基于皮肤组织转录组学和蛋白质组学测序揭示影响羊毛性状的关键基因  

Revealing The Key Genes Affecting Wool Traits on The Basis of Skin Tissue RNA-seq and Proteome Sequencing

作　　者：吴晋强 郝晓静 赵红霞[1] 董亚洁 王荣 张鹏翔 王海东[1] 赫晓燕[1] WU Jin-Qiang;HAO Xiao-Jing;ZHAO Hong-Xia;DONG Ya-Jie;WANG Rong;ZHANG Peng-Xiang;WANG Hai-Dong;HE Xiao-Yan(College of Animal Medicine,Shanxi Agricultural University,Taigu 030801,China)

机构地区：[1]山西农业大学动物医学学院,太谷030801

出　　处：《生物化学与生物物理进展》2023年第3期606-622,共17页Progress In Biochemistry and Biophysics

基　　金：supported by grants from The National Natural Science Foundation of China(31772690);the Natural Science Foundation of Shanxi Province(201701D121106)。

摘　　要：目的羊毛是高档纺织原料,羊毛的物理性质直接关系到羊毛品质。本研究旨在挖掘影响羊毛性状的基因,探索影响羊毛性状的复杂分子机制。方法本研究选取萨福克羊和小尾寒羊各3只作为试验样本,取背部皮肤组织,采用转录组学(RNA-seq)和蛋白质组学测序分析造成羊毛性状差异的基因、蛋白质及相关信号通路。结果转录组测序表明:测序完成后,共得到230406674个原始数据和222049370个干净数据,其中Q20碱基百分比为99.9%以上,Q30碱基百分比为98%以上。以差异倍数FC≥1.4或FC≤0.714且P<0.05作为标准,由此筛选出1213个差异表达基因(DEGs),其中萨福克羊与小尾寒羊相比,上调基因有644个,下调基因有569个。GO富集发现中间丝、钙离子结合、角蛋白丝显著富集,表明其可能与羊毛性状相关。KEGG富集发现,影响羊毛性状的信号通路可能是ECM-受体相互作用。蛋白质组测序表明:以差异倍数FC≥1.4或FC≤0.714且P<0.05作为标准,由此筛选出99个差异表达蛋白(DEPs),其中萨福克羊与小尾寒羊相比,上调蛋白有47个,下调蛋白有52个。GO富集发现中间丝等显著富集,表明其可能与羊毛性状相关。KEGG富集发现,影响羊毛性状的信号通路可能是过氧化物酶体增殖物激活受体(PPAR)信号通路和ECM-受体相互作用。转录组与蛋白质组联合分析发现:转录组和蛋白质组均检测到的显著差异基因共有15个,其中13个为正相关,2个为负相关。中间丝显著富集,其中涉及的KRT35、KRT13、KAP13-1-like基因可能是影响羊毛性状的关键候选基因,PPAR信号通路显著富集,可能是影响羊毛性状的关键候选通路,FABP4基因可能是影响羊毛性状的关键候选基因。结论KRT35可能影响羊毛直径和弯曲;KRT13可能影响羊毛分化;KAP13-1-like可能影响羊毛硬度和韧性;FABP4可能影响羊毛直径。这些结果将扩展对影响绵羊羊毛性状的复杂分子机制的理解,并Objective Wool is a high-grade raw textile material,and the physical properties of wool are directly related to the quality of the wool.The present study was to search for the genes affecting wool traits and to explore the complex molecular mechanism affecting wool traits.Methods This study selected 3 Suffolk sheep and 3 small-tailed Han sheep and took samples of their back skin tissue using RNA sequencing(RNA-seq)and proteome sequencing analysis of genes,proteins,and related signalling pathways that cause differences in wool traits.Results RNA-seq showed that after sequencing,230406674 raw data points and 222049370 clean data points were obtained,of which the percentage of Q20 bases was over 99.9%,and the percentage of Q30 bases was over 98%.With a fold change(FC)≥1.4 or FC≤0.714 and P<0.05 as the standard,1213 differentially expressed genes(DEGs)were screened out,among which there were 644 upregulated genes and 569 downregulated genes in Suffolk sheep in comparison with small-tailed Han sheep.The gene ontology(GO)enrichment found that intermediate filament,calcium ion binding,and keratin filament were significantly enriched,indicating that they might be related to wool traits.The Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment found that the signalling pathway affecting wool traits might be the ECM-receptor interaction.Proteome sequencing showed that with FC≥1.4 or FC≤0.714 and P<0.05 as the standard,99 differentially expressed proteins(DEPs)were screened out,among which there were 47 upregulated proteins and 52 downregulated proteins in Suffolk sheep in comparison with small-tailed Han sheep.The GO enrichment found that intermediate filament was significantly enriched,indicating that it might be related to wool traits.The KEGG enrichment found that the signalling pathways affecting wool traits might be the peroxisome proliferator-activated receptor(PPAR)and the ECM-receptor interaction.A combined analysis of RNA-seq and proteome sequencing found that a total of 15 significantly different genes

关 键 词：转录组测序 蛋白质组测序 萨福克羊 小尾寒羊 羊毛性状 

分 类 号：R318[医药卫生—生物医学工程] Q38[医药卫生—基础医学]