RNA sequencing analysis reveals that missense mutation in SOX10 is associated with iris color phenotype in quail.

To investigate the molecular mechanisms underlying the differences in iris color in quail, the transcriptome of iris tissue from black quail and Korean quail at day 10 of hatching was RNA sequenced in this study. The differentially expressed genes (DEGs) were screened, functionally annotated and enriched after the quality control and mapping of the raw data. RT-qPCR validation was performed using EIF2S3 as an internal reference gene. The screened SNPs were studied by bioinformatics analysis and iris color correlation analysis. The results showed that there were 425 upregulated genes and 364 downregulated genes in 789 DEGs. Gene Ontology (GO) enrichment analysis revealed that 139 DEGs were significantly enriched in 154 GO terms. The Kyoto Encyclopedia of Genes and Genomes enrichment results showed that the Notch signaling pathway, melanogenesis and tyrosine metabolism were associated with pigment synthesis (p < 0.05). The expression levels of the ASIP, MLPH, PMEL, TYR and SOX10 genes were significantly different in black quail iris and Korean quail iris, as verified by RT-qPCR. The SOX10 gene c.324G>C mutation, which caused the replacement of p.Glu108Asp, had a highly significant correlation with iris color in black quail and Korean quail, which may be one of the reasons for different in iris color between these two quail species.

Expression and Mutation of SLC45A2 Affects Iris Color in Quail.

Iris color is a prominent phenotypic feature of quail. To understand the mechanism of melanin deposition related to quail iris color, iris tissues were selected from Beijing white and Chinese yellow quail for transcriptome analysis. Differentially expressed genes (DEGs) associated with pigmentation were identified using RNA sequencing and validated by quantitative real-time polymerase chain reaction (RT-qPCR). The identified single nucleotide polymorphisms were studied using bioinformatics and iris color correlation analyses. A total of 485 DEGs were obtained, with 223 upregulated and 262 downregulated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. Thirty-two genes were annotated using the GO database. Three important pigment synthesis pathways (Notch signaling, melanogenesis, and tyrosine metabolism) were identified in quail iris tissue (P < 0.05). The expression levels of solute carrier family 45 member 2 (SLC45A2), tyrosinase-related protein 1, vitamin D receptor, opsin 5, and docking protein 5 were significantly different between Beijing white and Chinese yellow quail, as verified by RT-qPCR. The c.1061C>T mutation in SLC45A2, which caused a single amino acid change at position 354 (threonine to methionine), was significantly associated with iris color in Beijing white and Chinese yellow quail, and might be the main reason for the different iris colors between these two quail species.