genotype and environment, as well as the need to weigh other key traits such as disease resistance and reproductive capacity in addition to growth traits, make breeding strategies more challenging, and a more integrated research approach is urgently needed. In the future, grouper breeding will benefit from the continued construction of high-quality genomic resources, the deep integration of marker-assisted selection and genomic selection, and the introduction of advanced breeding technologies. These efforts will help achieve the breeding goals of rapid growth, strong stress resistance and high quality, and promote the development of aquaculture in a sustainable and efficient direction.
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