Insights into molecular mechanisms of skin color variation in hybrid F1 of wild-type rainbow trout ? × yellow mutant rainbow trout ? through whole transcriptome and ceRNA network analysis
Rainbow trout (Oncorhynchus mykiss) is a well-known economical fish globally, and its market value and acceptance are greatly influenced by skin color. However, the molecular mechanisms underlying skin color variation in rainbow trout remains largely unknown. In this study, we compared the expression profiles of whole transcriptome in dorsal skin from wild-type (WTrt) and yellow mutant rainbow trout (YMrt) that are F1 generation of WTrt ? × YMrt ?. A total of 115 differentially expressed (DE) mRNAs, 126 lncRNAs, 18 circRNAs and 56 miRNAs were identified, and several core genes (gch1, pts, slc2all, pax7a/pax7b, dgat2, plin6 and pnpla2)   involved in pteridine and carotenoid synthesis were significantly upregulated in YMrt. Interestingly, we found that melanogenesis-related genes tyr, dct, mitfa and pmel were also notably elevated in YMrt. Functional enrichment analysis revealed some pigmentation-related GO terms and KEGG pathways, including pteridine-containing compound biosynthetic process, pigment metabolic process, melanosome, melanosome transport, tyrosine metabolism and melanogenesis. Based on competing endogenous RNA analysis, there were 25 and 21 lncRNA-miRNA-mRNA networks targeted to gch1 and mitfa, such as LOC110496571-miR-96-x-gch1, LOC110508587- miR-182-x-gch1, LOC110494316-miR-21-y-mitfa and LOC110526055- miR-182-x-mitfa. Additionally, one (novel_circ_000056), eight (including novel_circ_005436 and novel_circ_005586) and three circRNAs (novel_circ_000382, novel_circ_002592 and novel_circ_005868) were found to regulate dgat2, gch1 and mitfa by targeting 21 miRNAs. This study provides a systematic perspective on the potential functions of these DEmRNAs and ncRNAs, and lays a foundation for further study on the molecular mechanisms governing rainbow trout skin color variation. Overall design: In this study, we compared the expression profiles of whole transcriptome in dorsal skin from wild-type (WTrt) and yellow mutant rainbow trout (YMrt) that are F1 generation of WTrt ? × YMrt ?.