Analysis of key genes in Hu wavy pattern lambskin based on transcriptome sequencing

doi:10.11686/cyxb2025290

Abstract

Abstract:

The aim of this study was to conduct transcriptome sequencing on Hu lambskins with 4/4 straight hairs and 4/4 wavy pattern， and to identify the key genes affecting lambskin traits. Skin tissues （n=4） were collected from the side of the body of 4/4 straight hair and 4/4 wavy pattern Hu lambs. Total RNA was extracted for transcriptome sequencing， and differentially expressed genes （DEGs） were screened and subjected to gene ontology （GO） and kyoto encyclopedia of genes and genomes （KEGG） enrichment analyses. Gene set enrichment analysis （GSEA） of the KEGG pathways was also conducted， and the DEGs encoding transcription factors （TFs） were identified. Seven DEGs were selected for verification of their transcript profiles by real-time fluorescence quantitative PCR （qRT-PCR）， and the transcript profiles of DEGs in the site of straight hair and wavy pattern in individual lambskin with different wavy areas were compared. Results showed that a total of 315 DEGs （threshold |log₂FC|≥1 and FDR<0.05） were screened out by comparing the transcriptomes of 4/4 straight hair and 4/4 wavy pattern lambskins. Of the 315 DEGs， 274 were down-regulated and 41 were up-regulated in wavy pattern lambskin compared with straight hair lambskin. The GO analysis revealed that DEGs were mainly enriched in 3771 items including extracellular structural tissues， extracellular matrix， and integrin binding. The KEGG analysis showed that DEGs were mainly enriched in 209 pathways including the cell adhesion molecules， PI3K-AKT signaling， and RAS signaling pathways. The GSEA results indicated that DEGs were mainly related to pathways such as histidine metabolism， renin secretion， and protein digestion and absorption. The enriched signaling pathways related to hair follicles， including the RAS， PI3K-AKT， and RAP1 signaling pathways， showed a down-regulated trend in the 4/4 wavy pattern lambskin compared with the 4/4 straight hair lambskin. Among the DEGs， 12 encoded TFs， of which two were up-regulated and 10 were down-regulated in wavy pattern lambskin compared with straight hair lambskin. The down-regulated TF DEGs included those encoding SRY-related high-mobility group box （SOX）， forkhead box （FOX）， and T-box （T-box） TFs. The transcript levels of the seven candidate genes determined by qRT-PCR were consistent with those determined from the transcriptome analysis， and confirmed significantly lower transcript levels of IGF1 and MFAP5 in wavy pattern skin regions than in straight hair skin regions in individuals with different pattern coverage areas. In conclusion， AEBP1， IGF1， MMP27， MFAP5， RPTN， SPI1， and THY1 were identified as important candidate genes affecting lambskin traits. These results lay a foundation for further understanding the molecular mechanism of the formation of wavy lambskin in Hu sheep.

Key words: Hu sheep, lambskin, hair follicle development, wool crimp, transcriptome sequencing

Jing XIE, Xu-ming MENG, Zhen CANG, Yun-tao HUA, Xian-yi ZHOU, Da-gan MAO. Analysis of key genes in Hu wavy pattern lambskin based on transcriptome sequencing[J]. Acta Prataculturae Sinica, 2026, 35(7): 188-200.

Figures/Tables 9

References 41

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基因 Gene	名称 Name	基因库编号 Genebank number	引物序列 Primer sequence （5′-3′）	产物长度 Product length （bp）
AEBP1	AE结合蛋白1AE binding protein 1	XM_012176971.5	F： CTCATGCAATACCTGTGCCG	142
AEBP1	AE结合蛋白1AE binding protein 1	XM_012176971.5	R： TCCCAAACTCTGAGCCCATC	142
IGF1	胰岛素样生长因子1Insulin-like growth factor 1	XM_027965761.2	F： TTCTATCTGGCCCTGTGCTTG	138
IGF1	胰岛素样生长因子1Insulin-like growth factor 1	XM_027965761.2	R： CCCCGTGGGCTTGTTGAAATA	138
MMP27	基质金属肽酶27Matrix metallopeptidase 27	XM_004015972.5	F： TGCTGTCTTGCCAGATTATCCC	149
MMP27	基质金属肽酶27Matrix metallopeptidase 27	XM_004015972.5	R： GGGTCACTTCATCATACCTCCAG	149
MFAP5	微纤维相关蛋白5Microfibril-associated protein 5	XM_015094961.3	F： TCAAGCCTTCTACCGATGACC	70
MFAP5	微纤维相关蛋白5Microfibril-associated protein 5	XM_015094961.3	R： TTCTCATCCCGGCACTCTGT	70
RPTN	重复素Repetin	XM_060396929.1	F： AGAATGGGGACTCCACCTCA	93
RPTN	重复素Repetin	XM_060396929.1	R： CTGGGTCATTTGGTCTCCTGA	93
SPI1	Spi-1原癌基因Spi-1 proto-oncogene	XM_027979753.3	F： CAACGCCAAACGCACGAATA	71
SPI1	Spi-1原癌基因Spi-1 proto-oncogene	XM_027979753.3	R： TCCCAGTAATGGTCGCTGTG	71
THY1	Thy-1细胞表面抗原Thy-1 cell surface antigen	XM_060399793.1	F： CCTCCTGCTGACAGTCTTACA	132
THY1	Thy-1细胞表面抗原Thy-1 cell surface antigen	XM_060399793.1	R： AACTCATACTGCATGGGCGT	132
GAPDH	甘油醛-3-磷酸脱氢酶Glyceraldehyde-3-phosphate dehydrogenase	NM_001190390.1	F： TCGGAGTGAACGGATTTGGC	76
GAPDH	甘油醛-3-磷酸脱氢酶Glyceraldehyde-3-phosphate dehydrogenase	NM_001190390.1	R： ACGATGTCCACTTTGCCAGT	76

基因 Gene	名称 Name	基因库编号 Genebank number	引物序列 Primer sequence （5′-3′）	产物长度 Product length （bp）
AEBP1	AE结合蛋白1AE binding protein 1	XM_012176971.5	F： CTCATGCAATACCTGTGCCG	142
AEBP1	AE结合蛋白1AE binding protein 1	XM_012176971.5	R： TCCCAAACTCTGAGCCCATC	142
IGF1	胰岛素样生长因子1Insulin-like growth factor 1	XM_027965761.2	F： TTCTATCTGGCCCTGTGCTTG	138
IGF1	胰岛素样生长因子1Insulin-like growth factor 1	XM_027965761.2	R： CCCCGTGGGCTTGTTGAAATA	138
MMP27	基质金属肽酶27Matrix metallopeptidase 27	XM_004015972.5	F： TGCTGTCTTGCCAGATTATCCC	149
MMP27	基质金属肽酶27Matrix metallopeptidase 27	XM_004015972.5	R： GGGTCACTTCATCATACCTCCAG	149
MFAP5	微纤维相关蛋白5Microfibril-associated protein 5	XM_015094961.3	F： TCAAGCCTTCTACCGATGACC	70
MFAP5	微纤维相关蛋白5Microfibril-associated protein 5	XM_015094961.3	R： TTCTCATCCCGGCACTCTGT	70
RPTN	重复素Repetin	XM_060396929.1	F： AGAATGGGGACTCCACCTCA	93
RPTN	重复素Repetin	XM_060396929.1	R： CTGGGTCATTTGGTCTCCTGA	93
SPI1	Spi-1原癌基因Spi-1 proto-oncogene	XM_027979753.3	F： CAACGCCAAACGCACGAATA	71
SPI1	Spi-1原癌基因Spi-1 proto-oncogene	XM_027979753.3	R： TCCCAGTAATGGTCGCTGTG	71
THY1	Thy-1细胞表面抗原Thy-1 cell surface antigen	XM_060399793.1	F： CCTCCTGCTGACAGTCTTACA	132
THY1	Thy-1细胞表面抗原Thy-1 cell surface antigen	XM_060399793.1	R： AACTCATACTGCATGGGCGT	132
GAPDH	甘油醛-3-磷酸脱氢酶Glyceraldehyde-3-phosphate dehydrogenase	NM_001190390.1	F： TCGGAGTGAACGGATTTGGC	76
GAPDH	甘油醛-3-磷酸脱氢酶Glyceraldehyde-3-phosphate dehydrogenase	NM_001190390.1	R： ACGATGTCCACTTTGCCAGT	76

样本名称Sample	原始测序读数Raw reads （bp）	过滤后读数Clean reads （bp）	Q20 （%）	Q30 （%）	GC含量GC content （%）
S₁	41094942	41094936	99.40	97.18	48.65
S₂	40508630	40508628	99.40	97.25	48.60
S₃	46929166	46924146	99.53	97.87	48.88
S₄	40044654	40044652	99.54	97.95	48.63
W₁	41862838	41859348	99.51	97.71	48.47
W₂	43925888	43925882	99.48	97.60	48.88
W₃	40125986	40125986	99.49	97.67	47.44
W₄	42378798	42375874	99.45	97.48	47.76

样本名称Sample	原始测序读数Raw reads （bp）	过滤后读数Clean reads （bp）	Q20 （%）	Q30 （%）	GC含量GC content （%）
S₁	41094942	41094936	99.40	97.18	48.65
S₂	40508630	40508628	99.40	97.25	48.60
S₃	46929166	46924146	99.53	97.87	48.88
S₄	40044654	40044652	99.54	97.95	48.63
W₁	41862838	41859348	99.51	97.71	48.47
W₂	43925888	43925882	99.48	97.60	48.88
W₃	40125986	40125986	99.49	97.67	47.44
W₄	42378798	42375874	99.45	97.48	47.76