International Journal of Molecular Zoology, 2025, Vol.15, No.1, 38-47 http://animalscipublisher.com/index.php/ijmz 43 By accurately predicting the breeding values of candidate individuals at an early stage, GS technology can shorten the generation interval and increase the speed of genetic improvement, which is more efficient than traditional pedigree-based selection methods (Sonesson and Meuwissen, 2009; Shan et al., 2021). 5.3 Evaluation and improvement of GS efficiency The genomic selection (GS) model used in grouper has shown very high accuracy. For traits like body weight and ammonia tolerance, the prediction accuracy can reach up to 96% (Shan et al., 2023). But to keep this level of accuracy over many generations, the training group and marker sets must be updated regularly (Sonesson and Meuwissen, 2009). Simulation studies show that if sibling testing is done in every generation, the accuracy stays stable. However, if testing happens less often, the accuracy drops. Using important SNP markers found through GWAS, along with fast and low-cost genotyping tools, can help lower the cost and time needed for genomic selection (GS). This makes GS more practical for use in commercial fish farms (Shan et al., 2021; 2023). Even though GS still costs more than older methods-because it needs both gene testing and trait measurements-it offers big benefits in the long run. These include faster genetic improvement and a lower risk of inbreeding (Sonesson and Meuwissen, 2009; Shan et al., 2021). 6 Case Studies in Grouper Fast-Growth Breeding 6.1 Identification of the fast-growing lineage of grouper In the breeding process of tomato grouper (Cephalopholis sonnerati), since the germplasm sources are mostly wild parents or mixed breeding models, farms often lack clear parent pairing information, resulting in bottlenecks in the genetic improvement of growth traits. To address this problem, Hsu et al. (2023) used PCR-based ISSRseq high-throughput genotyping technology to conduct assisted breeding research on fry without parental information. The study screened out 24 fastest and slowest growing individuals from a batch of more than 10 000 fry, and used SNP data to conduct genetic diversity assessment and pedigree structure analysis, confirming that the samples have high genetic differences. Through population structure division, principal component discriminant analysis (DAPC) and kinship network integration analysis, three genetic lineages were clearly identified, and one of the lineages was found to gather 92.3% of fast-growing individuals (Figure 2) (Hsu et al., 2024). This result shows that ISSRseq can not only make up for the lack of parental information, but also has the ability to divide families with high growth potential. In addition, the study also identified 53 lineage-specific molecular markers, most of which are concentrated in fast (F) and slow (S) lineages, providing a key tool for the subsequent construction of a stable genetic breeding system. 6.2 Hybrid groupers and heterosis research The natural population of grouper is limited, and hybrid breeding has become an effective means to improve its growth performance. For instance, the hybridization between striped grouper (E. fuscoguttatus) and giant grouper (E. lanceolatus) has produced several hybrid varieties with excellent growth performance. The growth rate of these hybrid fish is significantly higher than that of the parents. Studies have reported that their absolute weight growth rate can reach 1.6 times that of the mother, and their muscle yield is also better than that of the father (Bunlipatanon and Taynapun, 2017; Gong et al., 2025). Cao et al. (2024) combined full-length transcriptome sequencing with next-generation sequencing technology to deeply explore the molecular mechanism of growth advantage of hybrid grouper (Cromileptes altivelas × Epinephelus lanceolatus). The study pointed out that hybrids have a large number of growth-related differentially expressed genes (DEGs) in brain and muscle tissues, of which 15 core genes (such as PTEN, ACTC, FGFR3, etc.) play a key role in regulating the cytoskeleton and MAPK signaling pathways, especially PTENis considered to be a possible upstream regulatory factor (Figure 3) (Cao et al., 2024). Besides, hybrids are generally in an intermediate state between the parents in terms of expression levels, suggesting that their growth advantage may come from the "intermediate parent effect" of expression regulation.
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