Abstract

Sea cucumber ( Apostichopus japonicus ) displays considerable variation in growth rates under the same cultivation conditions, with a subset of individuals displaying a “growth stagnation” phenotype. After one year of laboratory cultivation from the same breeding population, normally growing (NG) individuals of A. japonicus averaged 38.02 ± 3.36 g, whereas stunted-growing (SG) individuals averaged 2.02 ± 0.360 g. To investigate the molecular basis of this growth divergence, transcriptomic profiling was performed on the body wall tissues of NG and SG individuals. A total of 816 differentially expressed genes (DEGs) were identified, including key genes related to growth, muscle function, motility, and cytoskeletal organization. NG individuals showed upregulation of growth-promoting genes such as HGFR and RAS . Whereas SG individuals exhibited significant upregulation of genes associated with muscle and cytoskeletal structure, including ACTG1 , MYHC , TITIN , and FLNB , reflecting compensatory or disordered activation rather than productive growth, as further supported by histological observations of abnormal muscle tissue. Furthermore, traditional Chinese medicine compounds, including Imperatae Rhizoma and Hedysarum multijugum Maxim , were identified as potential modulators of HGFR and RAS signaling. These findings provide new insights into the regulation of growth in A. japonicus and may lay the foundation for developing herbal-based strategies to mitigate growth retardation.