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

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Accounts of Chemical Research Pub Date : 2023-10-31 DOI:10.1111/age.13371

Shiwei Ren, Xiaohui Zhang, Youzhi Pang, Yanxia Qi, Linke Huo, Fanghu Wu, Yuanyuan Shang, Jinquan Xi

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Abstract

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.

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RNA测序分析表明SOX10的错义突变与鹌鹑虹膜颜色表型有关。

为了研究鹌鹑虹膜颜色差异的分子机制，本研究对孵化第10天黑鹌鹑和韩国鹌鹑虹膜组织的转录组进行了RNA测序。在对原始数据进行质量控制和绘图后，对差异表达基因（DEGs）进行筛选、功能注释和富集。使用EIF2S3作为内部参考基因进行RT-qPCR验证。通过生物信息学分析和虹膜颜色相关性分析对筛选出的SNPs进行研究。结果表明，789个DEG中有425个上调基因和364个下调基因。基因本体论（GO）富集分析显示，139个DEG在154个GO术语中显著富集。京都基因和基因组百科全书的富集结果表明，Notch信号通路、黑色素生成和酪氨酸代谢与色素合成有关（p 引起p.Glu108Asp替换的C突变与黑鹌鹑和韩国鹌鹑的虹膜颜色具有高度显著的相关性，这可能是这两种鹌鹑虹膜颜色不同的原因之一。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.

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