Comparative Transcriptomic Analysis Reveals Molecular Mechanisms Underlying Scale Adhesion Differences Between Carassius auratus indigentiaus and Carassius auratus gibelio

Scale adhesion strength is a key trait in aquaculture, directly influencing disease resistance, survival, and commercial value. The Dongting crucian carp (Carassius auratus indigentiaus, hereafter CaDT) is valued for its rapid growth and superior flesh quality but is characterized by loosely attached scales. In this study, we investigated the morphological and molecular basis underlying scale adhesion by comparing CaDT with the tight-scaled allogynogenetic gibel carp, Zhongke No. 3 (Carassius auratus gibelio, hereafter CaGB). Morphological analysis revealed a significantly lower scale-embedding ratio in CaDT compared to CaGB. To unravel the molecular mechanisms underpinning these phenotypic differences, a comparative transcriptomic analysis was conducted on scale sac, skin, and muscle tissues in CaDT and CaGB. In CaGB, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) in the critical scale sac tissue showed a significant upregulation of genes involved in ribosomal pathways. Specifically, key epithelial differentiation markers, including keratin 13 (krt13), keratin 15 (krt15), and metabolic genes, enolase 3-like (eno3l), and phosphoglycerate mutase 2 (pgam2) were significantly down-regulated in CaDT, which suggests a compromised epithelial cell differentiation capacity and reduced energetic and biosynthetic activity. Quantitative PCR (qPCR) validation across three tissues showed high concordance with the RNA-seq results, thereby confirming the reliability of the transcriptomic data. The results offer insight into the molecular basis for understanding scale adhesion traits, and provide valuable insights for selective breeding strategies to improve scale retention in aquaculture species.