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Zheng Y, Chen R, Yue C, Zhang Y, Guo S, Wang Y, Bai Z, Cai W, Hui T, Sun J, Zhang X, Wang Z. CeRNA regulates network and expression and SNP effect on NFKBIA of cashmere fineness. Anim Biotechnol 2023; 34:2863-2874. [PMID: 36165594 DOI: 10.1080/10495398.2022.2124165] [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] [Indexed: 11/01/2022]
Abstract
In this study, a total of 1140 Liaoning Cashmere Goats (LCG) were genotyped for single nucleotide polymorphism (SNP) of NFKBIA gene. There are 15 SNPs and 7 genotypes have been found, and G1547A (GG) genotype has been associated with cashmere fineness and cashmere yield. An integrated ceRNA regulatory network of NFKBIA gene was made. To prove NFKBIA and these non-coding RNAs (ncRNAs) may be related to cashmere fineness, we performed qPCR on these ncRNA in LCG coarse type skin (CT-LCG) and LCG fine type skin (FT-LCG). The result of qPCR showed lncRNA XLOC_011060 and ciRNA452 are at high expression level in CT-LCG, all miRNAs appear high expressed in FT-LCG, and mir-93 was the most significant difference between CT-LCG and FT-LCG. In addition, five miRNAs were selected for qPCR in different genotypes. The qPCR results showed that mir-93 might negatively regulate cashmere fineness and mir-17-5p may play a positive role in regulating cashmere fineness of individuals with G1355A (AG) genotype. These results demonstrated that NFKBIA gene is associated with cashmere fineness of LCG and G1547A (GG) genotype is the preferred marker genotype for cashmere fineness.
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Affiliation(s)
- Yuanyuan Zheng
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chang Yue
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yingchun Zhang
- Wenhua Road Primary School, Shenhe District, Shenyang, China
| | - Suping Guo
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanru Wang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Taiyu Hui
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jiaming Sun
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Tarasova EI, Frolov AN, Lebedev SV, Romanov MN. Landmark native breed of the Orenburg goats: progress in its breeding and genetics and future prospects. Anim Biotechnol 2023; 34:5139-5154. [PMID: 36495096 DOI: 10.1080/10495398.2022.2154221] [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] [Indexed: 12/14/2022]
Abstract
This paper reviews information about a unique and iconic breed of the Orenburg Oblast, the homeland and the only place where the best herds of Orenburg down-hair goats in Russia are concentrated. Three types of these small ruminant animals are widespread on the territory of the region: Orenburg purebred gray goats, Orenburg purebred white goats, as well as crossbred white goats of F1 White Don × White Orenburg. Currently, at the farms of the Orenburg region, animals are selected according to their phenotype, with selected traits being color, weight and length of down hair. In recent years, the Orenburg goat breed has become an object of genetic research using various marker systems including immunogenetic, microsatellite, mtDNA and SNP markers. Overall, these studies evidence about the uniqueness of the allele pool in the landmark native breed of the Orenburg goats, which is a complex dynamic genetic system, prioritizing its further in-depth genome research and breeding applications.
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Affiliation(s)
- Ekaterina I Tarasova
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
| | - Alexey N Frolov
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
| | - Svyatoslav V Lebedev
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Abioja M, Logunleko M, Majekodunmi B, Adekunle E, Shittu O, Odeyemi A, Nwosu E, Oke O, Iyasere O, Abiona J, Williams T, James I, Smith O, Daramola J. Roles of Candidate Genes in the Adaptation of Goats to Heat Stress: A Review. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Bai Z, Xu Y, Gu M, Cai W, Zhang Y, Qin Y, Chen R, Sun Y, Wu Y, Wang Z. Proteomic analysis of coarse and fine skin tissues of Liaoning cashmere goat. Funct Integr Genomics 2022; 22:503-513. [PMID: 35366687 DOI: 10.1007/s10142-022-00856-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
Abstract
Proteomics is the study of all proteins expressed by a cell or even an organism. However, knowledge of proteins that regulate the fineness of cashmere is limited. Liaoning cashmere goat (LCG) is a valuable genetic resource of China. The skin samples of Liaoning cashmere goats during the growing period were collected, performed tandem mass tag (TMT) method, and identified 117 differentially expressed proteins in CT_LCG (course type) and FT_LCG (fine type). To verify proteins differentially expressed in LCG, we performed PRM validation on three candidate proteins (ALB, SDC1, and ITGB4) in CT-LCG and FT-LCG. Furthermore, primary metabolic process and lysosome are most enriched in the GO and KEGG pathways, respectively. In addition, we also derived a protein-protein interaction (PPI) regulatory network from the perspective of bioinformatics. This study sought to elucidate the molecular mechanism of differential proteins regulating cashmere fineness of Liaoning cashmere goats by using TMT quantitative proteomics analysis. Differentially expressed proteins ALB and SDC1 may regulate cashmere fineness; ITGB4 can become a promising protein for further study. They can be used as key proteins to lay a foundation for studying cashmere fineness of Liaoning cashmere goats.
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Affiliation(s)
- Zhixian Bai
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yanan Xu
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Ming Gu
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Weidong Cai
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yu Zhang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuting Qin
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Rui Chen
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yinggang Sun
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yanzhi Wu
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zeying Wang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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Gao WZ, Xue HL, Yang JC. Proteomics analysis of the secondary hair follicle cycle in Liaoning cashmere goat. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits. Int J Genomics 2020; 2020:5940205. [PMID: 32904540 PMCID: PMC7456479 DOI: 10.1155/2020/5940205] [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: 03/11/2020] [Revised: 06/30/2020] [Accepted: 07/24/2020] [Indexed: 11/25/2022] Open
Abstract
Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.
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Nocelli C, Cappelli K, Capomaccio S, Pascucci L, Mercati F, Pazzaglia I, Mecocci S, Antonini M, Renieri C. Shedding light on cashmere goat hair follicle biology: from morphology analyses to transcriptomic landascape. BMC Genomics 2020; 21:458. [PMID: 32615938 PMCID: PMC7330943 DOI: 10.1186/s12864-020-06870-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 06/24/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cashmere goat is known for its precious undercoat. Being photoperiod-dictated, cashmere growth has been studied focusing mainly on hair follicle cycle phases (anagen, catagen and telogen). An accurate molecular knowledge of the goat hair follicle cycle, disentangling gene expression changes during phases and recognizing timing boundaries, could be useful to improve cashmere goat management and ultimately cashmere production. RESULTS To better describe goat's hair follicle transcriptome we applied RNA-sequencing to isolated hair follicles from five Italian cashmere goats, during the anagen and catagen phase, identifying total of 214 differentially expressed genes (DEGs): 97 were up-regulated while 117 were down-regulated in catagen with respect to anagen. Gene Ontology and pathway analysis were performed. We detected 144 significant pathways spanning from estrogen, pluripotency of stem cells, thermogenesis and fatty acid metabolism that were strongly expressed during the hair follicle phases analysed. Finally, we validated promising DEGs by RT-qPCR in the same set of samples as well as in hair follicles and entire skin biopsies of another cashmere goats cohort accounting for early anagen, anagen, early catagen, and catagen phases. CONCLUSIONS As in the isolated hair follicles, some target genes were homogenously modulated during the four hair follicle phases. Ceruloplasmin (CP) and Keratin 4 (K4), confirmed their clear cut expression between growing and resting phase. In fact, K4 was almost absent in catagen phases while CP was barely expressed in anagen phases. In particular, the strong expression of K4 in early anagen makes it an eligible marker to track the beginning of a new hair cycle, and therefore defining the optimum time for cashmere harvesting.
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Affiliation(s)
- Cristina Nocelli
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy
| | - Katia Cappelli
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
| | - Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
| | - Luisa Pascucci
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
| | - Francesca Mercati
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
| | - Irene Pazzaglia
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche, Via Salvemini 1, 06126 Perugia, Italy
| | - Samanta Mecocci
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
| | - Marco Antonini
- Italian National Agency for New Technology, Energy and Sustainable Economic Development, ENEA CR Casaccia—SSPT BIOAG Probio, S.M. di Galeria, 00123 Rome, Italy
| | - Carlo Renieri
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy
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Lv X, Chen L, He S, Liu C, Han B, Liu Z, Yusupu M, Blair H, Kenyon P, Morris S, Li W, Liu M. Effect of Nutritional Restriction on the Hair Follicles Development and Skin Transcriptome of Chinese Merino Sheep. Animals (Basel) 2020; 10:ani10061058. [PMID: 32575477 PMCID: PMC7341508 DOI: 10.3390/ani10061058] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
The high concentration of secondary branched wool follicles is a distinctive feature of the Merino sheep. At present, the molecular control of the development and branching of secondary wool follicles (SF) remains elusive. To reveal the potential genes associated with the development of hair follicles, we investigated the characteristics of prenatal and postnatal development of wool follicles, and the transcriptional expression profile in fetuses/lambs from dams under either maternal maintenance or sub-maintenance (75% maintenance) nutrition. The density of SF and the ratio of SF to primary wool follicles (PF) were reduced (p < 0.05) in fetuses from day 105 to 135 of gestation under sub-maintenance nutrition. Differentially expressed genes were enriched in the binding, single-organism process, cellular process, cell and cell part Gene Ontology (GO) functional categories and metabolism, apoptosis, and ribosome pathways. Four candidate genes, SFRP4, PITX1, BAMBI, and KRT16, which were involved in secondary wool follicles branching and development, were identified. Our results indicate that nutritional intervention imposed on pregnant ewes by short-term sub-maintenance nutrition could provide a strategy for the study of wool follicle development. Overall insight into the global gene expression associated with SF development can be used to investigate the underlying mechanisms of SF branching in Merino sheep.
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Affiliation(s)
- Xuefeng Lv
- College of Life Science and Technology, Xinjiang University, Urmuqi 830000, China;
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urmuqi 830000, China
| | - Lei Chen
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
| | - Sangang He
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
| | - Chenxi Liu
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
| | - Bin Han
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
| | - Zhilong Liu
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
| | - Mayila Yusupu
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
| | - Hugh Blair
- International Sheep Research Centre, School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (H.B.); (P.K.); (S.M.)
| | - Paul Kenyon
- International Sheep Research Centre, School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (H.B.); (P.K.); (S.M.)
| | - Stephen Morris
- International Sheep Research Centre, School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand; (H.B.); (P.K.); (S.M.)
| | - Wenrong Li
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
- Correspondence: (W.L.); (M.L.)
| | - Mingjun Liu
- Key Laboratory of Genetics, Breeding & Reproduction of Grass-Feeding Livestock, Ministry of Agriculture, Urmuqi 830000, China; (L.C.); (S.H.); (C.L.); (B.H.); (Z.L.); (M.Y.)
- Key Laboratory of Animal Biotechnology of Xinjiang Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urmuqi 830000, China
- Correspondence: (W.L.); (M.L.)
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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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Pazzaglia I, Mercati F, Antonini M, Capomaccio S, Cappelli K, Dall'Aglio C, La Terza A, Mozzicafreddo M, Nocelli C, Pallotti S, Pediconi D, Renieri C. PDGFA in Cashmere Goat: A Motivation for the Hair Follicle Stem Cells to Activate. Animals (Basel) 2019; 9:E38. [PMID: 30695990 PMCID: PMC6407032 DOI: 10.3390/ani9020038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
The cashmere hair follicle (HF) perpetually goes through cycles of growth, involution and rest. The photoperiod is the main factor in the control of seasonal coat change in cashmere goats while stem cells play a crucial role in the HF growth. Several factors, including Platelet-Derived Growth Factor A (PDGFA), Bone Morphogenetic Protein 2 (BMP2) and Lim-Homeobox gene 2 (LHX2) are implicated in HF morphogenesis and cycle. In this work, the mentioned molecules were investigated to evaluate their role in follicular cycle activation. The study was performed on skin samples collected at different periods of HF cycle and the molecular expression of PDGFA, BMP2 and LHX2 was evaluated by Real-Time PCR (qPCR) at each time point. Since PDGFA showed the most variation, the goat PDGFA gene was sequenced and the protein localization was investigated by immunohistochemistry together with PDGF receptor α (PDGFRα). PDGFA immunostaining was observed in the basal layer of the HF outer root sheath and the immunoreaction appeared stronger in the regressive HFs compared to those in the anagen phase according to qPCR analysis. PDGFRα was observed in the HF epithelium, proving the effect of PDGFA on the follicular structure. The data obtained suggest that PDGFA and BMP2 are both implicated in HF cycle in goat. In particular, PDGFA secreted by the HF is involved in the anagen activation.
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Affiliation(s)
- Irene Pazzaglia
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Pontoni 5, 62032 Camerino, Italy.
| | - Francesca Mercati
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy.
| | - Marco Antonini
- Italian National Agency for New Technology, Energy and Sustainable Economic Development, ENEA CR Casaccia-SSPT BIOAG Probio, S.M. di Galeria, 00123 Roma, Italy.
| | - Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy.
| | - Katia Cappelli
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy.
| | - Cecilia Dall'Aglio
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy.
| | - Antonietta La Terza
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Pontoni 5, 62032 Camerino, Italy.
| | - Matteo Mozzicafreddo
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Pontoni 5, 62032 Camerino, Italy.
| | - Cristina Nocelli
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Pontoni 5, 62032 Camerino, Italy.
| | - Stefano Pallotti
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Pontoni 5, 62032 Camerino, Italy.
| | - Dario Pediconi
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Pontoni 5, 62032 Camerino, Italy.
| | - Carlo Renieri
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy.
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12
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Zheng Y, Wang Z, Zhu Y, Wang W, Bai M, Jiao Q, Wang Y, Zhao S, Yin X, Guo D, Bai W. LncRNA-000133 from secondary hair follicle of Cashmere goat: identification, regulatory network and its effects on inductive property of dermal papilla cells. Anim Biotechnol 2019; 31:122-134. [PMID: 30632899 DOI: 10.1080/10495398.2018.1553788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs), a class of non-protein conding RNAs > 200 nt in length, were thought to play critical roles in regulating the expression of protein-coding genes. Here, we identified and characterized a novel lncRNA-000133 from the secondary hair follicle (SHF) of cashmere goat with its ceRNA network analysis, as well as, its potential effects on inductive property of dermal papilla cells were evaluated through overexpression analysis. Expression analysis indicated that lncRNA-000133 had a significantly higher expression at anagen than that at telogen in SHF of Cashmere goat, suggesting that lncRNA-000133 might be involved in the reconstruction of SHF with the formation and growth of cashmere fiber. Taken together with methylation analysis, we showed that 5' regulatory region methylation of the lncRNA-000133 gene might be involved in its expression suppression in SHF of Cashmere goat. The ceRNA regulatory network showed that a rich and complex regulatory relationship between lncRNA-000133 and related miRNAs with their target genes. The overexpression of lncRNA-000133 led to a significant increasing in the relative expression of ET-1, SCF, ALP and LEF1 in dermal papilla cells suggesting that lncRNA-000133 appears to contribute the inductive property of dermal papilla cells.
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Affiliation(s)
- Yuanyuan Zheng
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yubo Zhu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Wei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Man Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Qian Jiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yanru Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Sujun Zhao
- Sichuan Animal Science Academy, Chengdu, P. R. China
| | - Xianbo Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Dan Guo
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang, P. R. China
| | - Wenlin Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
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13
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Jiao Q, Yin RH, Zhao SJ, Wang ZY, Zhu YB, Wang W, Zheng YY, Yin XB, Guo D, Wang SQ, Zhu YX, Bai WL. Identification and molecular analysis of a lncRNA-HOTAIR transcript from secondary hair follicle of cashmere goat reveal integrated regulatory network with the expression regulated potentially by its promoter methylation. Gene 2018; 688:182-192. [PMID: 30521888 DOI: 10.1016/j.gene.2018.11.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/05/2018] [Accepted: 11/22/2018] [Indexed: 01/17/2023]
Abstract
The HOTAIR transcript is transcribed from the antisense strand within the HOXC gene cluster, and it is thought to play a role in regulating the inductive capacity of dermal papilla cells during the reconstruction of hair-follicle. In the current investigation, we firstly isolated and characterized a lncRNA-HOTAIR transcript from the secondary hair follicle of cashmere goat. Also, we analyzed its transcriptional pattern and methylation level of HOTAIR gene promoter in secondary hair follicle of cashmere goat during anagen and telogen stages. Nucleotide composition analysis indicated that the contents of Adenine (A) and Thymine (T) are higher than that of Guanine (G) and Cytosine (C) in lncRNA-HOTAIR transcript of cashmere goat with the highest frequency distribution of AG nucleotide pair (8.06%). The regulatory network analysis showed a directly or indirectly complex regulatory relationships between lncRNA-HOTAIR of cashmere goat and its potential target molecules: miRNAs, mRNAs and proteins. Also, we showed that lncRNA-HOTAIR was properly transcribed at both anagen and telogen stages of secondary hair follicle of cashmere goat with the anagen being significantly higher than telogen in its expression, which suggest that lncRNA-HOTAIR transcript might be involved in the reconstruction of secondary hair follicle with the formation and growth of cashmere fiber. Taken together with methylation analysis of HOTAIR gene promoter, our data suggest that the promoter methylation of HOTAIR gene most likely is involved in its transcriptional suppression in secondary hair follicle of cashmere goat.
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Affiliation(s)
- Qian Jiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Rong H Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Su J Zhao
- Sichuan Animal Science Academy, Chengdu 610066, PR China
| | - Ze Y Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Yu B Zhu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Wei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Yuan Y Zheng
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Xian B Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Dan Guo
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Shi Q Wang
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Yan X Zhu
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Wen L Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China.
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14
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Wang X, Liu J, Zhou G, Guo J, Yan H, Niu Y, Li Y, Yuan C, Geng R, Lan X, An X, Tian X, Zhou H, Song J, Jiang Y, Chen Y. Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits. Sci Rep 2016; 6:38932. [PMID: 27941843 PMCID: PMC5150979 DOI: 10.1038/srep38932] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/16/2016] [Indexed: 12/25/2022] Open
Abstract
The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity. Here, we generated medium-coverage (9–13×) sequences from eight domesticated goat breeds, representing morphologically or geographically specific populations, to identify genomic regions representing selection signatures. We discovered ~10 million single nucleotide polymorphisms (SNPs) for each breed. By combining two approaches, ZHp and di values, we identified 22 genomic regions that may have contributed to the phenotypes in coat color patterns, body size, cashmere traits, as well as high altitude adaptation in goat populations. Candidate genes underlying strong selection signatures including coloration (ASIP, KITLG, HTT, GNA11, and OSTM1), body size (TBX15, DGCR8, CDC25A, and RDH16), cashmere traits (LHX2, FGF9, and WNT2), and hypoxia adaptation (CDK2, SOCS2, NOXA1, and ENPEP) were identified. We also identified candidate functional SNPs within selected genes that may be important for each trait. Our results demonstrated the potential of using sequence data in identifying genomic regions that are responsible for agriculturally significant phenotypes in goats, which in turn can be used in the selection of goat breeds for environmental adaptation and domestication.
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Affiliation(s)
- Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jing Liu
- 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
| | - Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, 625000, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.,College of Life Science, Yulin University, Yulin, 719000, China
| | - Yiyuan Niu
- 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
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China
| | - Rongqing Geng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.,College of Pharmacy, Yancheng Teachers University, Yancheng, 224051, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | | | - Huangkai Zhou
- Guangzhou Gene de-novo Biotechnology Co. Ltd. Guangzhou, 510000, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742,USA
| | - Yu Jiang
- 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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