Differential gene expression in the intestines of Chinese mitten crabs with three carapace colors.

Background: Carapace color in Chinese mitten crab (Eriocheir sinensis) influences both commercial value and physiological traits, yet its molecular basis remains unclear. The intestine plays a key role in pigment absorption and metabolism, but its involvement in pigmentation has been understudied. This study aimed to investigate intestinal gene expression differences among red, white, and green carapace strains.

Methods and results: We sequenced intestinal RNA from red, white, and green morphs (n = 3 per group) on an Illumina NovaSeq platform. Following fastp quality control and Salmon quantification, 6,214 genes were identified as differentially expressed (|log2FC| ≥ 1, FDR < 0.05). Functional enrichment linked these genes to pigment transport and biosynthesis pathways, including ABC transporters, SLC carriers, carotenoid binding, and tyrosine metabolism. Seven representative DEGs (CRCN‑A1, CRCN-A2, ABCC4, ABCF1, slc23a1, slc49a4, TYROB) were validated by qRT‑PCR, with expression trends congruent to RNA‑seq results.

Conclusion: Intestinal gene expression contributes to carapace pigmentation through distinct carotenoid‑transport and melanin pathways. These insights offer molecular targets for selective breeding and functional validation.