Transcriptome Sequencing-Based Screening of Genes and Key Pathways Related to Hair Follicle Traits in Chicken Skin

doi:10.7668/hbnxb.20194317

Abstract

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

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.

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

Figures/Tables 10

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

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

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.

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

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.

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.

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.

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.

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

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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