Functional Analysis of NdBCO-like4 Gene in Pigmentation of Neocaridina denticulata sinensis

Cherry shrimp (Neocaridina denticulata sinensis) is one of the main ornamental shrimp because of its bright body color. β, β-carotene 9′,10′-dioxygenase (BCO2) is closely related to the body color produced by carotenoids. In order to study the role of NdBCO-like4 (homologous gene of BCO2) in the pigmentation of cherry shrimp, the expression profiles, RNA interference, and SNP genotyping were applied in this study. The NdBCO-like4 expression varied significantly among four color strains and five development stages (p < 0.05). The results showed that the NdBCO-like4 expression was the highest in the red strain and the lowest in the wild strain. During the embryonic development, the expression in the metanauplius stage was significantly lower than other stages (p < 0.05), and the expression of NdBCO-like4 was the highest in the membrane-zoea stage. In the metanauplius stage, the RNAi knockdown of NdBCO-like4 mediated the red pigment brightness value, and the pigment cell index in the treatment group was significantly lower than the control group (p < 0.05). After the first round of screening, a total of 8424 high-quality SNPs were obtained. There was one candidate SNP located on the NdBCO-like4 target gene, named G.1719G>A. The synonymous SNP exhibited significantly different genotype frequencies between the yellow and wild strains compared to other strains (p < 0.05), suggesting an association with these phenotypes. These results suggest that NdBCO-like4 has a close relation with carotenoid accumulation in cherry shrimp, providing valuable insights into the molecular mechanisms underlying pigmentation in this species.