A Comparative Analysis of the Growth Performance, Morphological Indicators, and Transcriptome Between Two Coastal Regions of China in the Mud Crab (Scylla paramamosain)

Abstract

The mud crab (Scylla paramamosain), a commercially important species in China, is widely distributed along the southeastern coast. This study compares the growth performance, morphological traits, and transcriptomic profiles of two geographically distinct populations from Sanmen County, Zhejiang (SMC) and Zhangpu County, Fujian (ZPC). Juvenile crabs collected from both regions were reared in ponds under identical conditions for 7 months. Key results showed that the SMC population exhibited significantly higher daily weight gain, specific growth rate (SGR), and propodus-to-cheliped length ratio compared to ZPC (p < 0.01 for both sexes). Transcriptomic analysis revealed 44 consistently upregulated differentially expressed genes (DEGs) in SMC individuals. Among these, Otop (Otopetrin 1), Smyd (SET and MYND domain containing), AM1159 (Cancer pagurus Cuticle protein AM1159), PPAF1 (PPAR gamma coactivator 1 α), and NARG2 (NMDA receptor regulated 2) were functionally linked to molting and growth regulation in crustaceans. Notably, two mTOR pathway-associated genes (QDPR [Quinoid dihydropteridine reductase] and NLRC 3 [NLR family CARD domain containing 3]) and several energy/nutrient metabolism genes were also upregulated in SMC. Enrichment analysis identified four active KEGG pathways in SMC: “Melanogenesis,” “Riboflavin metabolism,” “Choline metabolism,” and “Ribosome biogenesis.” These findings suggest that the superior growth performance of SMC crabs may stem from enhanced molting efficiency and nutrient allocation mechanisms. While QDPR and NLRC3 are hypothesized to mediate mTOR-driven metabolic regulation, further functional validation is required to establish their causative roles. This study provides molecular markers (Otop, Smyd, etc.) for selective breeding programs and a transcriptomic framework for understanding regional adaptation in marine crustaceans.