Comparative skin transcriptome between common carp and the variety Jinbian carp (Cyprinus carpiov. jinbian)

Abstract

Jinbian carp, a variety of common carp (Cyprinus carpio v. jinbian) with black skin colour and two yellow stripes on both sides of its dorsal fin, has become a popular economic fish species as an edible delicacy and for its unique coloration. However, the genetic background of Jinbian carp is not well documented and the molecular mechanism of the yellow or black colour variation of the skin of this fish is not yet clear. Therefore, it is essential to understand the molecular mechanism of colour variation using advanced technology. In this study, using wild and Jinbian common carp as experimental materials, we performed RNA sequencing transcriptomic analysis with regard to the yellow and black skin colour in these fish. As a result, we identified 162 differentially expressed genes (DEGs) between yellow (Y) and black (B) skin derived from the same Jinbian carp and 2,475 DEGs between yellow skin in Jinbian carp (Y) and black skin in wild common carp (W). Gene functional analysis revealed that most of DEGs were involved in pigmentation-related and metabolic pathways, among which we mainly focused on the cGMP-PKG signalling pathway and adrenergic signalling in the cardiomyocyte pathway. In addition, our transcriptome results suggested that genes associated with cysteine metabolism, including scavenger receptor cysteine-rich type 1 protein M130 (CACNA1E), cysteine N-palmitoyltransferase HHAT-like protein (HHATL) and soluble scavenger receptor cysteine-rich domain-containing protein (SSC5D) could serve as candidate genes for colour variation in Jinbian carp. In conclusion, our results identify candidate genes and potential pathways involved in colour variation and provide useful genetic information for further breeding of Jinbian carp.