International Journal of Aquaculture, 2025, Vol.15, No.5, 229-239 http://www.aquapublisher.com/index.php/ija 236 7 Comprehensive Strategy of Combining QTL and GWAS 7.1 Multiomics joint analysis methods (genomics, transcriptomics, epigenetics) One of the development directions of modern molecular breeding is to integrate different "omics" information and build a comprehensive trait regulation network. For shrimp growth traits, it is often difficult to fully explain the genetic mechanism by relying solely on a single QTL or GWAS, so data from multiple angles such as genomics, transcriptomics, and epigenetics need to be combined (Zhang et al., 2022). A successful case is Chen et al. (2024) combining traditional QTL analysis with transcriptome expression QTL (eQTL) to discover STEAP4, a hidden key gene. They determined the differentially expressed genes of fast-growing shrimp through the transcriptome, and then screened the differentially expressed genes within the QTL interval, and finally locked in STEAP4 and verified with RNA interference. This QTL+ transcriptome strategy greatly improves the efficiency and accuracy of candidate gene discovery and also provides examples for other traits. For non-modal species such as shrimp, multiomic association also facilitates functional annotation and pathway analysis. Since shrimp genome annotation is not as perfect as model organisms, the transcriptome can determine which genes in the QTL interval are expressed in the target tissues, and the locations of important regulatory elements can be found through ATAC-seq, etc., and the dispersed genes can be integrated into a collaborative network through co-expression analysis (Zhao et al., 2020). This information can help researchers identify the "core" gene nodes that truly drive traits in massive correlation signals. In addition, multiomics combination also provides tools for the study of hybridization advantages and interaction effects. 7.2 Advantages of combining QTL and GWAS in precision breeding Combining genetic analysis methods such as QTL and GWAS can give full play to the effect of complementary advantages in breeding practice, thereby promoting precise breeding. First, QTL studies are usually conducted at the family level, and can use high heritability to find main effect sites, but are limited to specific parent combinations; GWAS searches for natural variant influence traits at the population level, and the results are more applicable (Banka et al., 2024), but are more sensitive to small effect sites. By combining the two, on the one hand, the reliability of QTL positioning can be verified through GWAS, and on the other hand, the QTL results can be used to guide GWAS screening. For example, when QTL is located in a certain chromosomal region, focus on the apical signal in that region in GWAS, reducing the burden on multiple tests, and thus making it easier to reach significant levels. Secondly, in the prediction of breeding value, fusion QTL markers and genome-wide markers also have advantages. In actual breeding, several large-effect markers can be locked according to the GWAS results to implement MAS to quickly eliminate families with obvious slow growth, and then use genome-wide breeding value prediction (GBLUP, etc.) to make fine selections (Altaf and Tatar, 2024). This two-stage selection utilizes efficient screening of GWAS and comprehensive accuracy of genome-wide selection, allowing for better genetic gain than using one method alone. Combining QTL and GWAS helps resolve genetic architectures of complex traits, thereby developing multitrait improvement strategies (Francisco et al., 2021). Growth traits tend to be genetically related to other traits, such as growth and survival may be negatively correlated. 7.3 Future prospects for genetic improvement of shrimp Looking ahead, shrimp genetic improvement will enter a new era driven by molecular technology. Driven by studies such as QTL and GWAS, the genetic basis of our shrimp growth traits is gradually becoming clear. This provides a scientific basis for formulating a new generation of breeding programs. Molecular marker assisted selection (MAS) will be more widely used in shrimp breeding fields. Once the key site effect is verified, breeders can use molecular marker screening at the larval stage to accelerate the turnover of generations and improve the breeding accuracy. Meanwhile, genome-wide selection (GS) is expected to be carried out in large breeding companies. As mentioned earlier, SNP chips and supporting analysis methods have been developed in China. Combined with the characteristics of large reproduction and large family size of shrimps, as long as investment is guaranteed, GS can significantly improve the genetic progress rate. In addition to growth itself, future breeding goals will become more diverse, such as disease resistance, hypoxia resistance, high-quality meat quality, etc.
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