Integrative QTL Mapping and Transcriptomic Profiling Identify Growth-Associated QTL and Candidate Genes in Hong Kong Catfish (<em>Clarias fuscus</em>)

Growth traits are critical economic characteristics in aquaculture. This study aimed to identify candidate genes associated with the growth of C. fuscus by integrating QTL mapping for growth traits and RNA-seq analysis of differentially expressed genes (DEGs) between two extreme body size groups (big-sized group and small-sized group). QTL mapping was performed on eight growth traits—body weight, body height, body length, body width, orbital diameter, caudal peduncle length, caudal peduncle height, and pre-dorsal length—using 200 individuals from a full-sibling line. Seventeen growth-related QTL loci were identified across 8 linkage groups, explaining phenotypic variance ranging from 8.00% to 11.90%. A total of 162 functional genes were annotated within these QTL intervals. RNA-seq analysis identified 3,824 DEGs between the big-sized and small-sized groups, with 2,252 genes upregulated and 1,572 downregulated in the big group. By integrating QTL mapping and RNA-seq data, 27 candidate genes were identified, including myostatin (mstnb), epidermal growth factor receptor (egfr), and sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (serca1). These findings provide crucial insights into the genetic regulation of growth in C. fuscus and lay a foundation for future genetic selection strategies.