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

Abstract

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

CLC Number:

S831.2

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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Screening of Candidate Genes of Skin Color of Black-Bone Chicken Based on Transcriptome and Proteome

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