基于转录组测序研究调控黄羽肉鸡干毛性状关键基因和信号通路

doi:10.3864/j.issn.0578-1752.2024.01.014

Abstract

Abstract:

【Objective】 The study aimed to identify important candidate genes and signaling pathways associated with dry feather traits by comparing the morphological and gene expression differences between the feather follicles of dry and undried feathers. 【Method】 Three samples of skin tissue were selected from each of the undried and dried feathers. The histological examinations were used to compare the morphological differences between the feather follicles of dried and undried feathers. RNA-seq technology was employed to compare the differentially expressed genes (DEGs) between the two groups of skin samples. The accuracy of transcriptome results was validated by using the fluorescent quantitative PCR technique (RT-qPCR). 【Result】 By histological H.E staining, it was confirmed that the feather follicles of the undried feathers were in the growth phase, while the feather follicles of the dried feathers were in the resting phase. The feather follicle skin samples at the growth stage were used as controls, 942 DEGs were identified in resting feather follicle samples (|fold-change|>2 and P<0.05), including 384 significantly down-regulated DEGs and 558 upregulated DEGs. Gene ontology (Go) analysis suggested that the DEGs were significantly enriched in cell division, cycle regulation, and other related biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway results showed that the DEGs were related to MAPK, TGF-β, p53, and cell cycle-related signaling pathways. Protein-protein interaction (PPI) network was constructed and six hub genes were obtained by CytoHubba analysis, including CDK1, MAD2L1, BUB1, CCNB2, PLK1, and BUB1B. Gene Set Enrichment Analysis (GSEA) results indicated that the signaling pathways related to the tight junction, insulin, MAPK, TGF-β, and cell cycle-related pathways were significantly associated with the growth cycle of chicken feather follicles. The expression patterns of 8 DEGs detected by RT-qPCR were consistent with the RNA-seq results. 【Conclusion】 In summary, the dry feather traits of chickens were related to the development of feather follicle cycles. Signaling pathways such as MAPK and TGF-β might play important roles in feather growth and development by regulating the expression of cell cycle-related genes. The study provided clues for understanding the molecular regulatory mechanisms for dry feather traits in yellow-feathered broiler chickens.

Key words: chicken, dry feather, feather follicle, RNA-seq, gene, signaling pathway

JI GaiGe, CHEN ZhiWu, SHAN YanJu, LIU YiFan, TU YunJie, ZOU JianMin, ZHANG Ming, JU XiaoJun, SHU JingTing, ZHANG HaiTao, TANG YanFei, JIANG HuaLian. Study of Key Genes and Signaling Pathways Regulating Dry Feather Traits in Yellow-Feathered Broiler Chickens Based on Transcriptome Analysis[J].Scientia Agricultura Sinica, 2024, 57(1): 204-215.

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References 46

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基因 Gene symbol	序列号 Accession number	引物序列 Primer sequence (5′→3′)	产物长度 Product length (bp)
β-actin	NM_205518.2	F: GCTGAACTCCATCTTGGTTCCC R: TGCTTCTAGGGTCACTCGCA	150
BUB1	NM_001012870.1	F: GCTGAACTCCATCTTGGTTCCC R: TGCTTCTAGGGTCACTCGCA	112
BIRC5	NM_001012319.1	F:CTGGATAAAAAGCGGACCAA R: AACCTAAGGGCCCATGTTCT	246
CDK1	NM_205314.1	F:GGAACGCATGTCCAAAACTT R: GCAGGCAGGCAAAGATAAAG	236
NEK2	NM_001031050.2	F:ATGTCTTCCTGGATGGCAAG R: TCTGCCAACTCCTTCTGGTT	241
CDC6	XM_040691823.1	F:GTGTCCTCTCGGAGGTGTTT R: AGGCACTCTGTCTGGTCCAC	214
ANXA1	NM_206906.1	F:AAAAACTCCACCTGGCAATG R: CCACATAAAGCGACCAGGAT	193
BCL2	NM_205339.2	F: TGACACCTCGATCTCACAGG R: CATGCAACACACTGGGATTC	247
EDA2R	NM_001083360.1	F: ACCCTCATCAACCGCATCCA R: GCCTTGCGGTAAAACCCTGG	89
FZD4	NM_204099.1	F:AATGTCACCAAGATGCCCAACC R:AGACCGAACAAAGGAAGAACTGGA	130

样品 Sample	原始序列 Raw reads	有效序列 Clean reads	Q30 (%)	GC (%)	比对率 Mapped on reference	未比对率 Unmapped	唯一位置比对 Uniquely mapped
H1-1	40968048	38142462	92.33	48.605	36255024 (95.05%)	1887438 (4.95%)	35196169 (92.28%)
H1-2	46296028	43781388	93.07	49.900	41547151 (94.9%)	2234237 (5.1%)	40274977 (91.99%)
H1-3	48737026	45301826	92.01	48.995	42668140 (94.19%)	2633686 (5.81%)	41786822 (92.24%)
H2-1	46250350	43867410	93.33	49.985	41559772 (94.74%)	2307638 (5.26%)	40597907 (92.55%)
H2-2	43917200	40983494	92.28	49.945	38739383 (94.52%)	2244111 (5.48%)	37804671 (92.24%)
H2-3	42372910	39985456	93.17	49.750	38040749 (95.14%)	1944707 (4.86%)	36991013 (92.51%)

基因 Gene	MCC	基因 Gene	Degree	基因 Gene	MNC	基因 Gene	EPC
CDK1	5.11E+19	CDK1	56	CDK1	55	APITD1	85.564
BUB1	5.11E+19	PLK1	46	PLK1	46	AURKA	85.564
PLK1	5.11E+19	CCNB2	44	CCNB2	43	CDK1	85.564
CCNB2	5.11E+19	CENPE	43	CENPE	43	TPX2	85.564
NDC80	5.11E+19	BUB1	41	BUB1	41	BIRC5	85.564
CENPE	5.11E+19	NDC80	41	NDC80	41	MAD2L1	85.564
BUB1B	5.11E+19	BUB1B	37	BUB1B	37	BUB1	85.564
MAD2L1	5.11E+19	MAD2L1	34	KIF11	34	CCNB2	85.564
CENPF	5.11E+19	KIF11	34	MAD2L1	33	PLK1	85.564
INCENP	5.11E+19	AURKA	32	AURKA	31	BUB1B	85.564

Study of Key Genes and Signaling Pathways Regulating Dry Feather Traits in Yellow-Feathered Broiler Chickens Based on Transcriptome Analysis

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