基于转录组和蛋白组筛选乌骨鸡肤色性状候选基因

doi:10.11843/j.issn.0366-6964.2023.06.012

摘要/Abstract

摘要： 旨在基于转录组和蛋白组的联合分析,筛选影响乌骨鸡肤色性状的候选基因。本研究在HW1系黑羽乌骨鸡群体中选取150日龄的6只白肤个体和6只乌肤个体分为两组(white skin,WS和black skin,BS)作为试验样本,采集胸部皮肤组织,提取RNA和蛋白,进行高通量转录组测序(RNA-Seq)和蛋白组定量分析,筛选差异表达基因(differentially expressed genes, DEGs)和差异表达蛋白(differentially expressed proteins, DEPs),并对其进行实时荧光定量PCR(RT-qPCR)验证、功能富集分析和蛋白互作网络的构建与分析,进一步筛选与乌骨鸡肤色性状相关的候选基因。结果显示,转录组共鉴定到293个DEGs,蛋白组共鉴定到4个DEPs,其中重叠的基因有CRP、DCT、GPNMB。随机选择5个DEGs进行RT-qPCR验证,表达趋势与测序结果一致。富集分析表明,DEGs和DEPs显著富集在71个GO条目和4个KEGG通路中,包括黑素细胞分化、黑素体、黑素体膜和黑素原生成通路。接下来,通过Cytoscape软件的cytoHubba插件捕获到来自DEGs和DEPs构建的蛋白互作网络里的10个Hub基因,这些基因主要显著富集在免疫相关GO条目和通路中。进一步发现Hub基因与黑色素相关基因可构成两个子网络,这两个子网络可通过PTPRC、SOX10、GPNMB、CRP基因连接在一起。本研究最终筛选到11个乌骨鸡肤色性状相关的候选基因(SOX10、EDN3、EDNRB2、MLANA、OCA2、DCT、GPNMB、ASIP、RAB38、PTPRC、CRP),其可能在黑色素合成中起关键作用。总之,该研究可为今后探究乌骨鸡肤色性状的分子调控机制和分子育种改良提供理论依据。

关键词: 乌骨鸡, 肤色, 转录组, 蛋白组, 黑色素, 蛋白互作网络

Abstract: This study aimed to screen the candidate genes affecting skin color of Black-bone chicken based on the combination of transcriptome and proteome analysis. Six white skin (WS) chickens and six black skin (BS) chickens at 150 days of age were selected from HW1 Black-feather Black-bone chicken population in this study. Total RNA and protein were extracted from breast skin tissue, high-throughput transcriptome sequencing (RNA-Seq) and proteomics quantification analysis were performed. Next, the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with the skin color of Black-bone chicken were identified, and several DEGs were further verified by real-time fluorescent quantitative PCR (RT-qPCR). Finally, the candidate genes related to skin color trait of Black-bone chicken were further screened by combining functional enrichment analysis and protein-protein interaction network (PPI) analysis. The results showed that 293 DEGs were identified in the transcriptome and 4 DEPs were identified in the proteome, among which the overlapping genes were CRP, DCT and GPNMB. We then randomly validated 5 DEGs using RT-qPCR, which showed that RT-qPCR gene expression results were consistent with RNA-seq results. Enrichment analysis indicated that these DEGs and DEPs were significantly enriched in 71 GO terms and 4 KEGG pathways, including melanocyte differentiation, melanosome, melanosome membrane, and melanogenesis pathways. Subsequently, 10 Hub genes were captured by the cytoHubba plug-in of Cytoscape software from the PPI network constructed by DEGs and DEPs, and these genes were mainly enriched in immune-related GO terms and pathways. It was further found that Hub genes and melanin-related genes constituted two sub-networks, among which PTPRC, SOX10, GPNMB and CRP genes connected the two sub-networks. In all, 11 candidate genes related to skin color trait of Black-bone chicken were screened, including SOX10, EDN3, EDNRB2, MLANA, OCA2, DCT, GPNMB, ASIP, RAB38, PTPRC, CRP, which may play an important role in melanin synthesis process. In summary, this study provides a theoretical basis for the future exploration of the molecular regulation mechanism and the improvement of molecular breeding in Black-bone chicken skin color traits.

Key words: Black-bone chicken, skin color, transcriptome, proteome, melanin, protein-protein interaction network

中图分类号:

S831.2

刘航, 王欢欢, 葛莹, 张雷, 张伟武, 魏莹晖, 李庆海, 范京辉, 章学东. 基于转录组和蛋白组筛选乌骨鸡肤色性状候选基因[J]. 畜牧兽医学报, 2023, 54(6): 2320-2329.

LIU Hang, WANG Huanhuan, GE Ying, ZHANG Lei, ZHANG Weiwu, WEI Yinghui, LI Qinghai, FAN Jinghui, ZHANG Xuedong. Screening of Candidate Genes of Skin Color of Black-Bone Chicken Based on Transcriptome and Proteome[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2320-2329.

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