International Journal of Aquaculture, 2025, Vol.15, No.1, 29-36 http://www.aquapublisher.com/index.php/ija 33 6 Advances in QTL Mapping and Association Analysis 6.1 Quantitative trait loci (QTL) mapping for muscle growth traits Quantitative trait loci (QTL) localization is an important means to reveal the genetic basis of complex traits. Muscle-related QTL has been reported in freshwater fish such as tuna and bass. For example, in rainbow trout, researchers found QTLs related to muscle yield on chromosomes 14 and 16, which could explain up to 28.4% of phenotypic variation. In addition, a 7-month-old fish weight QTL detected in the same study was located on chromosome 9, explaining about 1.5% of the variation (Blay et al., 2021). Similarly, multiple pairs of QTL regions related to body weight and meat quality have also been found in other breeding fish species such as salmon and bass. These results indicate that growth traits are usually regulated by multiple genes, and QTL studies provide important clues for candidate gene screening. 6.2 Genome-wide association studies (GWAS) for flesh quality traits In recent years, with the development of high-throughput genotyping technology, genome-wide association research (GWAS) has been used to genetic analysis of fish meat traits. For example, in Atlantic salmon, GWAS analysis identified multiple loci on chromosomes 13, 18, and 20 related to muscle yield (bone loss yield) and found QTLs related to muscle fat content on chromosomes 9 and 10 (Blay et al., 2021). These findings suggest that specific chromosomal regions may contain key genes that affect fat deposition and muscle growth. Through GWAS, more accurate genetic markers can be identified at the population level, providing a basis for breeding plans for species such as bamboo shoots, shellfish, etc. 6.3 Candidate gene screening and functional validation Based on QTL and GWAS results, candidate genes in the associated region can be screened and functionally verified. Common muscle growth candidate genes include IGF1, GH receptors, myogenic regulators, etc. In addition, emerging candidate genes such as collagen family, muscle protein degradation enzymes and fat metabolic enzymes have also been concerned. The emergence of gene editing technologies such as CRISPR/Cas9 has provided convenience in verifying the function of candidate genes. For example, after targeted knockout of the MRF4 gene in tilapia, relevant studies have shown that the expression of the downstream myogenin factor Myogenin has almost doubled (Sukhan et al., 2024), demonstrating the regulatory effect of this gene on muscle development. This type of research model will have potential application value in bamboo shoot shell fish breeding. 7 Environmental and Nutritional Influences on Gene Expression 7.1 Effects of feed composition and nutritional regulation Feed nutritional composition has a significant effect on fish muscle growth and meat quality. For example, in the study of grass carp, the effects of forage and artificial feed were compared, and it was found that individuals who were raised in forage were larger in diameter, higher in muscle density, and tighter in meat; while the artificial feed feed group deposited more body fat and loose muscle tissue structure (Zhao et al., 2018). In addition, experiments on increasing the phosphorus content in feed showed that appropriate increase in phosphorus content can significantly improve the protein content and water-holding properties of grass carp muscles. These studies show that different feed formulas affect muscle mass by regulating metabolic pathways and gene expression levels. For bamboo shoot shellfish, optimizing the proportion of protein, fat and minerals, as well as supplementing specific functional nutrients (such as collagen or feed additives that induce muscle growth) may effectively improve growth performance and meat quality. 7.2 Impact of environmental factors such as temperature and dissolved oxygen Environmental conditions such as water temperature and dissolved oxygen will affect muscle growth and quality by affecting metabolic rate and stress levels. Higher water temperatures usually speed up metabolism and promote growth rates, but excessive or fluctuating temperatures can cause stress and affect muscle fiber development. Conversely, a low temperature environment may prolong the growth cycle but may increase the muscle fiber density. Insufficient dissolved oxygen can cause hypoxia stress, induce expression changes of related genes (such
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