Genes influencing deposition of melanin in breast muscle of the Xuefeng black bone chicken based on bioinformatic analysis.

IF 2.3 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Genome Pub Date : 2023-08-01 DOI:10.1139/gen-2022-0090
Mingming Xu, Shengguo Tang, Xu Liu, Yuying Deng, Changqing He, Songchang Guo, Xiangyong Qu
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引用次数: 1

Abstract

The Xuefeng black bone chicken (XFBC) represents an important poultry genetic resource. However, the darkness in breast muscle is heterogeneous. The molecular genetic mechanisms underlying melanogenesis of breast muscle in XFBC remains unclear. This study used RNA-seq to compare the difference in transcriptome between hyperpigmentation and hypopigmentation of breast muscle. Six cDNA libraries were constructed for hyperpigmentation and hypopigmentation groups in XFBC. We identified 395 differently expressed genes (DEGs) between hyperpigmentation and hypopigmentation group (P < 0.05, |log2FC|≥1). Gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated several differentially enriched biological functions and pathways involved in melanogenesis of the breast muscle. Gene set enrichment analysis (GSEA) GO analysis identified two significant gene sets, including the pathways of pigment metabolic process and transmembrane receptor protein tyrosine kinase activity. GSEA-KEGG analysis identified the process of tyrosine metabolism and several genes related with melanogenesis in breast muscle of the XFBC. The protein-protein interaction network was constructed and eight genes were clustered in the module. We identified nine hub genes, including TYR, TYRP1, DCT, GPR143, MLANA, SLC24A5, GPNMB, MLPH, and EDNRB2. Taken together, the DEGs and hub genes identified in the study provide a solid basis for the study of the genetic regulatory mechanisms involved the melanogenesis in the breast muscle of the XFBC.

影响雪峰黑骨鸡胸肌黑色素沉积的基因生物信息学分析
雪峰黑骨鸡(XFBC)是一种重要的家禽遗传资源。然而,乳房肌肉的暗度是不均匀的。XFBC患者乳房肌肉黑色素形成的分子遗传机制尚不清楚。本研究使用RNA-seq比较乳腺肌肉色素沉着和色素沉着的转录组差异。构建了XFBC色素沉着和色素沉着组的6个cDNA文库。我们鉴定出395个不同表达基因(DEGs)在色素沉着和色素沉着组之间(P 2FC|≥1)。基因本体(GO)富集和京都基因与基因组百科全书(KEGG)通路分析表明,在乳房肌肉黑色素形成过程中存在几种差异富集的生物学功能和通路。基因集富集分析(GSEA)鉴定出色素代谢途径和跨膜受体蛋白酪氨酸激酶活性两个重要基因集。GSEA-KEGG分析确定了XFBC胸肌中酪氨酸代谢过程和几个与黑色素生成相关的基因。构建了蛋白-蛋白相互作用网络,并将8个基因聚类在该模块中。我们鉴定出9个枢纽基因,包括TYR、TYRP1、DCT、GPR143、MLANA、SLC24A5、GPNMB、MLPH和EDNRB2。综上所述,本研究发现的DEGs和hub基因为研究XFBC胸肌黑色素形成的遗传调控机制提供了坚实的基础。
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
Genome
Genome 生物-生物工程与应用微生物
CiteScore
5.30
自引率
3.20%
发文量
42
审稿时长
6-12 weeks
期刊介绍: Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.
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