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Wang J, Wei W, Xing C, Wang H, Liu M, Xu J, He X, Liu Y, Guo X, Jiang R. Transcriptome and Weighted Gene Co-Expression Network Analysis for Feather Follicle Density in a Chinese Indigenous Breed. Animals (Basel) 2024; 14:173. [PMID: 38200904 PMCID: PMC10778273 DOI: 10.3390/ani14010173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
Feather follicle density plays an important role in appealing to consumers' first impressions when making purchasing decisions. However, the molecular network that contributes to this trait remains largely unknown. The aim of this study was to perform transcriptome and weighted gene co-expression network analyses to determine the candidate genes relating to feather follicle density in Wannan male chickens. In total, five hundred one-day-old Wannan male chickens were kept in a conventional cage system. Feather follicle density was recorded for each bird at 12 weeks of age. At 12 weeks, fifteen skin tissue samples were selected for weighted gene co-expression network analysis, of which six skin tissue samples (three birds in the H group and three birds in the L group) were selected for transcriptome analysis. The results showed that, in total, 95 DEGs were identified, and 56 genes were upregulated and 39 genes were downregulated in the high-feather-follicle-density group when compared with the low-feather-follicle-density group. Thirteen co-expression gene modules were identified. The red module was highly significantly negatively correlated with feather follicle density (p < 0.01), with a significant negative correlation coefficient of -0.72. In total, 103 hub genes from the red module were screened. Upon comparing the 103 hub genes with differentially expressed genes (DEGs), it was observed that 13 genes were common to both sets, including MELK, GTSE1, CDK1, HMMR, and CENPE. From the red module, FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 were selected as the most important genes. These genes were enriched in the DNA binding pathway, the heterocyclic compound binding pathway, the cell cycle pathway, and the oocyte meiosis pathway. This study suggests that FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 may be involved in regulating the development of feather follicle density in Wannan male chickens. The results of this study reveal the genetic structure and molecular regulatory network of feather follicle density in Wannan male chickens, and provide a basis for further elucidating the genetic regulatory mechanism and identifying molecular markers with breeding value.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (J.W.); (W.W.); (C.X.); (H.W.); (M.L.); (J.X.); (X.H.); (Y.L.); (X.G.)
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2
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Zhang L, Cai C, Liu X, Zhang X, An Z, Zhou E, Li J, Li Z, Li W, Sun G, Li G, Kang X, Han R, Jiang R. Multi-Stage Transcriptome Analysis Revealed the Growth Mechanism of Feathers and Hair Follicles during Induction Molting by Fasting in the Late Stage of Egg Laying. BIOLOGY 2023; 12:1345. [PMID: 37887055 PMCID: PMC10603888 DOI: 10.3390/biology12101345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/21/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023]
Abstract
Induced molting is a common method to obtain a new life in laying hens, in which periodic changes in feathers are the prominent feature. Nevertheless, its precise molecular mechanism remains unclear. In this study, feather and hair follicle samples were collected during fasting-induced physiological remodeling for hematoxylin-eosin staining, hormone changes and follicle traits, and transcriptome sequencing. Feather shedding was observed in F13 to R25, while newborns were observed in R3 to R32. Triiodothyronine and tetraiodothyronine were significantly elevated during feather shedding. The calcium content was significantly higher, and the ash content was significantly lower after the changeover. The determination of hair follicle traits revealed an increasing trend in pore density and a decrease in pore diameter after the resumption of feeding. According to RNA-seq results, several core genes were identified, including DSP, CDH1, PKP1, and PPCKB, which may have an impact on hair follicle growth. The focus was to discover that starvation may trigger changes in thyroid hormones, which in turn regulate feather molting through thyroid hormone synthesis, calcium signaling, and thyroid hormone signaling pathways. These data provide a valuable resource for the analysis of the molecular mechanisms underlying the cyclical growth of hair follicles in the skin during induced molting.
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Affiliation(s)
- Lujie Zhang
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Chunxia Cai
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Xinxin Liu
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Xiaoran Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Zhiyuan An
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Enyou Zhou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Jianzeng Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Wenting Li
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Guirong Sun
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Guoxi Li
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Xiangtao Kang
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Ruili Han
- The Shennong Laboratory, Zhengzhou 450002, China; (L.Z.); (C.C.); (X.L.); (W.L.); (G.S.); (G.L.); (X.K.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.Z.); (Z.A.); (E.Z.); (J.L.); (Z.L.)
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Ji G, Zhang M, Tu Y, Liu Y, Shan Y, Ju X, Zou J, Shu J, Sheng Z, Li H. Molecular Regulatory Mechanisms in Chicken Feather Follicle Morphogenesis. Genes (Basel) 2023; 14:1646. [PMID: 37628697 PMCID: PMC10454116 DOI: 10.3390/genes14081646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
In China, the sale of freshly slaughtered chickens is becoming increasingly popular in comparison with that of live chickens, and due to this emerging trend, the skin and feather follicle traits of yellow-feathered broilers have attracted a great deal of research attention. The feather follicle originates from the interaction between the epidermis and dermis in the early embryonic stage. Feather follicle morphogenesis is regulated by the Wnt, ectodysplasin (Eda), epidermal growth factor (EGF), fibroblast growth factor (FGF), bone morphogenetic protein (BMP), sonic hedgehog (Shh), Notch, and other signaling pathways that exist in epithelial and mesenchymal cells. The Wnt pathway is essential for feather follicle and feather morphogenesis. Eda interacts with Wnt to induce FGF expression, which attracts mesenchymal cell movement and aggregates to form feather follicle primordia. BMP acts as an inhibitor of the above signaling pathways to limit the size of the feather tract and distance between neighboring feather primordia in a dose-dependent manner. The Notch/Delta pathway can interact with the FGF pathway to promote feather bud formation. While not a part of the early morphogenesis of feather follicles, Shh and BMP signaling are involved in late feather branching. This review summarizes the roles of miRNAs/lncRNA in the regulation of feather follicle and feather growth and development and suggests topics that need to be solved in a future study. This review focuses on the regulatory mechanisms involved in feather follicle morphogenesis and analyzes the impact of SNP sites on feather follicle traits in poultry. This work may help us to understand the molecular regulatory networks influencing feather follicle growth and provide basic data for poultry carcass quality.
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Affiliation(s)
- Gaige Ji
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Ming Zhang
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Yunjie Tu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Yifan Liu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Yanju Shan
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Xiaojun Ju
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Jianmin Zou
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Jingting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Zhongwei Sheng
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Hua Li
- School of Life Science and Engineering, Foshan University, Foshan 528231, China
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Mabrouk I, Zhou Y, Wang S, Song Y, Fu X, Xu X, Liu T, Wang Y, Feng Z, Fu J, Ma J, Zhuang F, Cao H, Jin H, Wang J, Sun Y. Transcriptional Characteristics Showed That miR-144-y/FOXO3 Participates in Embryonic Skin and Feather Follicle Development in Zhedong White Goose. Animals (Basel) 2022; 12:ani12162099. [PMID: 36009690 PMCID: PMC9405214 DOI: 10.3390/ani12162099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Feather is one of the most valuable and economical products in goose farming and plays a crucial physiological role in birds. For avian biology and the poultry industry, it is essential to comprehend and regulate how skin and feather follicles develop during embryogenesis. This study showed that several key regulatory genes (FOXO3, CTGF, and PTCH1, among others) and miRNAs (miR-144-y) participated in the developmental process of the skin and feather follicles in Zhedong white goose. Our findings are particularly important because they will serve as a valuable resource for upcoming studies on down feathers in agricultural economic growth regarding complex molecular mechanisms and breeding techniques. Abstract Skin and feather follicle development are essential processes for goose embryonic growth. Transcriptome and next-generation sequencing (NGS) network analyses were performed to improve the genome of Zhedong White goose and discover the critical genes, miRNAs, and pathways involved in goose skin and feather follicle morphogenesis. Sequencing output generated 6,002,591,668 to 8,675,720,319 clean reads from fifteen libraries. There were 1234, 3024, 4416, and 5326 different genes showing differential expression in four stages, E10 vs. E13, E10 vs. E18, E10 vs. E23, and E10 vs. E28, respectively. The differentially expressed genes (DEGs) were found to be implicated in multiple biological processes and pathways associated with feather growth and development, such as the Wnt signaling pathway, cell adhesion molecules, ECM–receptor interaction signaling pathways, and cell cycle and DNA replication pathways, according to functional analysis. In total, 8276 DEGs were assembled into twenty gene profiles with diverse expression patterns. The reliability of transcriptome results was verified by real-time quantitative PCR by selecting seven DEGs and five miRNAs. The localization of forkhead box O3 (FOXO3), connective tissue growth factor (CTGF), protein parched homolog1 (PTCH1), and miR-144-y by in situ hybridization showed spatial-temporal expression patterns and that FOXO3 and miR-144-y have an antagonistic targeting relationship. The correlation coefficient of FOXO3 and miR-144-y was -0.948, showing a strong negative correlation. Dual-luciferase reporter assay results demonstrated that miR-144-y could bind to the expected location to suppress the expression of FOXO3, which supports that there is a targeting relationship between them. The detections in this report will provide critical insight into the complex molecular mechanisms and breeding practices underlying the developmental characteristics of skin and feather follicles in Zhedong white geese.
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Affiliation(s)
- Ichraf Mabrouk
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yuxuan Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Sihui Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yupu Song
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xianou Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xiaohui Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Tuoya Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yudong Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Ziqiang Feng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jinhong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jingyun Ma
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Fangming Zhuang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Heng Cao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Honglei Jin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jingbo Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yongfeng Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Animal Production, Product Quality and Security, Jilin Agricultural University, Ministry of Education, Changchun 130118, China
- Correspondence:
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Feng Z, Mabrouk I, Msuthwana P, Zhou Y, Song Y, Gong H, Li S, Min C, Ju A, Duan A, Niu J, Fu J, Yan X, Xu X, Li C, Sun Y. In ovo injection of CHIR-99021 promotes feather follicles development via activating Wnt/β-catenin signaling pathway during chick embryonic period. Poult Sci 2022; 101:101825. [PMID: 35381530 PMCID: PMC8980496 DOI: 10.1016/j.psj.2022.101825] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 01/11/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
The Wingless-types/beta-catenin (Wnt/β-catenin) signaling pathway plays an important role in embryonic development and affects the physiological development processes of feather follicles. To investigate the role of Wnt/β-catenin pathway in regulating feather follicles morphogenesis, in ovo injection of CHIR-99021, an activator of the Wnt/β-catenin signaling pathway, was conducted in chick embryo model. Initially, a total of 40 embryos were used to assess feather follicles morphogenesis and the expression of β-catenin (E9–E17). The histological results showed that feather follicle morphogenesis was mainly completed from E9 to E17. β-catenin was involved in the processing of the appearance of dermal cell condensation (E9) and the completion of the feather follicles morphogenesis (E17). Next, a total of 160 fertilized eggs were randomly divided into 8 groups for in ovo injection at E9, including a Normal Saline injected group (CON) and the 500, 1,000, 2,000, 5,000, 10,000, 50,000, and 100,000 ng CHIR-99021 groups. Dorsal skin tissue samples were collected at E17 for investigating feather follicles morphology and expressions of β-catenin and lymphoid enhancerbinding factor-1 (LEF1) at gene and protein levels. The results showed that feather follicle diameter in the injected groups were significantly (P < 0.05) increased with limit dose-independence compared to the CON group. CHIR-99021 significantly (P < 0.05) influenced the mRNA expressions of catenin beta-1 (CTNNB1) and downstream target LEF1. In ovo injection of CHIR-99021 caused that β-catenin and LEF1 were significantly (P < 0.05) increased followed the increased doses as determined by western blotting. The immunochemical results showed that β-catenin was detected in the dermal papilla of feather follicles. Given these results, this study suggests to developmental biology that in ovo injection of CHIR-99021 promoted feather follicles morphogenesis and development via activating Wnt/β-catenin signaling pathway and upregulating downstream target LEF1 during embryonic period in chick embryo model. Moreover, CHIR-99021 may be a strong candidate to promote the animal feather/hair industry, especially as a reference for bird feather production.
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Hu S, Li C, Wu D, Huo H, Bai H, Wu J. The Dynamic Change of Gene-Regulated Networks in Cashmere Goat Skin with Seasonal Variation. Biochem Genet 2021; 60:527-542. [PMID: 34304316 DOI: 10.1007/s10528-021-10114-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/13/2021] [Indexed: 11/26/2022]
Abstract
The Cashmere goat (Capra hircus) is renowned for its high-quality fiber production trait. The hair cycle in Cashmere goat has an annual rhythm. To deepen the understanding of the molecular foundation of annual rhythm in the skin of Cashmere goat, we did a comparative analysis of the Cashmere goat skin transcriptome all year round. 4002 Differentially expressed genes (DEGs) were identified with seasonal variations. 12 months transcriptome were divided into four developmental stages: Jan-Mar, Apr-Jul, Aug-Oct, and Nov-Dec based on gene expression patterns. 13 modules of highly correlated genes in skin were identified using WGCNA. Ten of these modules were consistent with the development stages. The gene function of those genes in each module was analyzed by functional enrichment. The results indicated that Wnt and Hedgehog signaling pathways were inhibited from January to March and activated from April to July. The cutaneous immune system of Cashmere goats has high activity from August to October. Fatty acid metabolism dominates goat skin from November to December. This study provides new information related to the annual skin development cycle, which could provide molecular biological significance for understanding the seasonal development and response to the annual rhythm of skin.
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Affiliation(s)
- Sile Hu
- College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
- Key Laboratory of Bioinformatics of Inner Mongolia University for Nationalities, Tongliao, 028000, China
- Inner Mongolia Engineering and Technical Research Center for Personalized Medicine, Tongliao, 028000, China
- Institute of Resource Biology and Ecology, College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Chun Li
- Key Laboratory of Bioinformatics of Inner Mongolia University for Nationalities, Tongliao, 028000, China
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Dubala Wu
- Key Laboratory of Bioinformatics of Inner Mongolia University for Nationalities, Tongliao, 028000, China
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Hongyan Huo
- College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Haihua Bai
- College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
- Inner Mongolia Engineering and Technical Research Center for Personalized Medicine, Tongliao, 028000, China
- Institute of Resource Biology and Ecology, College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Jianghong Wu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China.
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China.
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7
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Yuan X, Guo Q, Bai H, Jiang Y, Zhang Y, Liang W, Wang Z, Xu Q, Chang G, Chen G. Identification of key genes and pathways associated with duck ( Anas platyrhynchos) embryonic skin development using weighted gene co-expression network analysis. Genome 2020; 63:615-628. [PMID: 32956594 DOI: 10.1139/gen-2020-0054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Skin and feather follicle morphogenesis are important processes for duck development; however, the mechanisms underlying morphogenesis at the embryonic stage remain unclear. To improve the understanding of these processes, we used transcriptome and weighted gene co-expression network analyses to identify the critical genes and pathways involved in duck skin development. Five modules were found to be the most related to five key stages in skin development that span from embryonic day 8 (E8) to postnatal day 7 (D7). Using STEM software, 6519 genes from five modules were clustered into 10 profiles to reveal key genes. Above all, we obtained several key module genes including WNT3A, NOTCH1, SHH, BMP2, NOG, SMAD3, and TGFβ2. Furthermore, we revealed that several pathways play critical roles throughout the skin development process, including the Wnt pathway and cytoskeletal rearrangement-related pathways, whereas others are involved in specific stages of skin development, such as the Notch, Hedgehog, and TGF-beta signaling pathways. Overall, this study identified the pathways and genes that play critical roles in skin development, which may provide a basis for high-quality down-type meat duck breeding.
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Affiliation(s)
- Xiaoya Yuan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qixin Guo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yi Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Wenshuang Liang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qi Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
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A "Numerical Evo-Devo" Synthesis for the Identification of Pattern-Forming Factors. Cells 2020; 9:cells9081840. [PMID: 32764501 PMCID: PMC7463486 DOI: 10.3390/cells9081840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
Animals display extensive diversity in motifs adorning their coat, yet these patterns have reproducible orientation and periodicity within species or groups. Morphological variation has been traditionally used to dissect the genetic basis of evolutionary change, while pattern conservation and stability in both mathematical and organismal models has served to identify core developmental events. Two patterning theories, namely instruction and self-organisation, emerged from this work. Combined, they provide an appealing explanation for how natural patterns form and evolve, but in vivo factors underlying these mechanisms remain elusive. By bridging developmental biology and mathematics, novel frameworks recently allowed breakthroughs in our understanding of pattern establishment, unveiling how patterning strategies combine in space and time, or the importance of tissue morphogenesis in generating positional information. Adding results from surveys of natural variation to these empirical-modelling dialogues improves model inference, analysis, and in vivo testing. In this evo-devo-numerical synthesis, mathematical models have to reproduce not only given stable patterns but also the dynamics of their emergence, and the extent of inter-species variation in these dynamics through minimal parameter change. This integrative approach can help in disentangling molecular, cellular and mechanical interaction during pattern establishment.
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Sun L, Zhou T, Wan QH, Fang SG. Transcriptome Comparison Reveals Key Components of Nuptial Plumage Coloration in Crested Ibis. Biomolecules 2020; 10:E905. [PMID: 32549189 PMCID: PMC7356354 DOI: 10.3390/biom10060905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/02/2020] [Accepted: 06/13/2020] [Indexed: 11/16/2022] Open
Abstract
Nuptial plumage coloration is critical in the mating choice of the crested ibis. This species has a characteristic nuptial plumage that develops from the application of a black sticky substance, secreted by a patch of skin in the throat and neck region. We aimed to identify the genes regulating its coloring, by comparing skin transcriptomes between ibises during the breeding and nonbreeding seasons. In breeding season skins, key eumelanin synthesis genes, TYR, DCT, and TYRP1 were upregulated. Tyrosine metabolism, which is closely related to melanin synthesis, was also upregulated, as were transporter proteins belonging to multiple SLC families, which might act during melanosome transportation to keratinocytes. These results indicate that eumelanin is likely an important component of the black substance. In addition, we observed upregulation in lipid metabolism in breeding season skins. We suggest that the lipids contribute to an oil base, which imbues the black substance with water insolubility and enhances its adhesion to feather surfaces. In nonbreeding season skins, we observed upregulation in cell adhesion molecules, which play critical roles in cell interactions. A number of molecules involved in innervation and angiogenesis were upregulated, indicating an ongoing expansion of nerves and blood vessels in sampled skins. Feather β keratin, a basic component of avian feather filament, was also upregulated. These results are consistent with feather regeneration in the black skin of nonbreeding season ibises. Our results provide the first molecular evidence indicating that eumelanin is the key component of ibis coloration.
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Affiliation(s)
| | | | | | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (L.S.); (T.Z.); (Q.-H.W.)
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10
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Ji G, Zhang M, Liu Y, Shan Y, Tu Y, Ju X, Zou J, Shu J, Wu J, Xie J. A gene co‐expression network analysis of the candidate genes and molecular pathways associated with feather follicle traits of chicken skin. J Anim Breed Genet 2020; 138:122-134. [DOI: 10.1111/jbg.12481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/23/2020] [Accepted: 04/03/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Gai‐ge Ji
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Ming Zhang
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Yi‐fan Liu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Yan‐ju Shan
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Yun‐jie Tu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Xiao‐jun Ju
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Jian‐min Zou
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Jing‐ting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou China
| | - Jun‐feng Wu
- Jiangsu Li‐hua Animal Husbandry Company Jiangsu China
| | - Jin‐fang Xie
- Jiangxi Academy of Agricultural Sciences Nanchang China
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11
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Xie WY, Chen MJ, Jiang SG, Yan HC, Wang XQ, Gao CQ. Investigation of feather follicle morphogenesis and the expression of the Wnt/β-catenin signaling pathway in yellow-feathered broiler chick embryos. Br Poult Sci 2020; 61:557-565. [PMID: 32329625 DOI: 10.1080/00071668.2020.1758302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
1. This study investigated the pattern of feather follicle morphogenesis and the expression of the Wnt/β-catenin signalling pathway in the skin of yellow-feathered broiler chick embryos during feather development, using haematoxylin and eosin (H&E) staining and Western blot assays, respectively. 2. The results showed that the skin displayed protrusions during embryonic days E7-E9, feather buds elongated during E10-E11 with anterior-posterior and proximal-distal asymmetries, and the epidermis invaginated to form the primary feather follicles (Pfs) at E12. At E13, the formation of the feather follicle and the epidermis at the base of the feather bud further invaginated into the dermis. By E15, Pf formation was essentially complete, and secondary feather follicles (Sfs) appeared. It was speculated that Pfs and Sfs developed independently and that Pfs occurred earlier than Sfs. 3. Quantitative measurements of Pf density reached a maximum at E15 and then decreased gradually. Sf density started to increase from E15. 4. Protein expression levels of β-catenin, TCF4, cyclin D1, and c-Myc were significantly increased during E8-E12 (P < 0.05) and then decreased from E13 to the day of hatching (DOH) (P < 0.05). The result of the β-catenin immunolocalisation signal intensity assay was consistent with the result of the Western blot assay. 5. Collectively, the results indicated that the Wnt/β-catenin signalling pathway is essential for promoting the development of feather follicles, especially during E7-E15.
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Affiliation(s)
- W Y Xie
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , Guangzhou, China
| | - M J Chen
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , Guangzhou, China
| | - S G Jiang
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , Guangzhou, China
| | - H C Yan
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , Guangzhou, China
| | - X Q Wang
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , Guangzhou, China
| | - C Q Gao
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , Guangzhou, China
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12
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Comparison of nonlinear models to describe the feather growth and development curve in yellow-feathered chickens. Animal 2020; 14:1005-1013. [PMID: 31902381 DOI: 10.1017/s1751731119003082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Feathers play a critical role in thermoregulation and directly influence poultry production. Poor feathering adversely affects living appearance and carcass quality, thus reducing profits. However, producers tend to ignore the importance of feather development and do not know the laws of feather growth and development. The objective of this study was to fit growth curves to describe the growth and development of feathers in yellow-feathered broilers during the embryonic and posthatching periods using different nonlinear functions (Gompertz, logistic and Bertalanffy). Feather mass and length were determined during the embryonic development and posthatching stages to identify which growth model most accurately described the feather growth pattern. The results showed that chick embryos began to grow feathers at approximately embryonic (E) day 10, and the feathers grew rapidly from E13 to E17. There was little change from E17 to the day of hatching (DOH). During the embryonic period, the Gompertz function (Y = 798.48e-203 431exp(-0.87t), Akaike's information criterion (AIC) = -0.950 × 103, Bayesian information criterion (BIC) = -0.711 × 103 and mean square error (MSE) = 559.308) provided the best fit for the feather growth curve compared with the other two functions. After hatching, feather mass and length changed little from the DOH to day (D) 14, increased rapidly from D21 to D91 and then grew slowly after D91. The first stage of feather molting occurred from 2 to 3 weeks of age when the down feathers were mostly shed and replaced with juvenile feathers, and the second stage occurred at approximately 13 to 15 weeks of age. The three nonlinear functions could overall fit the feather growth curve well, but the Bertalanffy model (Y = 116.88 × (1-0.86e-0.02t)3, AIC = 1.065 × 105, BIC = 1.077 × 105 and MSE = 11.308) showed the highest degree of fit among the models. Therefore, the Gompertz model exhibited the best goodness of fit for the feather growth curve during the embryonic development, while the Bertalanffy model was the most suitable model due to its accurate ability to predict the growth and development of feathers during the growth period, which is an important commercial characteristic of yellow-feathered chickens.
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13
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Hu X, Zhang X, Liu Z, Li S, Zheng X, Nie Y, Tao Y, Zhou X, Wu W, Yang G, Zhao Q, Zhang Y, Xu Q, Mou C. Exploration of key regulators driving primary feather follicle induction in goose skin. Gene 2020; 731:144338. [PMID: 31923576 DOI: 10.1016/j.gene.2020.144338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
The primary feather follicles are universal skin appendages widely distributed in the skin of feathered birds. The morphogenesis and development of the primary feather follicles in goose skin remain largely unknown. Here, the induction of primary feather follicles in goose embryonic skin (pre-induction vs induction) was investigated by de novo transcriptome analyses to reveal 409 differentially expressed genes (DEGs). The DEGs were characterized to potentially regulate the de novo formation of feather follicle primordia consisting of placode (4 genes) and dermal condensate (12 genes), and the thickening of epidermis (5 genes) and dermal fibroblasts (17 genes), respectively. Further analyses enriched DEGs into GO terms represented as cell adhesion and KEGG pathways including Wnt and Hedgehog signaling pathways that are highly correlated with cell communication and molecular regulation. Six selected Wnt pathway genes were detected by qPCR with up-regulation in goose skin during the induction of primary feather follicles. The localization of WNT16, SFRP1 and FRZB by in situ hybridization showed weak expression in the primary feather primordia, whereas FZD1, LEF1 and DKK1 were expressed initially in the inter-follicular skin and feather follicle primordia, then mainly restricted in the feather primordia. The spatial-temporal expression patterns indicate that Wnt pathway genes DKK1, FZD1 and LEF1 are the important regulators functioned in the induction of primary feather follicle in goose skin. The dynamic molecular changes and specific gene expression patterns revealed in this report provide the general knowledge of primary feather follicle and skin development in waterfowl, and contribute to further understand the diversity of hair and feather development beyond the mouse and chicken models.
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Affiliation(s)
- Xuewen Hu
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Xiaokang Zhang
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Zhiwei Liu
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Shaomei Li
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Xinting Zheng
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Yangfan Nie
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Yingfeng Tao
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Xiaoliu Zhou
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Wenqing Wu
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Ge Yang
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Qianqian Zhao
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China
| | - Yang Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Qi Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Chunyan Mou
- Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430000, China.
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14
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Tao Y, Zhou X, Liu Z, Zhang X, Nie Y, Zheng X, Li S, Hu X, Yang G, Zhao Q, Mou C. Expression patterns of three JAK-STAT pathway genes in feather follicle development during chicken embryogenesis. Gene Expr Patterns 2019; 35:119078. [PMID: 31759166 DOI: 10.1016/j.gep.2019.119078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022]
Abstract
The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) (JAK-STAT) pathway is shown to restrain the hair follicles in catagen and telogen and prevent anagen reentry in murine hair follicle cycling. The early roles of JAK-STAT pathway genes in skin development remain uncharacterized in mouse and chicken models. Here, we revealed the expression patterns of three JAK-STAT pathway genes (JAK1, JAK2, and TYK2) in chicken embryonic skin at E6-E10 stages which are key to feather follicle morphogenesis. Multiple sequence alignment of the three genes from chicken and other species all showed a closely related homology with birds like quail and goose. Whole mount in situ hybridization (WISH) revealed weak expression of JAK1, JAK2, and TYK2 in chicken skin at E6 and E7, and followed with the focally restricted signals in the feather follicles of neck and body skin located dorsally at E8 for JAK1, E9 for TYK2 and E10 for JAK2 gene. All three genes displayed stronger expression in feather follicles of neck skin than that of body skin. The expression levels of JAK1 and TYK2 were much stronger than those of JAK2. Quantitative real-time PCR (qRT-PCR) analysis revealed the increased expression tendency for JAK2 both in the neck and body skin from E6 to E10, and the much stronger expression in neck and body skin at later stages (E8-E10) than earlier stages (E6 and E7) for JAK1 and TYK2. Overall, these findings suggest that JAK1 and TYK2, not JAK2 are important to specify the feather follicle primordia, and to arrange the proximal-distal axis of feather follicles, respectively, during the morphogenesis of feather follicles in embryonic chicken skin.
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Affiliation(s)
- Yingfeng Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Xiaoliu Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Zhiwei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Xiaokang Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Yangfan Nie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Xinting Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Shaomei Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Xuewen Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Ge Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Qianqian Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China
| | - Chunyan Mou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan, China.
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15
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Wang X, Li D, Song S, Zhang Y, Li Y, Wang X, Liu D, Zhang C, Cao Y, Fu Y, Han R, Li W, Liu X, Sun G, Li G, Tian Y, Li Z, Kang X. Combined transcriptomics and proteomics forecast analysis for potential genes regulating the Columbian plumage color in chickens. PLoS One 2019; 14:e0210850. [PMID: 31693656 PMCID: PMC6834273 DOI: 10.1371/journal.pone.0210850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 10/18/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Coloration is one of the most recognizable characteristics in chickens, and clarifying the coloration mechanisms will help us understand feather color formation. "Yufen I" is a commercial egg-laying chicken breed in China that was developed by a three-line cross using lines H, N and D. Columbian plumage is a typical feather character of the "Yufen I" H line. To elucidate the molecular mechanism underlying the pigmentation of Columbian plumage, this study utilizes high-throughput sequencing technology to compare the transcriptome and proteome differences in the follicular tissue of different feathers, including the dorsal neck with black and white striped feather follicles (Group A) and the ventral neck with white feather follicles (Group B) in the "Yufen I" H line. RESULTS In this study, we identified a total of 21,306 genes and 5,203 proteins in chicken feather follicles. Among these, 209 genes and 382 proteins were differentially expressed in two locations, Group A and Group B, respectively. A total of 8 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) were found to be involved in the melanogenesis pathway. Additionally, a specifically expressed MED23 gene and a differentially expressed GNAQ protein were involved in melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis mapped 190 DEGs and 322 DEPs to 175 and 242 pathways, respectively, and there were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed that the following pathways were activated: melanogenesis, cardiomyocyte adrenergic, calcium and cGMP-PKG. The expression of DEGs was validated by real-time quantitative polymerase chain reaction (qRT-PCR) that produced results similar to those from RNA-seq. In addition, we found that the expression of the MED23, FZD10, WNT7B and WNT11 genes peaked at approximately 8 weeks in the "Yufen I" H line, which is consistent with the molting cycle. As both groups showed significant differences in terms of the expression of the studied genes, this work opens up avenues for research in the future to assess their exact function in determining plumage color. CONCLUSION Common DEGs and DEPs were enriched in the melanogenesis pathway. MED23 and GNAQ were also reported to play a crucial role in melanin synthesis. In addition, this study is the first to reveal gene and protein variations in in the "Yufen I" H line during Columbian feather color development and to discover principal genes and proteins that will aid in functional genomics studies in the future. The results of the present study provide a significant conceptual basis for the future breeding schemes with the "Yufen I" H line and provide a basis for research on the mechanisms of feather pigmentation.
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Affiliation(s)
- Xinlei Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Sufang Song
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Yanhua Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuanfang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Danli Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chenxi Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yanfang Cao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yawei Fu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
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16
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Bailleul R, Curantz C, Desmarquet-Trin Dinh C, Hidalgo M, Touboul J, Manceau M. Symmetry breaking in the embryonic skin triggers directional and sequential plumage patterning. PLoS Biol 2019; 17:e3000448. [PMID: 31577791 PMCID: PMC6791559 DOI: 10.1371/journal.pbio.3000448] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 10/14/2019] [Accepted: 09/04/2019] [Indexed: 01/22/2023] Open
Abstract
The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns, yet drawing testable hypotheses from those often remains difficult. Consequently, little is known about pattern-forming events. Here, we surveyed plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins, together representing the three major taxa of the avian phylogeny, and built a unified model that not only reproduces final patterns but also intrinsically generates shared and varying directionality, sequence, and duration of patterning. We used in vivo and ex vivo experiments to test its parameter-based predictions. We showed that directional and sequential pattern progression depends on a species-specific prepattern: an initial break in surface symmetry launches a travelling front of sharply defined, oriented domains with self-organising capacity. This front propagates through the timely transfer of increased cell density mediated by cell proliferation, which controls overall patterning duration. These results show that universal mechanisms combining prepatterning and self-organisation govern the timely emergence of the plumage pattern in birds. A survey of plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins shows that their formation depends on a species-specific prepattern in the embryo and demonstrates that universal mechanisms govern the timely emergence of natural patterns in birds.
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Affiliation(s)
- Richard Bailleul
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
- Sorbonne Université, UPMC Univ Paris 06, Laboratoire Jacques-Louis Lions, Paris, France
| | - Camille Curantz
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
- Sorbonne Université, UPMC Univ Paris 06, Laboratoire Jacques-Louis Lions, Paris, France
| | - Carole Desmarquet-Trin Dinh
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
| | - Magdalena Hidalgo
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
| | - Jonathan Touboul
- Department of Mathematics and Volen National Center for Complex Systems, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail: (MM); (JT)
| | - Marie Manceau
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
- * E-mail: (MM); (JT)
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17
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Cooper RL, Thiery AP, Fletcher AG, Delbarre DJ, Rasch LJ, Fraser GJ. An ancient Turing-like patterning mechanism regulates skin denticle development in sharks. SCIENCE ADVANCES 2018; 4:eaau5484. [PMID: 30417097 PMCID: PMC6221541 DOI: 10.1126/sciadv.aau5484] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/12/2018] [Indexed: 05/02/2023]
Abstract
Vertebrates have a vast array of epithelial appendages, including scales, feathers, and hair. The developmental patterning of these diverse structures can be theoretically explained by Alan Turing's reaction-diffusion system. However, the role of this system in epithelial appendage patterning of early diverging lineages (compared to tetrapods), such as the cartilaginous fishes, is poorly understood. We investigate patterning of the unique tooth-like skin denticles of sharks, which closely relates to their hydrodynamic and protective functions. We demonstrate through simulation models that a Turing-like mechanism can explain shark denticle patterning and verify this system using gene expression analysis and gene pathway inhibition experiments. This mechanism bears remarkable similarity to avian feather patterning, suggesting deep homology of the system. We propose that a diverse range of vertebrate appendages, from shark denticles to avian feathers and mammalian hair, use this ancient and conserved system, with slight genetic modulation accounting for broad variations in patterning.
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Affiliation(s)
- Rory L. Cooper
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Alexandre P. Thiery
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | | | - Liam J. Rasch
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Human Developmental Biology Resource, Institute of Child Health, University College, London, UK
| | - Gareth J. Fraser
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Biology, University of Florida, Gainesville, FL, USA
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18
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Ng CS, Li WH. Genetic and Molecular Basis of Feather Diversity in Birds. Genome Biol Evol 2018; 10:2572-2586. [PMID: 30169786 PMCID: PMC6171735 DOI: 10.1093/gbe/evy180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2018] [Indexed: 12/16/2022] Open
Abstract
Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago
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