Transcriptome-based studies on the candidate genes related to body color yellowing in channel catfish (Ictalurus punctatus)

This experiment was aimed to screen the key factors regulating pigment cells and elucidate the potential mechanism of yellowing body color in the channel catfish. Three-channel catfish with all-black body color (NS group) and three channel catfish with yellow body color (YS group) were taken for transcript sequencing analysis using Illumina sequencing technology. The results showed that a total of 2368 significant differentially expressed genes (DEGs) were screened. Compared with the transcription expression genes in the NS group, there were 1003 up-regulated genes and 1365 down-regulated genes in the YS group. Seven DEGs related to pigment regulation were selected for qRT-PCR analysis, and the results confirmed that the transcriptome analysis was reliable. Furthermore, the DEGs were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and the results showed that most of the DEGs were involved in immune response, endocytosis, cell adhesion molecules, etc. Furthermore, analysis of Melanogenesis and Wnt signaling pathways and other pathways with links to pigment regulation obtained by KEGG enrichment revealed that genes that promote melanogenesis, such as etb, plc, and camk2 were significantly down-regulated. Nevertheless, genes that inhibit melanogenesis (nf-κb, tnf-α, ifn) and genes that promote yellow pigmentation (xdh) were significantly up-regulated. In summary, it is hypothesized that oxidative stress is an important factor contributing to the yellowing of the body color of channel catfish, thus causing the expression of genes related to melanogenesis (etb, plc, camk2), yellow pigmentation (xdh), and immune-antioxidant responses (nf-κb, tnf-α, ifn). •Transcriptional analysis of many DEGs between yellowing channel catfish and all-black channel catfish.•A total of 2368 DEGs were identified, out of which 1003 genes were upregulated and 1365 genes were downregulated.•Oxidative stress is an important factor contributing to the yellowing of the body color of channel catfish.