International Journal of Marine Science, 2025, Vol.15, No.3, 167-178 http://www.aquapublisher.com/index.php/ijms 170 response genes of abalone, including the heat shock protein family HSPs, the ubiquitin-proteasome system, etc., which were consistently upregulated in heat stresses in multiple species (Zhang et al., 2022). These genes have become important candidate targets for improving thermal resistance of abalone. Similarly, by comparing the gene expression of disease-resistant and susceptible lines, several immune-related candidate genes can also be screened out, such as pattern recognition receptors, antimicrobial peptides, etc. 3.3 Analysis of the association between phenotypic traits and genetic markers Association analysis is a method to use natural variation at the population level to detect the association between traits and genotypes. In abalone, due to the lack of a large number of pure varieties and systematic breeding pedigrees, association analysis is usually based on high-density molecular marker data from population or family. High-throughput sequencing produces SNP markers are widely used in abalone association analysis and genome selection studies. Taking the thermal resistance trait as an example, Korean scholars genotyped a group of variegated abalone populations, and used GWAS analysis to detect multiple SNP sites related to high temperature resistance survival rates, which explained about 8% of the phenotypic variations in total (Lin et al., 2022). In addition to quantitative traits, qualitative traits such as shell color and markings were also correlated analysis in abalone. The membrane pattern separation of the tripartite hybrid abalone coat mentioned above, that is, through correlation analysis, it was found that a region on chromosome 15 had a very significant impact on the marking phenotype. This discovery enables subsequent use of molecular markers to predict shell color marks of hybrid progeny and improve breeding selection efficiency. In addition, association analysis is also applied to growth and reproductive traits. 4 Application of Abalone Genomics and Omics Tools 4.1 Current status of abalone genome sequencing and annotation The genome of molluscs of abalone is relatively large and contains a high proportion of repeat sequences. However, the development of sequencing technology in recent years has promoted a breakthrough in sequencing of abalone genome. In 2017, researchers released the first genome sketch of Haliotis discussion hannai, with a total length of about 1.3 Gb and more than 23 000 genes encoding. Subsequently, the genomes of multiple species have been cracked one after another, especially in recent years, three-generation sequencing and Hi-C technology have been used to construct high-quality chromosomal-level abalone genomes (Figure 1) (Barkan et al., 2024). In terms of genomic annotation, a large number of genes and pathways related to traits are predicted in these sequences. Taking the Ezo abalone genome as an example, the annotation reveals that there are significantly amplified families of immune genes in its genome, such as detoxification enzymes, heat shock proteins, etc., which are related to the abalone's ability to adapt to environmental stress. The identification of candidate genes that affect shell color and growth (such as the matrilin gene associated with pearl formation) in the South African abalone genome provides clues to explain differences in morphological traits. It is worth mentioning that the Chinese scientific research team also conducted genome research on hybrid abalones. Zhao et al. used ternary hybrid abalone to construct the hybrid genome and compared the parent genome. They found that some fragments in the hybrid abalone genome have genetic contributions that tend to be biased towards a certain parent, which may explain the molecular basis of hybridization advantages (Zhao et al., 2023). 4.2 Application of transcriptomics in trait variation research By analyzing gene expression profiles, transcriptomics can directly reflect the relationship between trait phenotype and gene expression regulation. In the study of abalone trait variation, transcriptome sequencing (RNA-Seq) has become a common tool. Many transcriptome studies targeting specific traits reveal key genes and pathways. For example, in order to understand the anti-thermal mechanism of abalone, there have been several transcriptome studies at home and abroad comparing the expression changes of abalone tissue before and after heat stress treatment. Tripp-Valdez et al. conducted integrated analysis of the heat-stress transcriptomes of 7 abalone species and 3 hybrid species, and identified 74 differentially expressed genes that recurred in at least 7 studies, among which the majority of genes in HSP, ubiquitin-proteasome and protein folding processing pathways. These core genes are considered conservative elements of abalone's heat stress response and have
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