基于转录组测序筛选鸡皮肤毛囊性状相关基因和关键通路

doi:10.7668/hbnxb.20194317

摘要/Abstract

摘要：

旨在通过对崇仁麻鸡背部皮肤毛囊组织的转录组学分析,筛选关键的差异表达基因和信号通路,探讨鸡皮肤毛囊性状的分子调控机制。采用TRIzol法提取皮肤毛囊组织总RNA,通过Illumina平台进行转录组高通量测序(RNA-Seq)。最后采用实时荧光定量的方法对转录组测序进行验证。研究结果如下:共筛选出了3 856个差异表达基因,在公鸡(BGB vs YGB)比较组合中筛选出了971个差异表达基因,其中274个表达上调,697个表达下调。在母鸡(BMB vs YMB)比较组合中筛选出了3 529个差异表达基因,其中1 477个上调,2 052个下调。在公鸡、母鸡共同的差异表达基因中筛选出了3个与皮肤毛囊性状有关的高表达基因KRT75、KRT6A和KRT14。在GO功能显著富集中,BGB vs YGB比较组合富集到了516个GO term,BMB vs YMB比较组合富集到了1 020个GO term,基因主要集中参与细胞黏附等活动。显著富集了多条KEGG通路,在BGB vs YGB比较组合中富集了8条显著的KEGG通路,在BMB vs YMB比较组合中富集了20条显著的KEGG通路,筛选出了3条关键通路Wnt信号传导途径、神经活性配体-受体调控通路和TGF-β调控通路。荧光定量结果显示,随机选取的5个差异基因在皮肤毛囊中的表达与RNA-Seq走向趋势一致。综上所述,筛选的KRT75、KRT6A、KRT14基因可能影响鸡皮肤毛囊性状;神经活性配体-受体调控通路、Wnt信号通路和TGF-β信号通路均是调控鸡皮肤毛囊性状的重要通路。

关键词: 崇仁麻鸡, 皮肤毛囊, 转录组测序, 差异表达基因, 信号通路, 荧光定量

Abstract:

The aim was to screen key differentially expressed genes and signaling pathways and explore the molecular regulatory mechanisms of chicken skin follicle traits through transcriptomic analysis of the dorsal skin follicle tissues of Chongren partridge chicken.Total RNA of skin hair follicle tissue was extracted by TRIzol method,and transcriptome high-throughput sequencing(RNA-Seq)was performed by Illumina platform.Finally,the transcriptome sequencing was validated by Real-time fluorescence quantitative PCR.The results were as follows:A total of 3 856 differentially expressed genes were screened,and 971 differentially expressed genes were screened in the cockerel(BGB vs YGB)comparative combinations,of these,274 up-regulated and 697 down-regulated.There were 3 529 differentially expressed genes in comparative combinations of hen(BMB vs YMB),of these,1 477 up-regulated and 2 052 down-regulated.Three highly expressed genes,KRT75,KRT6A,and KRT14,associated with skin follicle traits,were screened among the common differentially expressed genes in roosters and hens.In the significant enrichment of GO functions,516 GO terms were enriched in the BGB vs YGB and 1 020 GO terms were enriched in the BMB vs YMB.Genes were mainly focused on activities involved in cell adhesion and cell activation.Significantly enriched multiple KEGG pathways,with 8 significant KEGG pathways enriched in the BGB vs YGB and 20 significant KEGG pathways enriched in the BMB vs YMB.Three key pathways,Wnt signaling pathway,neuroactive ligand-receptor regulatory pathway and TGF-β regulatory pathway,were screened.Fluorescence quantification showed that the expression of five randomly selected differential genes in skin hair follicles was consistent with the trend towards RNA-Seq.In summary,the screened KRT75,KRT6A,and KRT14 genes may affect chicken skin follicle traits;the neuroactive ligand-receptor regulatory pathway,the Wnt signaling pathway,and the TGF-β signaling pathway are important pathways that regulate follicular traits in chicken skin.

Key words: Chongren partridge chicken, Skin follicles, Transcriptome sequencing, Differentially expressed genes, Signaling pathway, Fluorescence quantification

陈春, 魏岳, 黄聪, 黎观红, 谢金防, 武艳平. 基于转录组测序筛选鸡皮肤毛囊性状相关基因和关键通路[J]. 华北农学报, 2023, 38(6): 218-227. doi: 10.7668/hbnxb.20194317.

CHEN Chun, WEI Yue, HUANG Cong, LI Guanhong, XIE Jinfang, WU Yanping. Transcriptome Sequencing-Based Screening of Genes and Key Pathways Related to Hair Follicle Traits in Chicken Skin[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(6): 218-227. doi: 10.7668/hbnxb.20194317.

http://www.hbnxb.net/CN/Y2023/V38/I6/218

图/表 10

表1 实时荧光定量引物设计

Tab.1 Design of Real-time fluorescent quantitative primers

基因 Gene	引物序列(5'—3') Sequence(5'—3')	产物长度/bp Product length	登录号 Accession number
BMP2	F:GGGCTACGAGTGCTGAGGGG	199	NC_052534
	R:CACCCCTACCGCAAAAGCCA
TGFβ1	F:CCATGAACCCTGTGCAGATGTCA	150	NC_052533
	R:GTTGTCCACAGTGCTGCAATTCC
Wnt7A	F:CCTTCACCTACGCCATCATTGCT	117	NC_052543
	R:CCTTGTGGTACTGTCCCTGCTTC
GABRP	F:GAACTCACCCAACTTTTGCGAGC	145	NC_052529
	R:CCGTTTCTCAGTCCTCGTGTTGT
PTPRO	F:TGACCACCTTCAGCCACAATAGC	139	NC_052532
	R:ACCAGCAGCAGTCCAATGAGAAG
β-actin	F:GATGCAGAAGGAGATCACAGCCC	149	NC_052545
	R:ACTCCTGCTTGCTGATCCACATC

图1 差异比较组合差异基因数目统计柱状图

Fig.1 Comparison of the number of differential genes in the combination of statistical bar chart

图2 差异基因韦恩图黄色.所有母鸡唯一的差异表达基因;紫色.所有公鸡唯一的差异表达基因;重叠区.所有公鸡和母鸡共有的差异表达基因。

Fig.2 Venn diagram of differential genes Yellow.Differentially expressed genes unique to all hens;Purple.Differentially expressed genes unique to all males;Overlapping area.Differentially expressed genes common to all males and females.

表2 关键差异表达基因

Tab.2 Key differentially expressed genes

基因 Gene	BMB vs YMB			BGB vs YGB
基因 Gene	差异倍数 log₂Foldchange	P值 P value	校正后P值 padj	差异倍数 log₂Foldchange	P值 P value	校正后P值 padj
S100A12	-7.16	7.25E-13	1.46E-10	-6.57	8.46E-19	4.18E-16
SYT13	-6.31	1.71E-09	2.08E-07	-5.35	6.88E-06	1.71E-12
NCF2	-5.90	8.82E-07	5.61E-05	-5.08	6.34E-22	4.99E-19
KRT75	13.86	4.47E-30	1.09E-27	8.38	2.04E-15	1.19E-13
KRT6A	13.80	2.13E-16	1.44E-14	8.32	1.26E-27	2.52E-25
KRT14	12.76	5.49E-08	1.01E-06	7.80	5.10E-11	1.59E-09

图3 BGB vs YGB比较组合GO富集分析柱状图 1.骨骼系统的发育;2.骨化;3.骨骼系统形态发生;4.附肢形态发生;5.肢体形态发生;6.附肢发育;7.胚胎附肢形态发生;8.生物组织发育;9.肢体发育;10.胚胎形态发生;11.细胞外基质;12.中间丝;13.中间丝细胞骨架;14.谷氨酸能突触;15.质膜蛋白质复合体;16.超分子纤维;17.超分子复合体;18.超分子聚合物;19.突触膜;20.细胞外基质成分;21.细胞骨架结构成分;22.无机阳离子跨膜转运体活性;23.阳离子通道活性;24.阳离子跨膜转运体活性;25.通道活性;26.被动跨膜转运体活性;27.底物特异性通道活性;28.金属离子跨膜转运体活性;29.受体调节器活性;30.离子门控通道活性。

Fig.3 Bar chart of BGB vs YGB GO enrichment analysis 1.Skeletal system development;2.Ossification;3.Skeletal system morphogenesis;4.Appendage morphogenesis;5.Limb morphogenesis;6.Appendage development;7.Embryonic appendage morphogenesis;8.Biological tissue development;9.Limb development;10.Embryonic morphogenesis;11.Extracellular matrix;12.Intermediate filaments;13.Intermediate filament cytoskeleton;14.Glutamatergic synapses;15.Plasma membrane protein complexes;16.Supramolecular fibers;17.Supramolecular complexes;18.Supramolecular polymers;19.Synaptic membranes;20.Extracellular matrix components;21.Cytoskeletal structural components;22.Inorganic cation transmembrane transporter activity;23.Cation channel activity;24.Cation transmembrane transporter activity;25.Channel activity;26.Passive transmembrane transporter activity;27.Substrate-specific channel activity;28.Metal ion transmembrane transporter activity;29.Receptor regulator activity;30.Ion-gated channel activity.

图4 BMB vs YMB比较组合GO富集分析柱状图 1.细胞-细胞黏附;2.细胞黏附的调控;3.细胞-细胞黏附的调控;4.趋向;5.趋化作用;6.细胞活化;7.白细胞活化;8.白细胞-细胞黏附;9.细胞活化调节;10.白细胞活化调控;11.中间丝;12.中间丝细胞骨架;13.细胞表面;14.质膜蛋白复合物;15.聚合细胞骨架纤维;16.受体复合物;17.质膜受体复合物;18.细胞接头;19.质膜外侧;20.膜侧;21.细胞骨架的结构成分;22.趋化因子活性;23.G蛋白偶联受体结合;24.趋化因子受体结合;25.G蛋白偶联受体活性;26.受体调节器活性;27.细胞因子受体活性;28.受体配体活性;29.嘌呤核苷酸受体活性;30.核苷酸受体活性。

Fig.4 Bar chart of BMB vs YMB GO enrichment analysis 1.Cell-cell adhesion;2.Regulation of cell adhesion;3.Regulation of cell-cell adhesion;4.Taxis;5.Chemotaxis;6.Cell activation;7.Leukocyte activation;8.Leukocyte cell-cell adhesion;9.Regulation of cell activation;10.Regulation of leukocyte activation;11.Intermediate filament;12.Intermediate filament cytoskeleton;13.Cell surface;14.Plasma membrane protein complex;15.Polymeric cytoskeletal fiber;16.Receptor complex;17.Plasma membrane receptor complex;18.Cell junction;19.External side of plasma membrane;20.Side of membrane;21.Structural constituent of cytoskeleton;22.Chemokine activity;23.G protein-coupled receptor binding;24.Chemokine receptor binding;25.G-protein-coupled receptor activity;26.Receptor regulator activity;27.Cytokine receptor activity;28.Receptor ligand activity;29.Purinergic nucleotide receptor activity;30.Nucleotide receptor activity.

图5 BGB vs YGB比较组合KEGG富集气泡图 1.神经活性配体-受体调控通路;2.Wnt信号通路;3.叶酸的生物合成;4.黑色素生成;5.谷胱甘肽代谢;6.TGF-β信号通路;7.类固醇激素的生物合成;8.甘氨酸、丝氨酸和苏氨酸代谢;9.半胱氨酸和蛋氨酸代谢;10.细胞色素 P450 对异种生物的代谢;11.硫代谢;12.钙信号途径;13.ECM 与受体的相互作用;14.丙氨酸、天门冬氨酸和谷氨酸代谢;15.氨基酸的生物合成;16.细胞黏附分子 (CAM);17.视黄醇代谢;18.细胞因子-细胞因子受体相互作用;19.精氨酸和脯氨酸代谢;20.刺猬信号通路。

Fig.5 Bubble diagram of KEGG enrichment of BGB vs YGB 1.Neuroactive ligand-receptor regulatory pathway;2.Wnt signaling pathway;3.Folate biosynthesis;4.Melanogenesis;5.Glutathione metabolism;6.TGF-β signaling pathway;7.Steroid hormone biosynthesis;8.Glycine,serine and threonine metabolism;9.Cysteine and methionine metabolism;10.Metabolism of xenobiotics by cytochrome P450;11.Sulfur metabolism;12.Calcium signaling pathway;13.ECM-receptor interaction;14.Alanine,aspartate and glutamate metabolism;15.Biosynthesis of amino acids;16.Cell adhesion molecules(CAMs);17.Retinol metabolism;18.Cytokine-cytokine receptor interaction;19.Arginine and proline metabolism;20.Hedgehog signaling pathway.

图6 BMB vs YMB比较组合KEGG富集气泡图 1.细胞黏附分子(CAM);2.细胞因子-细胞因子受体相互作用;3.ECM与受体的相互作用;4.亚油酸代谢;5.黑色素生成;6.花生四烯酸代谢;7.Wnt信号通路;8.溶酶体;9.神经活性配体与受体的相互作用;10.α-亚麻酸代谢;11.药物代谢-细胞色素P450;12.血管平滑肌收缩;13.吞噬细胞;14.PPAR信号通路;15.醚脂代谢;16.甘油磷脂代谢;17.谷胱甘肽代谢;18.细胞色素P450对异种生物的代谢;19.病灶黏附;20.血管内皮生长因子信号通路。

Fig.6 Bubble diagram of KEGG enrichment of BMB vs YMB 1.Cell adhesion molecules(CAMs);2.Cytokine-cytokine receptor interaction;3.ECM-receptor interaction;4.Linoleic acid metabolism;5.Melanogenesis;6.Arachidonic acid metabolism;7.Wnt signaling pathway;8.Lysosome;9.Neuroactive ligand-receptor Interaction;10.Alpha-linolenic acid metabolism;11.Drug metabolism-cytochrome P450;12.Vascular smooth muscle contraction;13.Phagosome;14.PPAR signaling pathway;15.Ether lipid metabolism;16.Glycerophospholipid metabolism;17.Glutathione metabolism;18.Meta-bolism of xenobiotics by cytochrome P450;19.Focal adhesion;20.Vascular endothelial growth factor signaling pathway.

表3 RNA-Seq差异表达基因

Tab.3 RNA-Seq differentially expressed genes

基因 Gene	KEGG通路 KEGG pathway	差异倍数(♂) log₂Foldchange	差异倍数(♀) log₂Foldchange	表达调节 Regulation
TGFβ1	TGF-β通路	2.11	2.39	上调
GABRP	神经活性配体与受体的相互作用	3.37	4.12	上调
PTPRC	细胞黏附分子	2.38	2.53	上调
Wnt7a	Wnt信号通路	-3.21	-5.51	下调
BMP2	TGF-β通路	-2.70	-3.82	下调

图7 差异表达基因相对表达量相同字母表示差异不显著(P>0.05),不同字母表示差异显著(P<0.05)。

Fig.7 Relative expression levels of differential expressed genes The same letter indicates a non-significant difference(P>0.05),and different letters indicate a significant difference(P<0.05).

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