International Journal of Aquaculture, 2025, Vol.15, No.2, 45-56 http://www.aquapublisher.com/index.php/ija 47 applications. One of the important directions is the development of CRISPR systems for different enzymes, such as Cas12a, Cas13, etc. Cas12a not only provides different PAM selection and viscous ends in DNA editing, but also its unique non-specific single-strand DNA degradation activity after cleavage is used in diagnostic fields such as rapid nucleic acid detection (such as novel coronavirus detection) in vitro (Agha et al., 2025). Cas13 acts on RNA and can be used to target degrade specific transcripts and achieve reversible gene silencing. It is known as the "molecular scalpel". There are also Cas protein-based transposase systems (such as Castro) that are exploring for insertion of larger fragments of DNA. Base editing is another revolutionary improvement in the field of CRISPR. The researchers fuse inactivated Cas9 (dCas9) with cytosine deaminase to construct CBE (cytosine base editor), which can convert specific bases C→T without cutting off DNA. Then there is ABE fusion with adenine deaminase to achieve A→G mutation. The latest original editing is even more powerful. Based on dCas9 fusion reverse transcriptase, it carries the editing template at the same time through a guide sequence to achieve multiple types of point mutation, insertion or deletion editing, which theoretically covers most mutation types. These precision editing tools are of great significance in the medical field and have the potential to improve complex traits of multigene control for aquaculture because they can accurately rewrite functional sites without introducing additional changes. 3 Progress in Genomic Characteristics and Research of Shrimp 3.1 Complexity of shrimp genome and its current sequencing status The genome of crustaceans is generally large and complex, and shrimp are no exception. Taking the currently dominant breeding of vannamei prawns (Litopenaeus vannamei), the diploid genome size is about 1.66 Gb and the encoding genes is about 25,596. The shrimp genome contains a large number of repeat sequences and microsatellites (Simple Sequence Repeats (SSRs), and it is reported that the proportion of repeat sequences exceeds 23%. High proportions of repetition and AT-rich complex regions increase the difficulty of genome assembly, often resulting in unsubsidized or omitted sequence fragments. It was not until the development of high-throughput sequencing and assembly algorithms in recent years that the whole genome sequencing of shrimps has made breakthrough progress. In 2019, Zhang Xiujuan and other research teams used three-generation sequencing (PacBio long reading and length technology) to construct the high-quality sketch genome of South American white shrimp for the first time, with N50 length reaching 0.605 Mb, which was a high level at that time. Subsequently, by introducing Hi-C assisted construction of chromosome-level assembly, tens of thousands of fragments were further anchored to 44 chromosomes, increasing Contig N50 to 42.89 Mb and genome coverage reached ~84.6% (Liao et al., 2025). 3.2 Identification of major economic traits related genes in shrimp The acquisition of genomic information makes it possible to locate genes that affect the importance of shrimp from a global perspective. In the shrimp farming industry, growth rate, disease resistance, environmental tolerance and reproductive ability are key traits that directly determine yield and profit. In recent years, through genome-wide association analysis (GWAS), quantitative trait loci (QTL) analysis and candidate gene methods, researchers have identified a batch of gene markers related to these traits. In terms of growth traits, Yu et al. conducted a genome scan of vannabinoid shrimp and found that several genomic regions were significantly related to growth traits. One of the prominent candidate genes is MMD2 (a protein related to fungal macrophage migration inhibitor), and subsequent functional studies have shown that the variation of this gene is closely related to shrimp growth differences (Bu et al., 2025). In terms of disease resistance, studies have found that certain microsatellite lengths in the vannabinoid shrimp genome are related to antiviral manifestations: individuals carrying shorter repeats show higher resistance to leukoplakia and iridescent viruses (Yin et al., 2023). This suggests that there are natural disease-resistant alleles in the shrimp population, which can be assisted in breeding through molecular markers. In terms of environmental tolerance, genes have also been reported. The study found that the SNP polymorphism of the Catalase gene of vannerbine shrimp is related to hypoxia tolerance. Some heat shock proteins and osmotic regulation-related genes have been shown to be upregulated in high-salt stress responses, suggesting that they may be involved in salt-tolerant traits (Luo et al., 2022). In terms of reproduction
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