Integrative mRNA-miRNA interaction analysis reveals the molecular mechanism of skin color variation between wild-type and yellow mutant rainbow trout (Oncorhynchus mykiss).

Rainbow trout (Oncorhynchus mykiss) is an important economic fish in China. Skin color affects the economic value of trout. However, the molecular mechanism of the skin color variation between wild-type (WR) and yellow mutant rainbow trout (YR) is unclear. We sequenced mRNAs and miRNAs of dorsal skin to identify key color variation-associated mRNAs and miRNAs between WR and YR. Overall, 2060 out of 3625 differentially expressed genes were upregulated in YR, and 196 out of 275 differentially expressed miRNAs were downregulated in WR. We identified three key YR-upregulated genes related to the formation of xanthophores (GCH1 , SLC2A11 , and SOX10). Interestingly, several genes related to melanogenesis (TYR , TYRP1 , TYRP2 , MC1R , MITF , PMEL , SLC45A2 , and OCA2) were downregulated in WR. Integrated analysis identified five miRNAs that target at least two skin color-related genes (miR-495-y, miR-543-y, miR-665-z, miR-433-y, and miR-382-x). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of target genes identified noncoding RNA metabolic process as the most significantly enriched GO term, and several metabolic pathways associated with skin color were enriched significantly, such as tyrosine metabolism, histidine metabolism, and vitamin B6 metabolism. Quantitative real-time PCR of selected mRNAs and miRNAs validated the reliability of the integrated analysis. This study provides in-depth insights into the molecular mechanism of skin color variation between WR and YR, which will accelerate the genetic selection and breeding of rainbow trout with consumer-favored traits. [Display omitted] • Comparative mRNA and miRNA expression was firstly conducted to identify key mRNAs and miRNAs that may be responsible for skin color variation between wild-type and yellow mutant rainbow trout. • Three key positive genes in the formation of xanthophores and several important genes related to melanogenesis were all up-regulated in yellow mutant rainbow trout. • Five miRNAs were identified that target at least two skin color related genes. • Several metabolic pathways related to skin color were significantly enriched. [ABSTRACT FROM AUTHOR]