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Zhang C, Qin Q, Liu Z, Wang Y, Lan M, Zhao D, Zhang J, Wang Z, Li J, Liu Z. Combining multiomics to analyze the molecular mechanism of hair follicle cycle change in cashmere goats from Inner Mongolia. Front Vet Sci 2024; 11:1405355. [PMID: 39036798 PMCID: PMC11257874 DOI: 10.3389/fvets.2024.1405355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/14/2024] [Indexed: 07/23/2024] Open
Abstract
Sheep body size can directly reflect the growth rates and fattening rates of sheep and is also an important index for measuring the growth performance of meat sheep.Inner Mongolia Cashmere Goat is a local excellent breed of cashmere and meat dual-purpose, which is a typical heterogeneous indumentum. The hair follicles cycle through periods of vigorous growth (anagen), a regression caused by apoptosis (catagen), and relative rest (telogen). At present, it is not clear which genes affect the cycle transformation of hair follicles and unclear how proteins impact the creation and expansion of hair follicles.we using multi-omics joint analysis methodologies to investigated the possible pathways of transformation and apoptosis in goat hair follicles. The results showed that 917,1,187, and 716 proteins were specifically expressed in anagen, catagen andtelogen. The result of gene ontology (GO) annotation showed that differentially expressed proteins (DEPs) are in different growth cycle periods, and enriched GO items are mostly related to the transformation of cells and proteins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment result indicated that the apoptosis process has a great impact on hair follicle's growth cycle. The results of the protein interaction network of differential proteins showed that the ribosomal protein family (RPL4, RPL8, RPS16, RPS18, RPS2, RPS27A, RPS3) was the core protein in the network. The results of combined transcriptome and proteomics analysis showed that there were 16,34, and 26 overlapped DEGs and DEPs in the comparison of anagen VS catagen, catagen VS telogen and anagen VS telogen, of which API5 plays an important role in regulating protein and gene expression levels. We focused on API5 and Ribosomal protein and found that API5 affected the apoptosis process of hair follicles, and ribosomal protein was highly expressed in the resting stage of hair follicles. They are both useful as molecular marker candidate genes to study hair follicle growth and apoptosis,and they both have an essential function in the cycle transition process of hair follicles. The results of this study may provide a theoretical basis for further research on the growth and development of hair follicles in Inner Mongolian Cashmere goats.
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Affiliation(s)
- Chongyan Zhang
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
| | - Qing Qin
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Zhichen Liu
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Yichuan Wang
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
| | - Mingxi Lan
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
| | - Dan Zhao
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Jingwen Zhang
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
| | - Zhixin Wang
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Jinquan Li
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Zhihong Liu
- Department of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
- Northern Agriculture and Livestock Husbandry Technical Innovation Center, Chinese Academy of Agricultural Sciences, Hohhot, China
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Wang L, Tian R, Wang G, Zhao M, Zhang Y, Li J. Proteomic analysis of fetal skin by iTRAQ reveals molecular signals underlying Inner Mongolia Cashmere goat hair follicle initiation. ALL LIFE 2023. [DOI: 10.1080/26895293.2023.2169363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Lele Wang
- Ulanqab of Medical College, Ulanqab, People’s Republic of China
| | - Rugang Tian
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, People’s Republic of China
| | - Gaofeng Wang
- Ulanqab Center for Animal Disease Control and Prevention, Ulanqab, People’s Republic of China
| | - Meng Zhao
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, People’s Republic of China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
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Hu T, Lv X, Getachew T, Mwacharo JM, Haile A, Quan K, Li Y, Wang S, Sun W. Effect of Sox18 on the Induction Ability of Dermal Papilla Cells in Hu Sheep. BIOLOGY 2022; 12:biology12010065. [PMID: 36671756 PMCID: PMC9855062 DOI: 10.3390/biology12010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/19/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Sox18 is a developmental gene that encodes transcription factors. It has been indicated as be a key gene affecting the growth and development of hair follicles, in which dermal papilla cells (DPCs) have been demonstrated to play an important role through their ability to induce the formation of hair follicles. Pre-laboratory studies have found that Sox18 is differentially expressed in the dermal papilla cells of different pattern types of Hu sheep. We speculated that Sox18 plays an important role in the dermal papilla cells of Hu sheep. In our study, we analyzed the effect of Sox18 on the induction ability of DPCs in order to elucidate the function and molecular mechanism of Sox18 in the DPCs of Hu sheep. We first identified the expression of Sox18 in the DPCs of Hu sheep by immunofluorescence staining. We then used alkaline phosphatase staining, cell morphology observations and RT-PCR to detect the effect of Sox18 on the induction of DPCs after overexpression of or interference with Sox18. We also used RT-PCR, WB and immunofluorescence staining to detect the effect of Sox18 on the Wnt/β-catenin signal pathway in DPCs. We found that Sox18 was specifically expressed in the DPCs of Hu sheep, and that Sox18 could enhance the alkaline phosphatase activity in the DPCs of Hu sheep and accelerate cell agglutination. The results of RT-PCR revealed that Sox18 promoted the mRNA expression of Versican, HHIP and FGFRI, and inhibited the mRNA expression of BMP4 and WIF1. Further studies showed that Sox18 promoted the expression of β-catenin and activated the Wnt/β-catenin signal pathway in DPCs. When the Wnt/β-catenin signal pathway of DPCs was activated, the induction ability of DPCs was enhanced. Overall, we believe that Sox18 could enhance the induction ability of DPCs in Hu sheep and regulate the induction ability of DPCs through the Wnt/β-catenin signal pathway.
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Affiliation(s)
- Tingyan Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyang Lv
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Tesfaye Getachew
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Joram M. Mwacharo
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Aynalem Haile
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450060, China
| | - Yutao Li
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia 4067, Australia
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- Correspondence: (S.W.); (W.S.)
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- “Innovative China” “Belt and Road” International Agricultural Technology Innovation Institute for Evaluation, Protection, and Improvement on Sheep Genetic Resource, Yangzhou University, Yangzhou 225009, China
- Correspondence: (S.W.); (W.S.)
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De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4472940. [PMID: 36408285 PMCID: PMC9668446 DOI: 10.1155/2022/4472940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022]
Abstract
The sequenced data availability opened new horizons related to buffalo genetic control of economic traits and genomic diversity. The visceral organs (brain, liver, etc.) significantly involved in energy metabolism, docility, or social interactions. We performed swamp buffalo transcriptomic profiling of 24 different tissues (brain and non-brain) to identify novel transcripts and analyzed the differentially expressed genes (DEGs) of brain vs. non-brain tissues with their functional annotation. We obtained 178.57 Gb clean transcriptomic data with GC contents 52.77%, reference genome alignment 95.36%, exonic coverage 88.49%. Totally, 26363 mRNAs transcripts including 5574 novel genes were obtained. Further, 7194 transcripts were detected as DEGs by comparing brain vs. non-brain tissues group, of which 3,999 were upregulated and 3,195 downregulated. These DEGs were functionally associated with cellular metabolic activities, signal transduction, cytoprotection, and structural and binding activities. The related functional pathways included cancer pathway, PI3k-Akt signaling, axon guidance, JAK-STAT signaling, basic cellular metabolism, thermogenesis, and oxidative phosphorylation. Our study provides an in-depth understanding of swamp buffalo transcriptomic data including DEGs potentially involved in basic cellular activities and development that helped to maintain their working capacity and social interaction with humans, and also, helpful to disclose the genetic architecture of different phenotypic traits and their gene expression regulation.
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Liu Z, Liu Z, Mu Q, Zhao M, Cai T, Xie Y, Zhao C, Qin Q, Zhang C, Xu X, Lan M, Zhang Y, Su R, Wang Z, Wang R, Wang Z, Li J, Zhao Y. Identification of key pathways and genes that regulate cashmere development in cashmere goats mediated by exogenous melatonin. Front Vet Sci 2022; 9:993773. [PMID: 36246326 PMCID: PMC9558121 DOI: 10.3389/fvets.2022.993773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The growth of secondary hair follicles in cashmere goats follows a seasonal cycle. Melatonin can regulate the cycle of cashmere growth. In this study, melatonin was implanted into live cashmere goats. After skin samples were collected, transcriptome sequencing and histological section observation were performed, and weighted gene co-expression network analysis (WGCNA) was used to identify key genes and establish an interaction network. A total of 14 co-expression modules were defined by WGCNA, and combined with previous analysis results, it was found that the blue module was related to the cycle of cashmere growth after melatonin implantation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the first initiation of exogenous melatonin-mediated cashmere development was related mainly to the signaling pathway regulating stem cell pluripotency and to the Hippo, TGF-beta and MAPK signaling pathways. Via combined differential gene expression analyses, 6 hub genes were identified: PDGFRA, WNT5A, PPP2R1A, BMPR2, BMPR1A, and SMAD1. This study provides a foundation for further research on the mechanism by which melatonin regulates cashmere growth.
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Affiliation(s)
- Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhichen Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Mu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Meng Zhao
- Inner Mongolia Autonomous Region Agriculture and Animal Husbandry Technology Extension Center, Hohhot, China
| | - Ting Cai
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yuchun Xie
- Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Cun Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Qin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Chongyan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolong Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingxi Lan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanhong Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
- *Correspondence: Yanhong Zhao
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Xu Y, Cai W, Chen R, Zhang X, Bai Z, Zhang Y, Qin Y, Gu M, Sun Y, Wu Y, Wang Z. Metabolomic Analysis and MRM Verification of Coarse and Fine Skin Tissues of Liaoning Cashmere Goat. Molecules 2022; 27:molecules27175483. [PMID: 36080249 PMCID: PMC9457707 DOI: 10.3390/molecules27175483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
One of the critical elements in evaluating the quality of cashmere is its fineness, but we still know little about how it is regulated at the metabolic level. In this paper, we use UHPLC–MS/MS detection and analysis technology to compare the difference in metabolites between coarse cashmere (CT_LCG) and fine cashmere (FT_LCG) skin of Liaoning cashmere goats. According to the data, under positive mode four metabolites were significantly up-regulated and seven were significantly down-regulated. In negative mode, seven metabolites were significantly up-regulated and fourteen metabolites were significantly down-regulated. The two groups’ most significant metabolites, Gly–Phe and taurochenodeoxycholate, may be crucial in controlling cashmere’s growth, development, and fineness. In addition, we enriched six KEGG pathways, of which cholesterol metabolism, primary bile acid biosynthesis, and bile secretion were enriched in positive and negative modes. These findings offer a new research idea for further study into the critical elements influencing cashmere’s fineness.
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Zhao B, Li J, Liu M, Yang N, Bao Z, Zhang X, Dai Y, Cai J, Chen Y, Wu X. DNA Methylation Mediates lncRNA2919 Regulation of Hair Follicle Regeneration. Int J Mol Sci 2022; 23:ijms23169481. [PMID: 36012763 PMCID: PMC9408817 DOI: 10.3390/ijms23169481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/12/2022] [Accepted: 08/20/2022] [Indexed: 11/20/2022] Open
Abstract
Hair follicles (HFs) are organs that periodically regenerate during the growth and development of mammals. Long non-coding RNAs (lncRNAs) are non-coding RNAs with crucial roles in many biological processes. Our previous study identified that lncRNA2919 is highly expressed in catagen during the HF cycle. In this study, the in vivo rabbit model was established using intradermal injection of adenovirus-mediated lncRNA2919. The results showed that lncRNA2919 decreased HF depth and density and contributed to HF regrowth, thereby indicating that lncRNA2919 plays a negative role in HF regeneration. Moreover, methylation levels of the lncRNA2919 promoter at different HF cycle stages were detected through bisulfite sequencing. The key CpG site that negatively correlates with lncRNA2919 expression during the HF cycle was identified. 5-Aza-dc-induced demethylation upregulated lncRNA2919 expression, and the core promoter region of lncRNA2919 was verified on the basis of luciferase activity. Furthermore, we found that DNA methylation could prevent the binding of EGR1 to the lncRNA2919 promoter region, thereby affecting the transcriptional expression of lncRNA2919. Collectively, DNA methylation inhibits the transcriptional expression of lncRNA2919, which plays a vital role in the HF cycle and HF regrowth. These findings contribute to the basic theory of epigenetics in HF biology and provide references for further research in HF disease treatment and animal wool production.
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Affiliation(s)
- Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yingying Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jiawei Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Y.C.); (X.W.)
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Y.C.); (X.W.)
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Wu C, Qin C, Fu X, Huang X, Tian K. Integrated analysis of lncRNAs and mRNAs by RNA-Seq in secondary hair follicle development and cycling (anagen, catagen and telogen) of Jiangnan cashmere goat (Capra hircus). BMC Vet Res 2022; 18:167. [PMID: 35524260 PMCID: PMC9074311 DOI: 10.1186/s12917-022-03253-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/18/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Among the world's finest natural fiber composites is derived from the secondary hair follicles (SHFs) of cashmere goats yield one of the world's best natural fibres. Their development and cycling are characterized by photoperiodism with diverse, well-orchestrated stimulatory and inhibitory signals. Long non-coding RNA (lncRNAs) and mRNAs play important roles in hair follicle (HF) development. However, not many studies have explored their specific functions in cashmere development and cycling. This study detected mRNAs and lncRNAs with their candidate genes and related pathways in SHF development and cycling of cashmere goat. We utilized RNA sequencing (RNA-Seq) and bioinformatics analysis on lncRNA and mRNA expressions in goat hair follicles to discover candidate genes and metabolic pathways that could affect development and cycling (anagen, catagen, and telogen). RESULTS We identified 228 differentially expressed (DE) mRNAs and 256 DE lncRNA. For mRNAs, catagen and anagen had 16 upregulated and 35 downregulated DEGs, catagen and telogen had 18 upregulated and 9 downregulated DEGs and telogen and anagen had 52 upregulated and 98 downregulated DEGs. LncRNA witnessed 22 upregulated and 39 downregulated DEGs for catagen and anagen, 36 upregulated and 29 downregulated DEGs for catagen and telogen as well as 66 upregulated and 97 downregulated DEGs for telogen and anagen. Several key genes, including MSTRG.5451.2, MSTRG.45465.3, MSTRG.11609.2, CHST1, SH3BP4, CDKN1A, GAREM1, GSK-3β, DEFB103A KRTAP9-2, YAP1, S100A7A, FA2H, LOC102190037, LOC102179090, LOC102173866, KRT2, KRT39, FAM167A, FAT4 and EGFL6 were shown to be potentially important in hair follicle development and cycling. They were related to, WNT/β-catenin, mTORC1, ERK/MAPK, Hedgehog, TGFβ, NFkB/p38MAPK, caspase-1, and interleukin (IL)-1a signaling pathways. CONCLUSION This work adds to existing understanding of the regulation of HF development and cycling in cashmere goats via lncRNAs and mRNAs. It also serves as theoretical foundation for future SHF research in cashmere goats.
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Affiliation(s)
- Cuiling Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China.,Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Chongkai Qin
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, 843000, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China.
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China. .,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China.
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Li YC, He DQ, Ma YH, Ma Q, Ding W, Chen YH, Zhang M, Luo F, Chen LY, Wang JK, Jiang L, Li YK, Tao JZ. Skin transcriptome analysis identifies the key genes underlying fur development in Chinese Tan sheep in the birth and Er-mao periods. Gene 2022; 820:146257. [PMID: 35143949 DOI: 10.1016/j.gene.2022.146257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 11/18/2022]
Abstract
Hair follicle development in Tan sheep differs significantly between the birth and Er-mao periods, but the underlying molecular mechanism is still unclear. We profiled the skin transcriptomes of Tan sheep in the birth and Er-mao periods via RNA-seq technology. The Tan sheep examined consisted of three sheep in the birth period and three sheep in the Er-mao period. A total of 364 differentially expressed genes (DEGs) in the skin of Tan sheep between the birth period and the Er-mao period were identified, among which 168 were upregulated and 196 were downregulated. Interestingly, the FOS proto-oncogene (FOS) (fold change = 22.67, P value = 2.15*10^-44) was the most significantly differentially expressed gene. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the FOS gene was significantly enriched in the signaling pathway related to hair follicle development. Immunohistochemical analysis showed that the FOS gene was expressed in the skin of Chinese Tan sheep at the birth and Er-mao periods, with significantly higher expression in the Er-mao period. Our findings suggest that the FOS gene promotes hair follicle development in Tan sheep.
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Affiliation(s)
- Ya Chao Li
- Agricultural College, Ning Xia University, Yin Chuan 750021, China; The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Dong Qian He
- Agricultural College, Ning Xia University, Yin Chuan 750021, China
| | - Yue Hui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Qin Ma
- Animal Science Institute of Ning Xia Agricultural and Forestry Academy, Yin Chuan 750002, China
| | - Wei Ding
- Animal Science Institute of Ning Xia Agricultural and Forestry Academy, Yin Chuan 750002, China
| | - Yong Hong Chen
- Agricultural College, Ning Xia University, Yin Chuan 750021, China
| | - Meng Zhang
- Agricultural College, Ning Xia University, Yin Chuan 750021, China
| | - Fang Luo
- Agricultural College, Ning Xia University, Yin Chuan 750021, China
| | - Li Yao Chen
- Agricultural College, Ning Xia University, Yin Chuan 750021, China
| | - Jun Kui Wang
- Agricultural College, Ning Xia University, Yin Chuan 750021, China
| | - Lin Jiang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Ying Kang Li
- Animal Science Institute of Ning Xia Agricultural and Forestry Academy, Yin Chuan 750002, China.
| | - Jin Zhong Tao
- Agricultural College, Ning Xia University, Yin Chuan 750021, China.
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10
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Identification and Molecular Analysis of m6A-circRNAs from Cashmere Goat Reveal Their Integrated Regulatory Network and Putative Functions in Secondary Hair Follicle during Anagen Stage. Animals (Basel) 2022; 12:ani12060694. [PMID: 35327094 PMCID: PMC8944478 DOI: 10.3390/ani12060694] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Cashmere is a natural, high-end textile material. It is derived from the secondary hair follicle (SHFs) tissue in the skin of cashmere goats. Previous studies have indicated that m6A modifications in circRNA molecules play important roles in a variety of cells through multiple mechanisms. However, little information is available on the expression profile and functional regulatory characteristics of m6A-modified circRNA (m6A-circRNA) in SHFs of cashmere goats. In this study, a total of 15 m6A-circRNAs were identified. Six of these m6A-circRNAs were revealed to have significantly higher expression in skin at anagen than at telogen. To gain insight into the potential regulatory mechanisms of the anagen up-regulated m6A-circRNAs, we constructed the regulatory networks along with related pathways in SHFs of cashmere goats. In addition, we found that the expression trends of four m6A-circRNAs in the SHFs during SHF cycles were highly similar to their host genes. However, the expression patterns of two m6A-circRNAs were inconsistent with the linear RNAs from their host genes in the SHFs of cashmere goats. These results will provide new insights to elucidate the biological functions and regulatory features of m6A-circRNA in SHF development and cashmere growth in goats. Abstract N6-methyladenosine (m6A) is the most abundant modification in linear RNA molecules. Over the last few years, interestingly, many circRNA molecules are also found to have extensive m6A modification sites with temporal and spatial specific expression patterns. To date, however, little information is available concerning the expression profiling and functional regulatory characteristics of m6A modified circRNAs (m6A-circRNAs) in secondary hair follicles (SHFs) of cashmere goats. In this study, a total of fifteen m6A-circRNAs were identified and characterized in the skin tissue of cashmere goats. Of these, six m6A-circRNAs were revealed to have significantly higher expression in skin at anagen compared with those at telogen. The constructed ceRNA network indicated a complicated regulatory relationship of the six anagen up-regulated m6A-circRNAs through miRNA mediated pathways. Several signaling pathways implicated in the physiological processes of hair follicles were enriched based on the potential regulatory genes of the six anagen up-regulated m6A-circRNAs, such as TGF-beta, axon guidance, ribosome, and stem cell pluripotency regulatory pathways, suggesting the analyzed m6A-circRNAs might be essentially involved in SHF development and cashmere growth in cashmere goats. Further, we showed that four m6A-circRNAs had highly similar expression trends to their host genes in SHFs of cashmere goats including m6A-circRNA-ZNF638, -TULP4, -DNAJB6, and -CAT. However, the expression patterns of two m6A-circRNAs (m6A-circRNA-STAM2 and -CAAP1) were inconsistent with the linear RNAs from their host genes in the SHFs of cashmere goats. These results provide novel information for eluci-dating the biological function and regulatory characteristics of the m6A-circRNAs in SHF development and cashmere growth in goats.
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11
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Qin Y, Xu Y, Zhang Y, Gu M, Cai W, Bai Z, Zhang X, Chen R, Sun Y, Wu Y, Wang Z. Transcriptomics analysis of cashmere fineness functional genes. Anim Biotechnol 2022:1-11. [PMID: 35253626 DOI: 10.1080/10495398.2022.2042306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Liaoning cashmere goat (LCG) is a famous cashmere goat breed in China. Cashmere fineness, as an important index to evaluate cashmere quality, is also one of the problems to be improved for Liaoning cashmere goats. Transcriptome studies all mRNA transcribed by a specific tissue or cell in a certain period. It is a key link in the study of gene expression regulation. It plays an important role in the analysis of biological growth and disease. Transcriptome is spatio-temporal specific, that is, gene expression varies in different tissues or at different times. Three coarser and three fine LCG skin samples were sequenced by RNA-seq technology, and a total of 427 differentially expressed genes were obtained, including 291 up-regulated genes and 136 down-regulated genes. In the experiment, we screened out 16 genes that had significant differences in the expression of coarse and fine cashmere of Liaoning cashmere goats, so it was inferred that these 16 genes might have regulatory effects on cashmere fineness. Moreover, GO gene set enrichment analysis revealed that differential genes mainly consist of immune response, MHC protein complex, Heme binding and other pathways. KEGG analysis showed that transplant-versus-host disease and allograft rejection were the main pathways of differential genes.
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Affiliation(s)
- Yuting Qin
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yinggang Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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12
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Li C, Feng C, Ma G, Fu S, Chen M, Zhang W, Li J. Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus. BMC Genomics 2022; 23:140. [PMID: 35172715 PMCID: PMC8848980 DOI: 10.1186/s12864-022-08331-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/19/2022] [Indexed: 12/29/2022] Open
Abstract
Background Cashmere goat is famous for its high-quality fibers. The growth of cashmere in secondary hair follicles exhibits a seasonal pattern arising from circannual changes in the natural photoperiod. Although several studies have compared and analyzed the differences in gene expression between different hair follicle growth stages, the selection of samples in these studies relies on research experience or morphological evidence. Distinguishing hair follicle growth cycle according to gene expression patterns may help to explore the regulation mechanisms related to cashmere growth and the effect of melatonin from a molecular level more accurately. Results In this study, we applied RNA-sequencing to the hair follicles of three normal and three melatonin-treated Inner Mongolian cashmere goats sampled every month during a whole hair follicle growth cycle. A total of 3559 and 988 genes were subjected as seasonal changing genes (SCGs) in the control and treated groups, respectively. The SCGs in the normal group were divided into three clusters, and their specific expression patterns help to group the hair follicle growth cycle into anagen, catagen and telogen stages. Some canonical pathways such as Wnt, TGF-beta and Hippo signaling pathways were detected as promoting the hair follicle growth, while Cell adhesion molecules (CAMs), Cytokine-cytokine receptor interaction, Jak-STAT, Fc epsilon RI, NOD-like receptor, Rap1, PI3K-Akt, cAMP, NF-kappa B and many immune-related pathways were detected in the catagen and telogen stages. The PI3K-Akt signaling, ECM-receptor interaction and Focal adhesion were found in the transition stage between telogen to anagen, which may serve as candidate biomarkers for telogen-anagen regeneration. A total of 16 signaling pathways, 145 pathway mRNAs, and 93 lncRNAs were enrolled to construct the pathway-mRNA-lncRNA network, which indicated the function of lncRNAs through interacting with their co-expressed mRNAs. Pairwise comparisons between the control and melatonin-treated groups also indicated 941 monthly differentially expressed genes (monthly DEGs). These monthly DEGs were mainly distributed from April and September, which revealed a potential signal pathway map regulating the anagen stage triggered by melatonin. Enrichment analysis showed that Wnt, Hedgehog, ECM, Chemokines and NF-kappa B signaling pathways may be involved in the regulation of non-quiescence and secondary shedding under the influence of melatonin. Conclusions Our study decoded the key regulators of the whole hair follicle growth cycle, laying the foundation for the control of hair follicle growth and improvement of cashmere yield. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08331-z.
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Affiliation(s)
- Chun Li
- College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Cong Feng
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangyuan Ma
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shaoyin Fu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010018, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, China.
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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13
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Wang Z, Wang Y, Hui T, Chen R, Xu Y, Zhang Y, Tian H, Wang W, Cong Y, Guo S, Zhu Y, Zhang X, Guo D, Bai M, Fan Y, Yue C, Bai Z, Sun J, Cai W, Zhang X, Gu M, Qin Y, Sun Y, Wu Y, Wu R, Dou X, Bai W, Zheng Y. Single-Cell Sequencing Reveals Differential Cell Types in Skin Tissues of Liaoning Cashmere Goats and Key Genes Related Potentially to the Fineness of Cashmere Fiber. Front Genet 2021; 12:726670. [PMID: 34858469 PMCID: PMC8631524 DOI: 10.3389/fgene.2021.726670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
Cashmere fineness is one of the important factors determining cashmere quality; however, our understanding of the regulation of cashmere fineness at the cellular level is limited. Here, we used single-cell RNA sequencing and computational models to identify 13 skin cell types in Liaoning cashmere goats. We also analyzed the molecular changes in the development process by cell trajectory analysis and revealed the maturation process in the gene expression profile in Liaoning cashmere goats. Weighted gene co-expression network analysis explored hub genes in cell clusters related to cashmere formation. Secondary hair follicle dermal papilla cells (SDPCs) play an important role in the growth and density of cashmere. ACTA2, a marker gene of SDPCs, was selected for immunofluorescence (IF) and Western blot (WB) verification. Our results indicate that ACTA2 is mainly expressed in SDPCs, and WB results show different expression levels. COL1A1 is a highly expressed gene in SDPCs, which was verified by IF and WB. We then selected CXCL8 of SDPCs to verify and prove the differential expression in the coarse and fine types of Liaoning cashmere goats. Therefore, the CXCL8 gene may regulate cashmere fineness. These genes may be involved in regulating the fineness of cashmere in goat SDPCs; our research provides new insights into the mechanism of cashmere growth and fineness regulation by cells.
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Affiliation(s)
- Zeying Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Yanru Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Taiyu Hui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - He Tian
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuyan Cong
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Suping Guo
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanxu Zhu
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xinghui Zhang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Dan Guo
- Liaoning Provincial Department of Science and Technology, Shenyang, China
| | - Man Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yixing Fan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chang Yue
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jiaming Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuting Qin
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yinggang Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Wenlin Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuanyuan Zheng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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14
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Ge W, Zhang W, Zhang Y, Zheng Y, Li F, Wang S, Liu J, Tan S, Yan Z, Wang L, Shen W, Qu L, Wang X. A Single-cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:437-451. [PMID: 34534715 PMCID: PMC8864196 DOI: 10.1016/j.gpb.2021.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/17/2021] [Accepted: 08/02/2021] [Indexed: 01/06/2023]
Abstract
Cashmere, also known as soft gold, is produced from the secondary hair follicles (SHFs) of cashmere goats. The number of SHFs determines the yield and quality of cashmere; therefore, it is of interest to investigate the transcriptional profiles present during cashmere goat hair follicle development. However, mechanisms underlying this development process remain largely unexplored, and studies regarding hair follicle development mostly use a murine research model. In this study, to provide a comprehensive understanding of cellular heterogeneity and cell fate decisions, single-cell RNA sequencing was performed on 19,705 single cells of the dorsal skin from cashmere goat fetuses at induction (embryonic day 60; E60), organogenesis (E90), and cytodifferentiation (E120) stages. For the first time, unsupervised clustering analysis identified 16 cell clusters, and their corresponding cell types were also characterized. Based on lineage inference, a detailed molecular landscape was revealed along the dermal and epidermal cell lineage developmental pathways. Notably, our current data also confirmed the heterogeneity of dermal papillae from different hair follicle types, which was further validated by immunofluorescence analysis. The current study identifies different biomarkers during cashmere goat hair follicle development and has implications for cashmere goat breeding in the future.
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Affiliation(s)
- Wei Ge
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weidong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuelang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yujie Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shanhe Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; College of Animal Science & Technology, Yangzhou University, Yangzhou 225000, China
| | - Jinwang Liu
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Shaojing Tan
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Zihui Yan
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Lu Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Lei Qu
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Xin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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15
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Maleki M, Khelghati N, Alemi F, Younesi S, Asemi Z, Abolhasan R, Bazdar M, Samadi-Kafil H, Yousefi B. Multiple interactions between melatonin and non-coding RNAs in cancer biology. Chem Biol Drug Des 2021; 98:323-340. [PMID: 33905613 DOI: 10.1111/cbdd.13849] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022]
Abstract
The melatonin hormone secreted by the pineal gland is involved in physiological functions such as growth and maturation, circadian cycles, and biological activities including antioxidants, anti-tumor, and anti-ischemia. Melatonin not only interacts with proteins but also has functional effects on regulatory RNAs such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). In this study, we overview various physiological and pathological conditions affecting melatonin through lncRNA and miRNA. The information compiled herein will serve as a solid foundation to formulate ideas for future mechanistic studies on melatonin. It will also provide a chance to more clarify the emerging functions of the non-coding transcriptome.
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Affiliation(s)
- Masomeh Maleki
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Nafiseh Khelghati
- Department of Clinical Biochemistry, Urmia University of Medical Sciences, Urmia, Iran
| | - Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Simin Younesi
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Vic., Australia
| | - Zatollah Asemi
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Vic., Australia.,Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Rozita Abolhasan
- Stem Cell and Regenerative Medicine Institute (SCARM), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahtab Bazdar
- Department of Clinical Biochemistry, Urmia University of Medical Sciences, Urmia, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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16
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Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection. PLoS One 2021; 16:e0248405. [PMID: 33720948 PMCID: PMC7959398 DOI: 10.1371/journal.pone.0248405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal nematodes (GIN) are an important constraint in small ruminant production. Genetic selection for resistant animals is a potential sustainable control strategy. Advances in molecular genetics have led to the identification of several molecular genetic markers associated with genes affecting economic relevant traits. In this study, the variants in the genome of Creole goats resistant or susceptible to GIN were discovered from RNA-sequencing. We identified SNPs, insertions and deletions that distinguish the two genotypes, resistant and susceptible and we characterized these variants through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype with 78% of the genes involved in this pathway showing genomic variants. These genomic variants are expected to provide useful resources especially for molecular breeding for GIN resistance in goats.
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17
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Yang F, Liu Z, Zhao M, Mu Q, Che T, Xie Y, Ma L, Mi L, Li J, Zhao Y. Skin transcriptome reveals the periodic changes in genes underlying cashmere (ground hair) follicle transition in cashmere goats. BMC Genomics 2020; 21:392. [PMID: 32503427 PMCID: PMC7275469 DOI: 10.1186/s12864-020-06779-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
Background Cashmere goats make an outstanding contribution to the livestock textile industry and their cashmere is famous for its slenderness and softness and has been extensively studied. However, there are few reports on the molecular regulatory mechanisms of the secondary hair follicle growth cycle in cashmere goats. In order to explore the regular transition through the follicle cycle and the role of key genes in this cycle, we used a transcriptome sequencing technique to sequence the skin of Inner Mongolian cashmere goats during different months. We analyzed the variation and difference in genes throughout the whole hair follicle cycle. We then verified the regulatory mechanism of the cashmere goat secondary hair follicle growth cycle using fluorescence quantitative PCR. Results The growth cycle of cashmere hair could be divided into three distinct periods: a growth period (March–September), a regression period (September–December), and a resting period (December–March). The results of differential gene analyses showed that March was the most significant month. Cluster analysis of gene expression throughout the whole growth cycle further supported the key nodes of the three periods of cashmere growth, and the differential gene expression of keratin corresponding to the ground haircashmere growth cycle further supported the results from tissue slices. Quantitative fluorescence analysis showed that KAP3–1, KRTAP 8–1, and KRTAP 24–1 genes had close positive correlation with the cashmere growth cycle, and their regulation was consistent with the growth cycle of cashmere. Conclusion The growth cycle of cashmere cashmere could be divided into three distinct periods: a growth period (March–September), a regression period (September–December) and a resting period (December–March). March was considered to be the beginning of the cycle. KAP and KRTAP showed close positive correlation with the growth cycle of secondary hair follicle cashmere growth, and their regulation was consistent with the cashmere growth cycle. But hair follicle development-related genes are expressed earlier than cashmere growth, indicating that cycle regulation could alter the temporal growth of cashmere. This study laid a theoretical foundation for the study of the cashmere development cycle and provided evidence for key genes during transition through the cashmere cycle. Our study provides a theoretical basis for cashmere goat breeding.
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Affiliation(s)
- Feng Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Meng Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Qing Mu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tianyu Che
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yuchun Xie
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lina Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lu Mi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Yanhong Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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18
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Su R, Gong G, Zhang L, Yan X, Wang F, Zhang L, Qiao X, Li X, Li J. Screening the key genes of hair follicle growth cycle in Inner Mongolian Cashmere goat based on RNA sequencing. Arch Anim Breed 2020; 63:155-164. [PMID: 32490151 PMCID: PMC7256851 DOI: 10.5194/aab-63-155-2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/07/2020] [Indexed: 12/23/2022] Open
Abstract
Inner Mongolian Cashmere goat is an excellent local breed
selected for the dual-purpose of cashmere and meat. There are three lines of Inner
Mongolian Cashmere goat: Erlangshan, Alashan and Aerbasi. Cashmere is a kind
of precious textile raw material with a high price. Cashmere is derived from
secondary hair follicle (SHF), while hair is derived from primary hair
follicle (PHF). The growth cycle of SHF of cashmere goat is 1 year, and it
can be divided into three different stages: anagen, catagen and telogen. In
this study, we tried to find some important influence factors of SHF growth
cycle in skin tissue from Inner Mongolian Cashmere goats by RNA sequencing
(RNA-Seq). Three female Aerbasi Inner Mongolian Cashmere goats (2 years old)
were used as experimental samples in this study. Skin samples were collected
in September (anagen), December (catagen) and March (telogen) at dorsal side
from cashmere goats. Results showed that over 511 396 044 raw reads and
487 729 890 clean reads were obtained from sequence data. In total, 51
different expression genes (DEGs) including 29 downregulated genes and 22 upregulated genes were enriched in anagen–catagen comparing group. The 443 DEGs
contained 117 downregulated genes and 326 upregulated genes that were enriched
in catagen–telogen comparing group. In telogen–anagen comparing group, 779
DEGs were enriched including 582 downregulated genes and 197 upregulated
genes. The result of gene ontology (GO) annotation showed that DEGs are in
different growth cycle periods, and enriched GO items are mostly related to the
transformation of cell and protein. The Kyoto Encyclopedia of Genes and Genomes
(KEGG) enrichment result indicated that metabolic process has a great impact on
SHF growth cycle. Based on the results of a comprehensive analysis of
differentially expressed genes, GO enrichment and KEGG enrichment, we found
that FGF5, FGFR1 and RRAS had an effect on the hair follicle growth cycle. The results of
this study may provide a theoretical basis for further research on the
growth and development of SHF in Inner Mongolian Cashmere goats.
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Affiliation(s)
- Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, 010018, China.,Engineering Research Center for Goat Genetics and Breeding, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Gao Gong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Lingtian Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Fenghong Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Lei Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Xian Qiao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Xiaokai Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, 010018, China.,Engineering Research Center for Goat Genetics and Breeding, Hohhot, Inner Mongolia Autonomous Region, 010018, China
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19
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Discovery of genes and proteins possibly regulating mean wool fibre diameter using cDNA microarray and proteomic approaches. Sci Rep 2020; 10:7726. [PMID: 32382132 PMCID: PMC7206055 DOI: 10.1038/s41598-020-64903-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/30/2020] [Indexed: 01/06/2023] Open
Abstract
Wool fibre diameter (WFD) is one of the wool traits with higher economic impact. However, the main genes specifically regulating WFD remain unidentified. In this current work we have used Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin, bearing more wool, in Aohan fine wool sheep, a Chinese indigenous breed, and compared them with that of small tail Han sheep, a sheep bread with coarse wool. Microarray analyses showed that most of the genes likely determining wool diameter could be classified into a few categories, including immune response, regulation of receptor binding and growth factor activity. Certain gene families might play a role in hair growth regulation. These include growth factors, immune cytokines, solute carrier families, cellular respiration and glucose transport amongst others. Proteomic analyses also identified scores of differentially expressed proteins.
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20
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He N, Su R, Wang Z, Zhang Y, Li J. Exploring differentially expressed genes between anagen and telogen secondary hair follicle stem cells from the Cashmere goat (Capra hircus) by RNA-Seq. PLoS One 2020; 15:e0231376. [PMID: 32298297 PMCID: PMC7162518 DOI: 10.1371/journal.pone.0231376] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/23/2020] [Indexed: 12/17/2022] Open
Abstract
Hair follicle stem cells (HFSCs) have been shown to be essential in the development and regeneration of hair follicles (HFs). The Inner Mongolia Cashmere goat (Capra hircus) has two types of HFs, primary and secondary, with cashmere being produced from the secondary hair follicle. To identify the genes associated with cashmere growth, transcriptome profiling of anagen and telogen secondary HFSCs was performed by RNA-Seq. The RNA-Seq analysis generated over 58 million clean reads from each group, with 2717 differentially expressed genes (DEGs) detected between anagen and telogen, including 1500 upregulated and 1217 downregulated DEGs. A large number of DEGs were predominantly associated with cell part, cellular process, binding, biological regulation and organelle. In addition, the PI3K-Akt, MAPK, Ras and Rap1 signaling pathways may be involved in the growth of HFSCs cultured in vitro. The RNA-Seq results showed that the well-defined HFSC signature genes and cell cycle-associated genes showed no significant differences between anagen and telogen HFSCs, indicating a relatively quiescent cellular state of the HFSCs cultured in vitro. These results are useful for future studies of complex molecular mechanisms of hair follicle cycling in cashmere goats.
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Affiliation(s)
- Nimantana He
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Agriculture Research Center, Chifeng University, Chifeng, Inner Mongolia, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, Inner Mongolia Autonomous Region, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, Inner Mongolia Autonomous Region, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, Inner Mongolia Autonomous Region, China
- * E-mail:
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21
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Identification and characterization of circRNAs in the skin during wool follicle development in Aohan fine wool sheep. BMC Genomics 2020; 21:187. [PMID: 32111155 PMCID: PMC7048093 DOI: 10.1186/s12864-020-6599-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/20/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important to improve wool quality and yield. Circular RNAs (circRNAs) are widely expressed non-coding RNAs that can act as competitive endogenous RNAs (ceRNAs) to bind to miRNAs. Although circRNAs have been studied in many fields, research on their activity in sheep wool follicles is limited. To understand the regulation of circRNAs in the growth of fine wool in sheep, we used RNA-Seq to identify circRNAs in sheep shoulder skin samples at three developmental stages: embryonic day 90 (E90d), embryonic day 120 (E120d), and at birth (Birth). RESULTS We identified 8753 circRNAs and found that 918 were differentially-expressed. We then analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we identified the source genes of circRNAs, which were mainly enriched in cellular component organization, regulation of primary metabolic processes, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predicted interactions between 17 circRNAs and eight miRNAs, using miRanda software. Based on the significant pathways, we speculate that circ_0005720, circ_0001754, circ_0008036, circ_0004032, circ_0005174, circ_0005519, and circ_0007826 might play an important role in regulating wool follicle growth in AFWS. Seven circRNAs were randomly selected to validate the RNA-Seq results, using qRT-PCR. CONCLUSION Our results provide more information about circRNAs regulation of wool follicle development in AFWS, and establish a solid foundation for future research.
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22
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Comparative study on seasonal hair follicle cycling by analysis of the transcriptomes from cashmere and milk goats. Genomics 2019; 112:332-345. [PMID: 30779940 DOI: 10.1016/j.ygeno.2019.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 01/06/2023]
Abstract
Guard hair and cashmere undercoat are developed from primary and secondary hair follicle, respectively. Little is known about the gene expression differences between primary and secondary hair follicle cycling. In this study, we obtained RNA-seq data from cashmere and milk goats grown at four different seasons. We studied the differentially expressed genes (DEGs) during the yearly hair follicle cycling, and between cashmere and milk goats. WNT, NOTCH, MAPK, BMP, TGFβ and Hedgehog signaling pathways were involved in hair follicle cycling in both cashmere and milk goat. However, Milk goat DEGs between different months were significantly more than cashmere goat DEGs, with the largest difference being identified in December. Some expression dynamics were confirmed by quantitative PCR and western blot, and immunohistochemistry. This study offers new information sources related to hair follicle cycling in milk and cashmere goats, which could be applicable to improve the wool production and quality.
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23
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Analyses of histological and transcriptome differences in the skin of short-hair and long-hair rabbits. BMC Genomics 2019; 20:140. [PMID: 30770723 PMCID: PMC6377753 DOI: 10.1186/s12864-019-5503-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/31/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Hair fibre length is an important economic trait of rabbits in fur production. However, molecular mechanisms regulating rabbit hair growth have remained elusive. RESULTS Here we aimed to characterise the skin traits and gene expression profiles of short-hair and long-hair rabbits by histological and transcriptome analyses. Haematoxylin-eosin staining was performed to observe the histological structure of the skin of short-hair and long-hair rabbits. Compared to that in short-hair rabbits, a significantly longer anagen phase was observed in long-hair rabbits. In addition, by RNA sequencing, we identified 951 genes that were expressed at significantly different levels in the skin of short-hair and long-hair rabbits. Nine significantly differentially expressed genes were validated by quantitative real-time polymerase chain reaction. A gene ontology analysis revealed that epidermis development, hair follicle development, and lipid metabolic process were significantly enriched. Further, we identified potential functional genes regulating follicle development, lipid metabolic, and apoptosis as well as important pathways including extracellular matrix-receptor interaction and basal cell carcinoma pathway. CONCLUSIONS The present study provides transcriptome evidence for the differences in hair growth between short-hair and long-hair rabbits and reveals that lipid metabolism and apoptosis might constitute major factors contributing to hair length.
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24
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Su R, Fan Y, Qiao X, Li X, Zhang L, Li C, Li J. Transcriptomic analysis reveals critical genes for the hair follicle of Inner Mongolia cashmere goat from catagen to telogen. PLoS One 2018; 13:e0204404. [PMID: 30356261 PMCID: PMC6200190 DOI: 10.1371/journal.pone.0204404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
There are two main types of hair follicle in Inner Mongolia Cashmere goats, the primary hair follicle (PHF) producing hair fibers and the secondary hair follicle (SHF) producing cashmere fibers. Of both fibers from cashmere-bearing goats in Aerbasi, Inner Mongolia, the timing of cyclical phases for the cashmere have been well clarified but hair fibers have been less noticeable. Herein, we evaluated transcriptome of PHF and SHF from the same three goats in Aerbasi at the catagen- and telogen phase of cashmere growth. We totally found 1977 DEGs between PHFs at the telogen and catagen phases of SHF, 1199 DEGs between telogen- and catagen SHF, 2629 DEGs between PHF at the catagen phase of SHF and catagen SHF, and 755 DEGs between PHF at the telogen phase of SHF and telogen SHF. By analyzing gene functions based on GO and KEGG database, we found that the DEGs have functions in muscle contraction and muscle filament sliding between catagen- and telogen SHF, indicating that arrector pilli muscles might play a role on the transition from catagen to telogen. Moreover, considering that the enriched GO and KEGG categories of the DEGs between PHF and SHF, we suggested that part of PHF might rest in their own anagen phase when SHF are at catagen, but PHF might enter into the telogen phase at SHF’s telogen. Finally, we highly recommended the several potential genes acting as the regulators of the transition between growth phases including IL17RB and eight members of ZNF. These results provide insight into molecular mechanisms on the transition of SHF from catagen to telogen together with PHF’s growth situation at SHF’s catagen and telogen in Inner Mongolia Cashmere goats.
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Affiliation(s)
- Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Yixing Fan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xian Qiao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaokai Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lei Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Chun Li
- College of Animal Science, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
- * E-mail:
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25
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Li C, Li Y, Zhou G, Gao Y, Ma S, Chen Y, Song J, Wang X. Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cycling. BMC Genomics 2018; 19:638. [PMID: 30153818 PMCID: PMC6114738 DOI: 10.1186/s12864-018-5002-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/08/2018] [Indexed: 01/07/2023] Open
Abstract
Background Hair follicles (HFs), upon development, undergo repetitive cycles of growth (anagen), regression (catagen), and rest (telogen). The transition between the stages is determined by multiple molecular signals, including DNA methylation, which plays important roles in mammalian cellular identity and is essential for the development of HFs. Secondary hair follicles (SHFs) in cashmere goat exhibit classic cyclic hair development, and little has been done on a genome-wide scale to examine potentially methylated genes involved in the hair cyclic transition. Results Genome-wide DNA methylation profiles between skin tissues sampled during the anagen and telogen stages in cashmere goats were investigated using whole-genome bisulfite sequencing (WGBS). The methylation status was observed to be higher in the skin samples with HFs in the telogen than those in the anagen stage. A total of 1311 differentially methylated regions (DMRs) were identified between the two groups, which contained 493 fully annotated DMR-related genes (DMGs) (269 Hyper- DMGs and 224 Hypo-DMGs). Furthermore, a significant over-representation of the functional categories for DMGs related to immune response and intercellular crosstalk during hair cycling was observed. By integrating DNA methylation and mRNA expression data, we revealed that four genes (FMN1, PCOLCE, SPTLC3, and COL5A1) are crucial factors for elucidating epigenetic mechanisms contributing to the telogen-to-anagen transition. Conclusion Our study provided systematic methylome maps pertaining to the hair cycling stages (anagen vs telogen) at a single-base resolution, and revealed stage-specific methylation loci during cashmere growth or quiescence. Furthermore, we identified epigenetically regulated genes that are potentially involved in HF development and growth in cashmere goats, and likely in other mammal species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5002-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ye Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Sen Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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26
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Ge W, Wang SH, Sun B, Zhang YL, Shen W, Khatib H, Wang X. Melatonin promotes Cashmere goat (Capra hircus) secondary hair follicle growth: a view from integrated analysis of long non-coding and coding RNAs. Cell Cycle 2018; 17:1255-1267. [PMID: 29895193 DOI: 10.1080/15384101.2018.1471318] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The role of melatonin in promoting the yield of Cashmere goat wool has been demonstrated for decades though there remains a lack of knowledge regarding melatonin mediated hair follicle growth. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are widely transcribed in the genome and play ubiquitous roles in regulating biological processes. However, the role of lncRNAs in regulating melatonin mediated hair follicle growth remains unclear. In this study, we established an in vitro Cashmere goat secondary hair follicle culture system, and demonstrated that 500 ng/L melatonin exposure promoted hair follicle fiber growth. Based on long intergenic RNA sequencing, we demonstrated that melatonin promoted hair follicle elongation via regulating genes involved in focal adhesion and extracellular matrix receptor pathways and further cis predicting of lncRNAs targeted genes indicated that melatonin mediated lncRNAs mainly targeted vascular smooth muscle contraction and signaling pathways regulating the pluripotency of stem cells. We proposed that melatonin exposure not only perturbed key signals secreted from hair follicle stem cells to regulate hair follicle development, but also mediated lncRNAs mainly targeted to pathways involved in the microvascular system and extracellular matrix, which constitute the highly orchestrated microenvironment for hair follicle stem cell. Taken together, our findings here provide a profound view of lncRNAs in regulating Cashmere goat hair follicle circadian rhythms and broaden our knowledge on melatonin mediated hair follicle morphological changes.
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Affiliation(s)
- Wei Ge
- a College of Animal Science & Technology , Northwest A&F University , Yangling , China
| | - Shan-He Wang
- a College of Animal Science & Technology , Northwest A&F University , Yangling , China
| | - Bing Sun
- a College of Animal Science & Technology , Northwest A&F University , Yangling , China
| | - Yue-Lang Zhang
- a College of Animal Science & Technology , Northwest A&F University , Yangling , China
| | - Wei Shen
- b College of Life Sciences, Institute of Reproductive Sciences , Qingdao Agricultural University , Qingdao , China
| | - Hasan Khatib
- c Department of Animal Sciences , University of Wisconsin-Madison , Madison , WI , USA
| | - Xin Wang
- a College of Animal Science & Technology , Northwest A&F University , Yangling , China
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27
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Construction of lentiviral RNAi vector of PPARγ gene in cashmere goats and comparison with the transcriptome analysis of adipose cells treatments. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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28
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Li X, Su R, Wan W, Zhang W, Jiang H, Qiao X, Fan Y, Zhang Y, Wang R, Liu Z, Wang Z, Liu B, Ma Y, Zhang H, Zhao Q, Zhong T, Di R, Jiang Y, Chen W, Wang W, Dong Y, Li J. Identification of selection signals by large-scale whole-genome resequencing of cashmere goats. Sci Rep 2017; 7:15142. [PMID: 29123196 PMCID: PMC5680388 DOI: 10.1038/s41598-017-15516-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/27/2017] [Indexed: 01/14/2023] Open
Abstract
Inner Mongolia and Liaoning cashmere goats are two outstanding Chinese multipurpose breeds that adapt well to the semi-arid temperate grassland. These two breeds are characterized by their soft cashmere fibers, thus making them great models to identify genomic regions that are associated with cashmere fiber traits. Whole-genome sequencing of 70 cashmere goats produced more than 5.52 million single-nucleotide polymorphisms and 710,600 short insertions and deletions. Further analysis of these genetic variants showed some population-specific molecular markers for the two cashmere goat breeds that are otherwise phenotypically similar. By analyzing FST and θπ outlier values, we identified 135 genomic regions that were associated with cashmere fiber traits within the cashmere goat populations. These selected genomic regions contained genes, which are potential involved in the production of cashmere fiber, such as FGF5, SGK3, IGFBP7, OXTR, and ROCK1. Gene ontology enrichment analysis of identified short insertions and deletions also showed enrichment in keratinocyte differentiation and epidermal cell differentiation. These findings demonstrate that this genomic resource will facilitate the breeding of cashmere goat and other Capra species in future.
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Affiliation(s)
- Xiaokai Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Wenting Wan
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Huaizhi Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Xian Qiao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yixing Fan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Bin Liu
- Institute of Animal Husbandry, Academy of Agriculture and Stockbreeding Sciences, Hohhot, Inner Mongolia, 010030, China
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianjun Zhao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ran Di
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Wei Chen
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China. .,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China.
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
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29
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Zhao B, Chen Y, Yan X, Hao Y, Zhu J, Weng Q, Wu X. Gene expression profiling analysis reveals fur development in rex rabbits (Oryctolagus cuniculus). Genome 2017; 60:1060-1067. [PMID: 28850794 DOI: 10.1139/gen-2017-0003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fur is an important economic trait in rabbits. The identification of genes that influence fur development and knowledge regarding the actions of these genes provides useful tools for improving fur quality. However, the mechanism of fur development is unclear. To obtain candidate genes related to fur development, the transcriptomes of tissues from backs and bellies of Chinchilla rex rabbits were compared. Of the genes analyzed, 336 showed altered expression in the two groups (285 upregulated and 51 downregulated, P ≤ 0.05, fold-change ≥2 or ≤0.5). Using GO and KEGG to obtain gene classes that were differentially enriched, we found several genes to be involved in many important biological processes. In addition, we identified several signaling pathways involved in fur development, including the Wnt and MAPK signaling pathways, revealing mechanisms of skin and hair follicle development, and epidermal cell and keratinocytes differentiation. The obtained rabbit transcriptome and differentially expressed gene profiling data provided comprehensive gene expression information for SFRP2, FRZB, CACNG1, SLC25A4, and SLC16A3. To validate the RNA-seq data, the expression levels of eight differentially expressed genes involved in fur development were confirmed by qRT-PCR. The results of rabbit transcriptomic profiling provide a basis for understanding the molecular mechanisms of fur development.
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Affiliation(s)
- BoHao Zhao
- a The Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yang Chen
- a The Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - XiaoRong Yan
- a The Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ye Hao
- a The Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jie Zhu
- a The Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - QiaoQing Weng
- b Zhejiang Yuyao Xinnong Rabbit Industry Co., Ltd., Yuyao, Zhejiang 315400, China
| | - XinSheng Wu
- a The Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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Bai WL, Zhao SJ, Wang ZY, Zhu YB, Dang YL, Cong YY, Xue HL, Wang W, Deng L, Guo D, Wang SQ, Zhu YX, Yin RH. LncRNAs in Secondary Hair Follicle of Cashmere Goat: Identification, Expression, and Their Regulatory Network in Wnt Signaling Pathway. Anim Biotechnol 2017; 29:199-211. [PMID: 28846493 DOI: 10.1080/10495398.2017.1356731] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a novel class of eukaryotic transcripts. They are thought to act as a critical regulator of protein-coding gene expression. Herein, we identified and characterized 13 putative lncRNAs from the expressed sequence tags from secondary hair follicle of Cashmere goat. Furthermore, we investigated their transcriptional pattern in secondary hair follicle of Liaoning Cashmere goat during telogen and anagen phases. Also, we generated intracellular regulatory networks of upregulated lncRNAs at anagen in Wnt signaling pathway based on bioinformatics analysis. The relative expression of six putative lncRNAs (lncRNA-599618, -599556, -599554, -599547, -599531, and -599509) at the anagen phase is significantly higher than that at telogen. Compared with anagen, the relative expression of four putative lncRNAs (lncRNA-599528, -599518, -599511, and -599497) was found to be significantly upregulated at telogen phase. The network generated showed that a rich and complex regulatory relationship of the putative lncRNAs and related miRNAs with their target genes in Wnt signaling pathway. Our results from the present study provided a foundation for further elucidating the functional and regulatory mechanisms of these putative lncRNAs in the development of secondary hair follicle and cashmere fiber growth of Cashmere goat.
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Affiliation(s)
- Wen L Bai
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Su J Zhao
- b Institute of Biotechnology , Sichuan Animal Science Academy , Chengdu , P. R. China
| | - Ze Y Wang
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Yu B Zhu
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Yun L Dang
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Yu Y Cong
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Hui L Xue
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Wei Wang
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Liang Deng
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Dan Guo
- c Academy of Animal Husbandry Science of Liaoning Province , Liaoyang , P. R. China
| | - Shi Q Wang
- c Academy of Animal Husbandry Science of Liaoning Province , Liaoyang , P. R. China
| | - Yan X Zhu
- c Academy of Animal Husbandry Science of Liaoning Province , Liaoyang , P. R. China
| | - Rong H Yin
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
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Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages. PLoS One 2017; 12:e0182602. [PMID: 28800357 PMCID: PMC5553645 DOI: 10.1371/journal.pone.0182602] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/23/2017] [Indexed: 11/24/2022] Open
Abstract
Intramuscular fat (IMF) content and fatty acid composition of longissimus dorsi muscle (LM) change with growth, which partially determines the flavor and nutritional value of goat (Capra hircus) meat. However, unlike cattle, little information is available on the transcriptome-wide changes during different postnatal stages in small ruminants, especially goats. In this study, the sequencing reads of goat LM tissues collected from kid, youth, and adult period were mapped to the goat genome. Results showed that out of total 24 689 Unigenes, 20 435 Unigenes were annotated. Based on expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM), 111 annotated differentially expressed genes (DEGs) were identified among different postnatal stages, which were subsequently assigned to 16 possible expression patterns by series-cluster analysis. Functional classification by Gene Ontology (GO) analysis was used for selecting the genes showing highest expression related to lipid metabolism. Finally, we identified the node genes for lipid metabolism regulation using co-expression analysis. In conclusion, these data may uncover candidate genes having functional roles in regulation of goat muscle development and lipid metabolism during the various growth stages in goats.
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Guo H, Cheng G, Li Y, Zhang H, Qin K. A Screen for Key Genes and Pathways Involved in High-Quality Brush Hair in the Yangtze River Delta White Goat. PLoS One 2017; 12:e0169820. [PMID: 28125615 PMCID: PMC5268778 DOI: 10.1371/journal.pone.0169820] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/22/2016] [Indexed: 11/19/2022] Open
Abstract
The Yangtze River Delta White Goat is the only goat breed that produces high-quality brush hair, or type III hair, which is specialized for use in top-grade writing brushes. There has been little research, especially molecular research, on the traits that result in high-quality brush hair in the Yangtze River Delta White Goat. To explore the molecular mechanisms of the formation of high-quality brush hair, High-throughput RNA-Seq technology was used to compare skin samples from Yangtze River Delta White Goats that produce high-quality hair and non high-quality hair for identification of the important genes and related pathways that might influence the hair quality traits. The results showed that 295 genes were expressed differentially between the goats with higher and lower hair quality, respectively. Of those genes, 132 were up-regulated, 62 were down-regulated, and 101 were expressed exclusively in the goats with high-quality brush hair. Gene Ontology and Metabolic Pathway Significant Enrichment analyses of the differentially expressed genes indicated that the MAP3K1, DUSP1, DUSP6 and the MAPK signaling pathway might play important roles in the traits important for high-quality brush hair.
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Affiliation(s)
- Haiyan Guo
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohu Cheng
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yongjun Li
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- * E-mail:
| | - Hao Zhang
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kangle Qin
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Ji XY, Wang JX, Liu B, Zheng ZQ, Fu SY, Tarekegn GM, Bai X, Bai YS, Li H, Zhang WG. Comparative Transcriptome Analysis Reveals that a Ubiquitin-Mediated Proteolysis Pathway Is Important for Primary and Secondary Hair Follicle Development in Cashmere Goats. PLoS One 2016; 11:e0156124. [PMID: 27695037 PMCID: PMC5047472 DOI: 10.1371/journal.pone.0156124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
Background The fleece of cashmere goats contains two distinct populations of fibers, a short and fine non-medullated insulating cashmere fiber and a long and coarse medullated guard hair. The former is produced by secondary follicles (SFs) and the later by primary follicles (PFs). Evidence suggests that the induction of PFs and SFs may require different signaling pathways. The regulation of BMP2/4 signaling by noggin and Edar signaling via Downless genes are essential for the induction of SFs and PFs, respectively. However, these differently expressed genes of the signaling pathway cannot directly distinguish between the PFs and SFs. Results In this study, we selected RNA samples from 11 PFs and 7 SFs that included 145,525 exons. The pathway analysis of 4512 differentially expressed exons revealed that the most statistically significant metabolic pathway was related to the ubiquitin–mediated proteolysis pathway (UMPP) (P<3.32x 10−7). In addition, the 51 exons of the UMPP that were differentially expressed between the different types of hair follicle (HFs) were compared by cluster analysis. This resulted in the PFs and SFs being divided into two classes. The expression level of two selected exons was analyzed by qRT-PCR, and the results indicated that the expression patterns were consistent with the deep sequencing results obtained by RNA-Seq. Conclusions Based on the comparative transcriptome analysis of 18 HFs from cashmere goats, a large number of differentially expressed exons were identified using a high-throughput sequencing approach. This study suggests that UMPP activation is a prominent signaling pathway for distinguishing the PFs and SFs of cashmere goats. It is also a meaningful contribution to the theoretical basis of the biological study of the HFs of cashmere goats and other mammals.
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Affiliation(s)
- Xiao-yang Ji
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Institute of ATCG, Nei Mongol Bio-Information, Hohhot, 010020, China
| | - Jian-xun Wang
- Animal Research institution of Animal Science Academy of XinJiang Uygur Autonomous Region, Urumqi, 830001, China
| | - Bin Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Institute of ATCG, Nei Mongol Bio-Information, Hohhot, 010020, China
| | - Zhu-qing Zheng
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Institute of ATCG, Nei Mongol Bio-Information, Hohhot, 010020, China
| | - Shao-yin Fu
- Institute of ATCG, Nei Mongol Bio-Information, Hohhot, 010020, China
- Inner Mongolia Academy of Agricultural & Animal Husbandry Science, Hohhot, 010031, China
| | - Getinet Mekuriaw Tarekegn
- Department of Microbial, Cellular and molecular biology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Animal production and Technology, Biotechnology Research Institute, Bahir Dar University, Addis Ababa, Ethiopia
| | - Xue Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Institute of ATCG, Nei Mongol Bio-Information, Hohhot, 010020, China
| | - Yong-sheng Bai
- Department of Biology, The Center for Genomic Advocacy, Indiana State University, Terre Haute, Indiana, 47809, United States of America
- * E-mail: (WZ); (YB); (HL)
| | - Heng Li
- College of Life Sciences Inner Mongolia Agricultural University, Hohhot, 010018, China
- * E-mail: (WZ); (YB); (HL)
| | - Wen-guang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Institute of ATCG, Nei Mongol Bio-Information, Hohhot, 010020, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- * E-mail: (WZ); (YB); (HL)
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Zhao J, Liu N, Liu K, He J, Yu J, Bu R, Cheng M, De W, Liu J, Li H. Identification of genes and proteins associated with anagen wool growth. Anim Genet 2016; 48:67-79. [PMID: 27611105 DOI: 10.1111/age.12480] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 02/03/2023]
Abstract
Identifying genes of major effect for wool growth would offer strategies for improving the quality and increasing the yield of fine wool. In this study, we employed the Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin (more wool growing) in Aohan fine wool sheep (a Chinese indigenous breed) in comparison with groin skin (no wool growing) at the anagen stage of the wool follicle. A microarray study revealed that 4772 probes were differentially expressed, including 2071 upregulated and 2701 downregulated probes, in the comparisons of body side skin vs. groin skin (S/G). The microarray results were verified by means of quantitative PCR. A total of 1099 probes were assigned to unique genes/transcripts. The number of distinct genes/transcripts (annotated) was 926, of which 352 were upregulated and 574 were downregulated. In S/G, 13 genes were upregulated by more than 10 fold, whereas 60 genes were downregulated by more than 10 fold. Further analysis revealed that the majority of the genes possibly related to the wool growth could be assigned to categories including regulation of cell division, intermediate filament, cytoskeletal part and growth factor activity. Several potential gene families may participate in hair growth regulation, including fibroblast growth factors, transforming growth factor-β, WNTs, insulin-like growth factor, vascular endothelial growth factors and so on. Proteomic analysis also revealed 196 differentially expressed protein points, of which 121 were identified as single protein points.
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Affiliation(s)
- J Zhao
- Qingdao Agricultural University, Qingdao, 266109, China.,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.,China Agricultural University, Beijing, 100193, China
| | - N Liu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - K Liu
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
| | - J He
- Qingdao Agricultural University, Qingdao, 266109, China
| | - J Yu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - R Bu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - M Cheng
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
| | - W De
- Nanjing Medical University, Nanjing, 210029, China
| | - J Liu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - H Li
- Qingdao Agricultural University, Qingdao, 266109, China.,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
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36
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Zhao J, Li H, Liu K, Zhang B, Li P, He J, Cheng M, De W, Liu J, Zhao Y, Yang L, Liu N. Identification of differentially expressed genes affecting hair and cashmere growth in the Laiwu black goat by microarray. Mol Med Rep 2016; 14:3823-31. [DOI: 10.3892/mmr.2016.5728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 06/30/2016] [Indexed: 11/05/2022] Open
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37
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Gao Y, Wang X, Yan H, Zeng J, Ma S, Niu Y, Zhou G, Jiang Y, Chen Y. Comparative Transcriptome Analysis of Fetal Skin Reveals Key Genes Related to Hair Follicle Morphogenesis in Cashmere Goats. PLoS One 2016; 11:e0151118. [PMID: 26959817 PMCID: PMC4784850 DOI: 10.1371/journal.pone.0151118] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/22/2016] [Indexed: 11/18/2022] Open
Abstract
Cashmere goat skin contains two types of hair follicles (HF): primary hair follicles (PHF) and secondary hair follicles (SHF). Although multiple genetic determinants associated with HF formation have been identified, the molecules that determine the independent morphogenesis of HF in cashmere goats remain elusive. The growth and development of SHF directly influence the quantity and quality of cashmere production. Here, we report the transcriptome profiling analysis of nine skin samples from cashmere goats using 60- and 120-day-old embryos (E60 and E120, respectively), as well as newborns (NB), through RNA-sequencing (RNA-seq). HF morphological changes indicated that PHF were initiated at E60, with maturation from E120, while differentiation of SHF was identified at E120 until formation of cashmere occurred after birth (NB). The RNA-sequencing analysis generated over 20.6 million clean reads from each mRNA library. The number of differentially expressed genes (DEGs) in E60 vs. E120, E120 vs. NB, and E60 vs. NB were 1,024, 0 and 1,801, respectively, indicating that no significant differences were found at transcriptomic levels between E120 and NB. Key genes including B4GALT4, TNC, a-integrin, and FGFR1, were up-regulated and expressed in HF initiation from E60 to E120, while regulatory genes such as GPRC5D, PAD3, HOXC13, PRR9, VSIG8, LRRC15, LHX2, MSX-2, and FOXN1 were up-regulated and expressed in HF keratinisation and hair shaft differentiation from E120 and NB to E60. Several genes belonging to the KRT and KRTAP gene families were detected throughout the three HF developmental stages. The transcriptional trajectory analyses of all DEGs indicated that immune privilege, glycosaminoglycan biosynthesis, extracellular matrix receptor interaction, and growth factor receptors all played dominant roles in the epithelial-mesenchymal interface and HF formation. We found that the Wnt, transforming growth factor-beta/bone morphogenetic protein, and Notch family members played vital roles in HF differentiation and maturation. The DEGs we found could be attributed to the generation and development of HF, and thus will be critically important for improving the quantity and quality of fleece production in animals for fibres.
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Affiliation(s)
- Ye Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
- College of Life Science, Yulin University, Yulin, People’s Republic of China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
- College of Life Science, Yulin University, Yulin, People’s Republic of China
| | - Jie Zeng
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
| | - Sen Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
| | - Yiyuan Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, People’s Republic of China
- * E-mail:
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A Microarray-Based Analysis Reveals that a Short Photoperiod Promotes Hair Growth in the Arbas Cashmere Goat. PLoS One 2016; 11:e0147124. [PMID: 26814503 PMCID: PMC4731399 DOI: 10.1371/journal.pone.0147124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/29/2015] [Indexed: 12/11/2022] Open
Abstract
Many animals exhibit different behaviors in different seasons. The photoperiod can have effects on migration, breeding, fur growth, and other processes. The cyclic growth of the fur and feathers of some species of mammals and birds, respectively, is stimulated by the photoperiod as a result of hormone-dependent regulation of the nervous system. To further examine this phenomenon, we evaluated the Arbas Cashmere goat (Capra hircus), a species that is often used in this type of research. The goats were exposed to an experimentally controlled short photoperiod to study the regulation of cyclic cashmere growth. Exposure to a short photoperiod extended the anagen phase of the Cashmere goat hair follicle to increase cashmere production. Assessments of tissue sections indicated that the short photoperiod significantly induced cashmere growth. This conclusion was supported by a comparison of the differences in gene expression between the short photoperiod and natural conditions using gene chip technology. Using the gene chip data, we identified genes that showed altered expression under the short photoperiod compared to natural conditions, and these genes were found to be involved in the biological processes of hair follicle growth, structural composition of the hair follicle, and the morphogenesis of the surrounding skin appendages. Knowledge about differences in the expression of these genes as well as their functions and periodic regulation patterns increases our understanding of Cashmere goat hair follicle growth. This study also provides preliminary data that may be useful for the development of an artificial method to improve cashmere production by controlling the light cycle, which has practical significance for livestock breeding.
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Deng T, Pang C, Lu X, Zhu P, Duan A, Tan Z, Huang J, Li H, Chen M, Liang X. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One 2016; 11:e0147132. [PMID: 26766209 PMCID: PMC4713091 DOI: 10.1371/journal.pone.0147132] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/29/2015] [Indexed: 01/11/2023] Open
Abstract
The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
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Affiliation(s)
- Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Chunying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xingrong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Peng Zhu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Anqin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Zhengzhun Tan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Jian Huang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Hui Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Mingtan Chen
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
- * E-mail:
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40
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Wang YH, Zhang CL, Plath M, Fang XT, Lan XY, Zhou Y, Chen H. Global transcriptional profiling of longissimus thoracis muscle tissue in fetal and juvenile domestic goat using RNA sequencing. Anim Genet 2015; 46:655-65. [PMID: 26364974 DOI: 10.1111/age.12338] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2015] [Indexed: 01/05/2023]
Abstract
Domestic goats are important meat production animals; however, data from transcriptional profiling of skeletal muscle tissue in goat have thus far been scarce. We used comparative transcriptional profiling based on RNA sequencing of longissimus thoracis muscle tissue obtained from fetal goat muscle tissue (27 512 850 clean cDNA reads) and 6-month-old goat muscle tissue (27 582 908 reads) to identify genes that are differentially expressed, novel transcript units and alternative splicing events. Gene annotation revealed that 15 960 and 14 981 genes were expressed in the fetal and juvenile libraries respectively. We detected 6432 differentially expressed genes and, when considering GO terms, found 34, 27 and 55 terms to be significantly enriched in molecular function, cellular component and biological process categories respectively. Pathway analysis revealed that larger numbers of differentially expressed genes were enriched in fetal myogenesis or cell proliferation and differentiation-related pathways (such as Wnt), genes involved in the cell cycle and the Notch signaling pathway, and most of the differentially expressed genes involved in these pathways were downregulated in the juvenile goat library. These genes may be involved in various regulation mechanisms during muscle tissue differentiation between the two development stages examined herein. The identified novel transcript units, including both non-coding and coding RNA, as well as alternative splicing events increase the level of complexity of regulation mechanisms during muscle tissue formation and differentiation. Our study provides a comparative transcriptome analysis on goat muscle tissue, which will provide a valuable genomic resource for future studies investigating the molecular basis of skeletal muscle development.
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Affiliation(s)
- Y H Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China.,Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - C L Zhang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - M Plath
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China
| | - X T Fang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - X Y Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China
| | - Y Zhou
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China
| | - H Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China
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Expression profiling reveals genes involved in the regulation of wool follicle bulb regression and regeneration in sheep. Int J Mol Sci 2015; 16:9152-66. [PMID: 25915029 PMCID: PMC4463583 DOI: 10.3390/ijms16059152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 01/04/2023] Open
Abstract
Wool is an important material in textile manufacturing. In order to investigate the intrinsic factors that regulate wool follicle cycling and wool fiber properties, Illumina sequencing was performed on wool follicle bulb samples from the middle anagen, catagen and late telogen/early anagen phases. In total, 13,898 genes were identified. KRTs and KRTAPs are the most highly expressed gene families in wool follicle bulb. In addition, 438 and 203 genes were identified to be differentially expressed in wool follicle bulb samples from the middle anagen phase compared to the catagen phase and the samples from the catagen phase compared to the late telogen/early anagen phase, respectively. Finally, our data revealed that two groups of genes presenting distinct expression patterns during the phase transformation may have important roles for wool follicle bulb regression and regeneration. In conclusion, our results demonstrated the gene expression patterns in the wool follicle bulb and add new data towards an understanding of the mechanisms involved in wool fiber growth in sheep.
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Chen HY, Shen H, Jia B, Zhang YS, Wang XH, Zeng XC. Differential gene expression in ovaries of Qira black sheep and Hetian sheep using RNA-Seq technique. PLoS One 2015; 10:e0120170. [PMID: 25790350 PMCID: PMC4366253 DOI: 10.1371/journal.pone.0120170] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
The Qira black sheep and the Hetian sheep are two local breeds in the Northwest of China, which are characterized by high-fecundity and low-fecundity breed respectively. The elucidation of mRNA expression profiles in the ovaries among different sheep breeds representing fecundity extremes will helpful for identification and utilization of major prolificacy genes in sheep. In the present study, we performed RNA-seq technology to compare the difference in ovarian mRNA expression profiles between Qira black sheep and Hetian sheep. From the Qira black sheep and the Hetian sheep libraries, we obtained a total of 11,747,582 and 11,879,968 sequencing reads, respectively. After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively. A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep. Eight differentially expressed genes were randomly selected for validation by real-time RT-PCR. This study provides a basic data for future research of the sheep reproduction.
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Affiliation(s)
- Han Ying Chen
- School of Pharmacy, Shihezi University, Shihezi, Xinjiang, China
| | - Hong Shen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Bin Jia
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yong Sheng Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Xu Hai Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Xian Cun Zeng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
- * E-mail:
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43
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The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/904281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.
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44
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Geng R, Wang L, Wang X, Chen Y. Cyclic expression of Lhx2 is involved in secondary hair follicle development in cashmere goat. Gene Expr Patterns 2014; 16:31-5. [PMID: 25128627 DOI: 10.1016/j.gep.2014.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 11/25/2022]
Abstract
Lhx2, a member of LIM homeobox transcription factors, plays a key role in normal tissue development. However, the molecular mechanism of Lhx2 gene in the regulation of the secondary hair follicle cycling in cashmere goat remains largely unknown. In the present study, the Lhx2 gene was cloned and characterized in cashmere goat. The cloned cDNA of Lhx2 was 1233 bp in length, encoding for proteins of 406 amino acids which contained all functionally important domains conserved among vertebrate Lhx2 gene. Tissue distribution analysis showed that Lhx2 mRNA was highly expressed in the skin and low expressed in all other tissues. Immunohistochemical localization revealed that Lhx2 was expressed in secondary hair follicles. Analysis of expression profiles of Lhx2 mRNA during different development stages in secondary hair follicles showed that the highest expression was observed at the anagen stage, while the lowest expression was detected at the telogen stage. The expression tendency during the development stages was that it increased from telogen to anagen, decreased from anagen to catagen, and decreased from catagen to telogen. The expression pattern of Lhx2 protein and mRNA was similar. The mRNA and protein expression of Lhx2 were consistent throughout the development cycle in secondary hair follicles. These findings provided a better understanding of the function of Lhx2 and suggested that the cyclic expression of Lhx2 might play important roles during secondary hair follicle development in cashmere goat.
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Affiliation(s)
- Rongqing Geng
- College of Life Science and Technology, Yancheng Teachers University, Yancheng 224051, China
| | - Lanping Wang
- College of Life Science and Technology, Yancheng Teachers University, Yancheng 224051, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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45
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Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. The sheep genome illuminates biology of the rumen and lipid metabolism. Science 2014; 344:1168-1173. [PMID: 24904168 DOI: 10.1126/science.1252806] [Citation(s) in RCA: 315] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.
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Affiliation(s)
- Yu Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.,College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Min Xie
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Richard Talbot
- Ediburgh Genomics, University of Edinburgh, Easter Bush, Midlothian EH 25 9RG, UK
| | - Jillian F Maddox
- Department of Veterinary Science, University of Melbourne, Victoria 3010, Australia
| | - Thomas Faraut
- INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France
| | - Chunhua Wu
- Utah State University, Logan, UT 84322-1435-1435, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Wenguang Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Inner Mongolia Agricultural University, Hohhot 010018, China.,Institute of ATCG, Nei Mongol Bio-Information, Hohhot, China
| | - Jo-Ann Stanton
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Wesley C Barris
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Thibaut Hourlier
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Bronwen L Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - David L Adelson
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Chao Bian
- BGI-Shenzhen, Shenzhen 518083, China
| | - Graham R Cam
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Udaya DeSilva
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Karen Dixen
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | | | - Ian R Franklin
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Shaoyin Fu
- Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Rui Guan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Margaret A Highland
- USDA-ARS Animal Disease Research Unit, Pullman, WA 99164 USA.,Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA 99164 USA
| | - Michael E Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Aaron B Ingham
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Tian Lv
- BGI-Shenzhen, Shenzhen 518083, China
| | - Tittu Mathew
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sean McWilliam
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Moira Menzies
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | | | - David Robelin
- INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France
| | - Bertrand Servin
- INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France
| | - David Townley
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | | | - Bin Wei
- BGI-Shenzhen, Shenzhen 518083, China.,Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Stephen N White
- USDA-ARS Animal Disease Research Unit, Pullman, WA 99164 USA.,Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA 99164 USA
| | | | - Chen Ye
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou,730050,China
| | - Peng Zeng
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jacob B Hansen
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Karsten Kristensen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Huw E Jones
- Biosciences KTN, The Roslin Institute, Easter Bush, Midlothian, EH25 9RG, UK
| | - V Hutton Oddy
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - John C McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - James Kijas
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China.,Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.,Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Macau University of Science and Technology, Macau 999078, China
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alan L Archibald
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH 25 9RG, UK
| | | | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Brian P Dalrymple
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
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Identification of differentially expressed miRNAs between white and black hair follicles by RNA-sequencing in the goat (Capra hircus). Int J Mol Sci 2014; 15:9531-45. [PMID: 24879525 PMCID: PMC4100108 DOI: 10.3390/ijms15069531] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 01/30/2023] Open
Abstract
MicroRNAs (miRNAs) play a key role in many biological processes by regulating gene expression at the post-transcriptional level. A number of miRNAs have been identified from livestock species. However, compared with other animals, such as pigs and cows, the number of miRNAs identified in goats is quite low, particularly in hair follicles. In this study, to investigate the functional roles of miRNAs in goat hair follicles of goats with different coat colors, we sequenced miRNAs from two hair follicles samples (white and black) using Solexa sequencing. A total of 35,604,016 reads were obtained, which included 30,878,637 clean reads (86.73%). MiRDeep2 software identified 214 miRNAs. Among them, 205 were conserved among species and nine were novel miRNAs. Furthermore, DESeq software identified six differentially expressed miRNAs. Quantitative PCR confirmed differential expression of two miRNAs, miR-10b and miR-211. KEGG pathways were analyzed using the DAVID website for the predicted target genes of the differentially expressed miRNAs. Several signaling pathways including Notch and MAPK pathways may affect the process of coat color formation. Our study showed that the identified miRNAs might play an essential role in black and white follicle formation in goats.
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47
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Zhu B, Xu T, Yuan J, Guo X, Liu D. Transcriptome sequencing reveals differences between primary and secondary hair follicle-derived dermal papilla cells of the Cashmere goat (Capra hircus). PLoS One 2013; 8:e76282. [PMID: 24069460 PMCID: PMC3777969 DOI: 10.1371/journal.pone.0076282] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/22/2013] [Indexed: 12/30/2022] Open
Abstract
The dermal papilla is thought to establish the character and control the size of hair follicles. Inner Mongolia Cashmere goats (Capra hircus) have a double coat comprising the primary and secondary hair follicles, which have dramatically different sizes and textures. The Cashmere goat is rapidly becoming a potent model for hair follicle morphogenesis research. In this study, we established two dermal papilla cell lines during the anagen phase of the hair growth cycle from the primary and secondary hair follicles and clarified the similarities and differences in their morphology and growth characteristics. High-throughput transcriptome sequencing was used to identify gene expression differences between the two dermal papilla cell lines. Many of the differentially expressed genes are involved in vascularization, ECM-receptor interaction and Wnt/β-catenin/Lef1 signaling pathways, which intimately associated with hair follicle morphogenesis. These findings provide valuable information for research on postnatal morphogenesis of hair follicles.
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Affiliation(s)
- Bing Zhu
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, China
| | - Teng Xu
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, China
| | - Jianlong Yuan
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, China
| | - Xudong Guo
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, China
- * E-mail: (XG); (DL)
| | - Dongjun Liu
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, China
- * E-mail: (XG); (DL)
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48
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Kang X, Liu G, Liu Y, Xu Q, Zhang M, Fang M. Transcriptome profile at different physiological stages reveals potential mode for curly fleece in Chinese tan sheep. PLoS One 2013; 8:e71763. [PMID: 23990983 PMCID: PMC3753335 DOI: 10.1371/journal.pone.0071763] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 07/04/2013] [Indexed: 01/28/2023] Open
Abstract
Tan sheep (Ovis aries), a Chinese indigenous breed, has special curly fleece after birth, especially at one month old. However, this unique phenotype disappears gradually with age and the underlying reasons of trait evolvement are still unknown. In this study, skin transcriptome data was used to study this issue. In total 51,215 transcripts including described transcripts and transfrags were identified. Pathway analysis of the top 100 most highly expressed transcripts, which included TCHH and keratin gene family members, such as KRT25, KRT5, KRT71, KRT14 and others, showed pathways known to be relevant to hair/fleece development and function. Six hundred differentially expressed (DE) transcripts were detected at two different physiological ages (one-month-old with curly fleece and 48-month-old without curly fleece) and were categorized into three major functional groups: cellular component, molecular function, and biological process. The top six functional categories included cell, cell part, cellular process, binding, intracellular, metabolic process. The detected differentially expressed genes were particularly involved in signal, signal peptide, disulfide bond, glycoprotein and secreted terms, respectively. Further splicing isoform analysis showed that the metallothionein 3 isoform was up-regulated in Tan lamb skin, indicating that it may be related to the conformation of curly fleece in Chinese Tan lamb. The hair-related important differentially expressed genes (SPINK4, FGF21, ESRα, EphA3, NTNG1 and GPR110) were confirmed by qPCR analysis. We deduced that the differences existed in expressed transcripts, splice isoforms and GO categories between the two different physiological stages, which might constitute the major reasons for explaining the trait evolvement of curly fleece in Chinese Tan sheep. This study provides some clues for elucidating the molecular mechanism of fleece change with age in Chinese Tan sheep, as well as supplying some potential values for understanding human hair disorder and texture changes.
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Affiliation(s)
- Xiaolong Kang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Agriculture, Ningxia University, Yinchuan, People’s Republic of China
| | - Gang Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yufang Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qinqin Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ming Zhang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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