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Mullakkalparambil Velayudhan S, Sejian V, Devaraj C, Manjunathareddy GB, Ruban W, Kadam V, König S, Bhatta R. Novel Insights to Assess Climate Resilience in Goats Using a Holistic Approach of Skin-Based Advanced NGS Technologies. Int J Mol Sci 2023; 24:10319. [PMID: 37373465 DOI: 10.3390/ijms241210319] [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: 05/30/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
A novel study was conducted to elucidate heat-stress responses on a number of hair- and skin-based traits in two indigenous goat breeds using a holistic approach that considered a number of phenotypic and genomic variables. The two goat breeds, Kanni Aadu and Kodi Aadu, were subjected to a simulated heat-stress study using the climate chambers. Four groups consisting of six goats each (KAC, Kaani Aadu control; KAH, Kanni Aadu heat stress; KOC, Kodi Aadu control; and KOH, Kodi Aadu heat stress) were considered for the study. The impact of heat stress on caprine skin tissue along with a comparative assessment of the thermal resilience of the two goat breeds was assessed. The variables considered were hair characteristics, hair cortisol, hair follicle quantitative PCR (qPCR), sweating (sweating rate and active sweat gland measurement), skin histometry, skin-surface infrared thermography (IRT), skin 16S rRNA V3-V4 metagenomics, skin transcriptomics, and skin bisulfite sequencing. Heat stress significantly influenced the hair fiber characteristics (fiber length) and hair follicle qPCR profile (Heat-shock protein 70 (HSP70), HSP90, and HSP110). Significantly higher sweating rate, activated sweat gland number, skin epithelium, and sweat gland number (histometry) were observed in heat stressed goats. The skin microbiota was also observed to be significantly altered due to heat stress, with a relatively higher alteration being noticed in Kanni Aadu goats than in Kodi Aadi goats. Furthermore, the transcriptomics and epigenetics analysis also pointed towards the significant impact of heat stress at the cellular and molecular levels in caprine skin tissue. The higher proportion of differentially expressed genes (DEGs) along with higher differentially methylated regions (DMRs) in Kanni Aadu goats due to heat stress when compared to Kodi Aadu goats pointed towards the better resilience of the latter breed. A number of established skin, adaptation, and immune-response genes were also observed to be significantly expressed/methylated. Additionally, the influence of heat stress at the genomic level was also predicted to result in significant functional alterations. This novel study thereby highlights the impact of heat stress on the caprine skin tissue and also the difference in thermal resilience exhibited by the two indigenous goat breeds, with Kodi Aadu goats being more resilient.
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Affiliation(s)
| | - Veerasamy Sejian
- Rajiv Gandhi Institute of Veterinary Education and Research, Kurumbapet, Pondicherry 605008, India
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
| | - Chinnasamy Devaraj
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
| | | | - Wilfred Ruban
- Department of Livestock Product Technology, Hebbal Veterinary College, Karnataka Veterinary Animal and Fishery Sciences University, Hebbal, Bangalore 560024, India
| | - Vinod Kadam
- Textile Manufacturing and Textile Chemistry Division, Central Sheep and Wool Research Institute, Avikanagar, Malpura 304501, India
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstr. 21b, 35390 Giessen, Germany
| | - Raghavendra Bhatta
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
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Sun X, Jiang J, Wang G, Zhou P, Li J, Chen C, Liu L, Li N, Xia Y, Ren H. Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China. Anim Biosci 2023; 36:191-199. [PMID: 35760404 PMCID: PMC9834730 DOI: 10.5713/ab.21.0577] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/18/2022] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE This study aimed to investigate the significant single nucleotide polymorphisms (SNPs) and genes associated with nine reproduction and morphological traits in three breed populations of Chinese goats. METHODS The genome-wide association of nine reproduction and morphological traits (litter size, nipple number, wattle, skin color, coat color, black dorsal line, beard, beard length, and hind leg hair) were analyzed in three Chinese native goat breeds (n = 336) using an Illumina Goat SNP50 Beadchip. RESULTS A total of 17 genome-wide or chromosome-wide significant SNPs associated with one reproduction trait (litter size) and six morphological traits (wattle, coat color, black dorsal line, beard, beard length, and hind leg hair) were identified in three Chinese native goat breeds, and the candidate genes were annotated. The significant SNPs and corresponding putative candidate genes for each trait are as follows: two SNPs located on chromosomes 6 (CSN3) and 24 (TCF4) for litter size trait; two SNPs located on chromosome 9 (KATNA1) and 1 (UBASH3A) for wattle trait; three SNPs located on chromosome 26 (SORCS3), 24 (DYM), and 20 (PDE4D) for coat color trait; two SNPs located on chromosome 18 (TCF25) and 15 (CLMP) for black dorsal line trait; four SNPs located on chromosome 8, 2 (PAX3), 5 (PIK3C2G), and 28 (PLA2G12B and OIT3) for beard trait; one SNP located on chromosome 18 (KCNG4) for beard length trait; three SNPs located on chromosome 17 (GLRB and GRIA2), 28 (PGBD5), and 4 for hind leg hair trait. In contrast, there were no SNPs identified for nipple number and skin color. CONCLUSION The significant SNPs or genes identified in this study provided novel insights into the genetic mechanism underlying important reproduction and morphological traits of three local goat breeds in Southern China as well as further potential applications for breeding goats.
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Affiliation(s)
- Xiaoyan Sun
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China
| | - Jing Jiang
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Peng Zhou
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Jie Li
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Cancan Chen
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Liangjia Liu
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Nianfu Li
- Youyang County Livestock Industry Development Center, Chongqing, 409800,
China
| | - Yuanyou Xia
- Youyang County Livestock Industry Development Center, Chongqing, 409800,
China
| | - Hangxing Ren
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China,Corresponding Author: Hangxing Ren, Tel: +86-023-46777341, E-mail:
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Li Y, Hu Y, Cheng P, Chen S. Identification of Potential Blind-Side Hypermelanosis-Related lncRNA–miRNA–mRNA Regulatory Network in a Flatfish Species, Chinese Tongue Sole (Cynoglossus semilaevis). Front Genet 2022; 12:817117. [PMID: 35186018 PMCID: PMC8850641 DOI: 10.3389/fgene.2021.817117] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Blind-side hypermelanosis has emerged as a major concern in commercial rearing environments of the flatfish aquaculture industry. To date, the underlying molecular mechanisms are not well understood. To fill this gap, in this study, whole transcriptomic sequencing and analyses were performed using normal skins and hypermelanic skins of the blind side of Chinese tongue sole (Cynoglossus semilaevis). Differentially expressed long non-coding RNAs (DElncRNAs), miRNAs (DEmiRNAs), and differentially expressed genes as well as their competing endogenous RNA (ceRNA) networks were identified. A total of 34 DElncRNAs, 226 DEmiRNAs, and 610 DEGs were identified. Finally, lncRNA–miRNA–mRNA regulatory networks (involving 29 DElncRNAs, 106 DEmiRNAs, and 162 DEGs) associated with blind-side hypermelanosis were constructed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of 162 DEGs in ceRNA networks identified DEGs (e.g., oca2, mc1r, and ihhb) in pigmentation-related biological processes and DEGs (e.g., ca4, glul, and fut9) in nitrogen metabolism, glycosphingolipid biosynthesis, and folate biosynthesis pathways, as well as their corresponding DElncRNAs and DEmiRNAs to potentially play key regulatory roles in blind-side hypermelanosis. In conclusion, this is the first study on the ceRNA regulatory network associated with blind-side hypermelanosis in flatfish. These new findings expand the spectrum of non-coding regulatory mechanisms underpinning blind-side hypermelanosis, which facilitates the further exploration of molecular regulatory mechanisms of malpigmentation in flatfish.
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Affiliation(s)
- Yangzhen Li
- Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- *Correspondence: Yangzhen Li,
| | - Yuanri Hu
- Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Peng Cheng
- Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Songlin Chen
- Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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Qin H, Chen Y, Wang S, Ge S, Pang Q. The role of KLF4 in melanogenesis and homeostasis in sheep melanocytes. Acta Histochem 2022; 124:151839. [PMID: 34998218 DOI: 10.1016/j.acthis.2021.151839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/01/2022]
Abstract
KLF4 expression has been associated with hair color in mammals and has also been found to regulate melanoma cell growth. Here, we assessed the influence of KLF4 on coat color formation and melanocytes. We found that KLF4 was highly expressed in the black skin of sheep both at the mRNA and protein levels compared with white skin. KLF4 immunostaining further showed that KLF4 protein was mainly expressed in epidermal, outer root, and hair bulb regions. In sheep melanocytes, the proliferation of melanocytes was inhibited by KLF4 overexpression and this decrease in cell proliferation was coupled with induction of the S phase, cell cycle arrest, and apoptosis. In vitro cell migration assays showed that KLF4 suppressed cell migration. In addition, KLF4 overexpression significantly increased melanin production and pigment-related gene expression. Collectively, our findings show that KLF4 is important for coat color formation and melanocyte homeostasis.
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Jian H, Zu P, Rao Y, Li W, Mou T, Lin J, Zhang F. Comparative analysis of melanin deposition between Chishui silky fowl and Taihe silky fowl. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1981911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Huafeng Jian
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Panyu Zu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Yongchao Rao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Wei Li
- Guizhou Province Management Station of Livestock Genetic Resources, Guiyang, People’s Republic of China
| | - Tenghui Mou
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Jiadong Lin
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Fuping Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
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Discovery of genes and proteins possibly regulating mean wool fibre diameter using cDNA microarray and proteomic approaches. Sci Rep 2020; 10:7726. [PMID: 32382132 PMCID: PMC7206055 DOI: 10.1038/s41598-020-64903-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/30/2020] [Indexed: 01/06/2023] Open
Abstract
Wool fibre diameter (WFD) is one of the wool traits with higher economic impact. However, the main genes specifically regulating WFD remain unidentified. In this current work we have used Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin, bearing more wool, in Aohan fine wool sheep, a Chinese indigenous breed, and compared them with that of small tail Han sheep, a sheep bread with coarse wool. Microarray analyses showed that most of the genes likely determining wool diameter could be classified into a few categories, including immune response, regulation of receptor binding and growth factor activity. Certain gene families might play a role in hair growth regulation. These include growth factors, immune cytokines, solute carrier families, cellular respiration and glucose transport amongst others. Proteomic analyses also identified scores of differentially expressed proteins.
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Chen Y, Gong Q, Lai J, Song M, Liu Y, Wu Y, Ai J, Long Z. Transcriptome analysis identifies candidate genes associated with skin color variation in Triplophysa siluroides. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100682. [PMID: 32248074 DOI: 10.1016/j.cbd.2020.100682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 12/18/2022]
Abstract
In vertebrates, skin pigmentation is the most diverse phenotypic trait, and it is produced by a complex biological process that is often genetically controlled. Recently, two different colors (the typical brown and orange varieties) of Triplophysa siluroides, a species restricted to Yellow River drainage in China, were discovered. In the present study, the skin, brain and liver transcriptomes of T. siluroides of both colors were sequenced to search for genes related to skin pigmentation. Transcriptome sequencing generated 1,484,197,774 clean reads, resulting in a total of 222.6 Gb of sequence. The reads were assembled into 470,788 unigenes with a mean length of 1550 bp and an N50 size of 2944 bp. Functional annotation of the unigene dataset showed that 214,507, 304,161, 112,886, 179,074, 180,064, 184,837 and 82,081 unigenes were significantly matched to entries in the Nr protein, Nt, KO, Swiss-Prot, Pfam, GO and KOG databases, respectively. A differential expression analysis revealed that 2774, 3552 and 1529 unigenes were upregulated and 2720, 2663 and 1103 unigenes were downregulated in the skin, brain and liver of orange-skinned T. siluroides, respectively. Several genes that play key roles in pigmentation, i.e., Agouti, Slc45a2, Cbs, Mift and Slc7a11, showed significantly differential expression between brown and orange fish. In addition, we detected 158,863 simple sequence repeats (SSRs) in the T. siluroides transcriptome, and a total of 201,338 single-nucleotide polymorphisms (SNPs) were discovered in the different transcriptomes. The present results will facilitate further study of the molecular mechanisms of skin pigmentation and marker-assisted breeding of fish with valuable skin colors.
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Affiliation(s)
- Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Quan Gong
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China.
| | - Mingjiang Song
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Yingbin Wu
- Sichuan Juhai Fishery Technology Co., Ltd., Chengdu 610000, China
| | - Jiagui Ai
- Sichuan Juhai Fishery Technology Co., Ltd., Chengdu 610000, China
| | - Zhihai Long
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China.
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Xiong Q, Tao H, Zhang N, Zhang L, Wang G, Li X, Suo X, Zhang F, Liu Y, Chen M. Skin transcriptome profiles associated with black- and white-coated regions in Boer and Macheng black crossbred goats. Genomics 2019; 112:1853-1860. [PMID: 31678151 DOI: 10.1016/j.ygeno.2019.10.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 11/19/2022]
Abstract
To increase the current understanding of the gene-expression profiles in different skin regions associated with different coat colors and identify key genes for the regulation of color patterns in goats, we used the Illumina RNA-Seq method to compare the skin transcriptomes of the black- and white-coated regions containing hair follicles from the Boer and Macheng Black crossbred goat, which has a black head and a white body. Six cDNA libraries derived from skin samples of the white-coated region (n = 3) and black-coated region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for skin samples from black- and white-coated regions, respectively, of which 75.39% and 76.05% were covered in the genome database. A total of 165 differentially expressed genes (DEGs) were detected between these two color regions, among which 110 were upregulated and 55 were downregulated in the skin samples of white- vs. black-coated regions. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of these DEGs may play an important role in controlling the pigmentation of skin or hair follicles. We identified three key DEGs, i.e., Agouti, DCT, and TYRP1, in the pathway related to melanogenesis in the different skin regions of the crossbred goat. DCT and TYRP1 were downregulated and Agouti was upregulated in the skin of the white-coated region, suggesting a lack of mature melanocytes in this region and that Agouti might play a key developmental role in color-pattern formation. All data sets (Gene Expression Omnibus) are available via public repositories. In addition, MC1R was genotyped in 200 crossbred goats with a black head and neck. Loss-of-function mutations in MC1R as well as homozygosity for the mutant alleles were widely found in this population. The MC1R gene did not seem to play a major role in determining the black head and neck in our crossbred goats. Our study provides insights into the transcriptional regulation of two distinct coat colors, which might serve as a key resource for understanding coat color pigmentation in goats. The region-specific expression of Agouti may be associated with the distribution of pigments across the body in Boer and Macheng Black crossbred goats.
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Affiliation(s)
- Qi Xiong
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Hu Tao
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Nian Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Liqing Zhang
- Hubei Livestock and Poultry Breeding Centre, Wuhan 430070, China
| | - Guiqiang Wang
- Hubei Livestock and Poultry Breeding Centre, Wuhan 430070, China
| | - Xiaofeng Li
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Xiaojun Suo
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Feng Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Yang Liu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Mingxin Chen
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China.
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Peng Y, Wang Y, Wang R, Geng L, Ma R, Zhang C, Liu Z, Gong Y, Li J, Li X. Exploring differentially expressed genes associated with coat color in goat skin using RNA-seq. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2018-0026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fur color in domestic goats is an important, genetically determined characteristic that is associated with economic value. This study was designed to perform a comprehensive expression profiling of genes expressed in the skin tissues from Laiwu Black goat and Lubei White goat. Comparisons of black and white goat skin transcriptomes revealed 102 differentially expressed genes (DEGs), of which 38 were upregulated and 64 downregulated in black skin compared with white skin. Among the DEGs, we identified six genes involved in pigmentation, including agouti signaling protein (ASIP), CAMP responsive element binding protein 3-like 1 (CREB3L1), dopachrome tautomerase (DCT), premelanosome protein (PMEL), transient receptor potential cation channel subfamily M member 1 (TRPM1), and tyrosinase-related protein 1 (TYRP1). Notably, there were no significant differences in the expression of melanocortin 1 receptor, microphthalmia-associated transcription factor, tyrosinase, and KIT proto-oncogene receptor tyrosine kinase between the black and white skin samples, whereas ASIP expression was detected only in white skin. PMEL, TRPM1, TYRP1, and DCT showed higher expression in black goat skin, but ASIP and CREB3L1 had higher expression in white goat skin. Quantitative polymerase chain reaction results for PMEL, TRPM1, DCT, TYRP1, and CREB3L1 expression were consistent with those for RNA-seq. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goats, and provide a foundation for future studies.
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Affiliation(s)
- Yongdong Peng
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Yaqi Wang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Ruining Wang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Liying Geng
- College of Animal Science and Technology, Agricultural University of Hebei Province, Baoding, Hebei 071001, People’s Republic of China
| | - Ruxue Ma
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Chuansheng Zhang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Zhengzhu Liu
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Yuanfang Gong
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Jingshi Li
- College of Animal Science and Technology, Agricultural University of Hebei Province, Baoding, Hebei 071001, People’s Republic of China
| | - Xianglong Li
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
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11
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Koseniuk A, Ropka-Molik K, Rubiś D, Smołucha G. Genetic background of coat colour in sheep. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-173-2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The coat colour of animals is an extremely important trait that affects their
behaviour and is decisive for survival in the natural environment. In farm
animal breeding, as a result of the selection of a certain coat colour type,
animals are characterized by a much greater variety of coat types. This makes
them an appropriate model in research in this field. A very important aspect
of the coat colour types of farm animals is distinguishing between breeds and
varieties based on this trait. Furthermore, for the sheep breeds which are
kept for skins and wool, coat/skin colour is an important economic trait.
Until now the study of coat colour inheritance in sheep proved the dominance
of white colour over pigmented/black coat or skin and of black over brown.
Due to the current knowledge of the molecular basis of ovine coat colour
inheritance, there is no molecular test to distinguish coat colour types in
sheep although some are available for other species, such as cattle, dogs,
and horses. Understanding the genetic background of variation in one of the
most important phenotypic traits in livestock would help to identify new
genes which have a great effect on the coat colour type. Considering that
coat colour variation is a crucial trait for discriminating between breeds
(including sheep), it is important to broaden our knowledge of the genetic
background of pigmentation. The results may be used in the future to
determine the genetic pattern of a breed. Until now, identified candidate
genes that have a significant impact on colour type in mammals mainly code
for factors located in melanocytes. The proposed candidate genes code for the
melanocortin 1 receptor (MC1R), agouti signaling
protein (ASIP), tyrosinase-related protein 1 (TYRP1),
microphthalmia-associated transcription factor MITF, and v-kit
Hardy–Zuckerman 4 feline sarcoma viral oncogene homologue (KIT).
However, there is still no conclusive evidence of established polymorphisms
for specific coat colour types in sheep.
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12
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Peng Y, Liu X, Geng L, Ma R, Li L, Li J, Zhang C, Liu Z, Gong Y, Li X. Illumina-sequencing based transcriptome study of coat color phenotypes in domestic goats. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0543-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Zhao J, Liu N, Liu K, He J, Yu J, Bu R, Cheng M, De W, Liu J, Li H. Identification of genes and proteins associated with anagen wool growth. Anim Genet 2016; 48:67-79. [PMID: 27611105 DOI: 10.1111/age.12480] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 02/03/2023]
Abstract
Identifying genes of major effect for wool growth would offer strategies for improving the quality and increasing the yield of fine wool. In this study, we employed the Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin (more wool growing) in Aohan fine wool sheep (a Chinese indigenous breed) in comparison with groin skin (no wool growing) at the anagen stage of the wool follicle. A microarray study revealed that 4772 probes were differentially expressed, including 2071 upregulated and 2701 downregulated probes, in the comparisons of body side skin vs. groin skin (S/G). The microarray results were verified by means of quantitative PCR. A total of 1099 probes were assigned to unique genes/transcripts. The number of distinct genes/transcripts (annotated) was 926, of which 352 were upregulated and 574 were downregulated. In S/G, 13 genes were upregulated by more than 10 fold, whereas 60 genes were downregulated by more than 10 fold. Further analysis revealed that the majority of the genes possibly related to the wool growth could be assigned to categories including regulation of cell division, intermediate filament, cytoskeletal part and growth factor activity. Several potential gene families may participate in hair growth regulation, including fibroblast growth factors, transforming growth factor-β, WNTs, insulin-like growth factor, vascular endothelial growth factors and so on. Proteomic analysis also revealed 196 differentially expressed protein points, of which 121 were identified as single protein points.
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Affiliation(s)
- J Zhao
- Qingdao Agricultural University, Qingdao, 266109, China.,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.,China Agricultural University, Beijing, 100193, China
| | - N Liu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - K Liu
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
| | - J He
- Qingdao Agricultural University, Qingdao, 266109, China
| | - J Yu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - R Bu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - M Cheng
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
| | - W De
- Nanjing Medical University, Nanjing, 210029, China
| | - J Liu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - H Li
- Qingdao Agricultural University, Qingdao, 266109, China.,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
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Zhao J, Li H, Liu K, Zhang B, Li P, He J, Cheng M, De W, Liu J, Zhao Y, Yang L, Liu N. Identification of differentially expressed genes affecting hair and cashmere growth in the Laiwu black goat by microarray. Mol Med Rep 2016; 14:3823-31. [DOI: 10.3892/mmr.2016.5728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 06/30/2016] [Indexed: 11/05/2022] Open
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15
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Skin transcriptome profiles associated with skin color in chickens. PLoS One 2015; 10:e0127301. [PMID: 26030885 PMCID: PMC4452617 DOI: 10.1371/journal.pone.0127301] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 04/14/2015] [Indexed: 12/20/2022] Open
Abstract
Nutritional and medicinal benefits have been attributed to the consumption of tissues from the black-boned chickens in oriental countries. Lueyang black-boned chicken is one of the native chicken breeds. However, some birds may instead have white or lighter skin, which directly causes economic losses every year. Previous studies of pigmentation have focused on a number of genes that may play important roles in coat color regulation. Illumina2000 sequencing technology was used to catalog the global gene expression profiles in the skin of the Lueyang chicken with white versus black skin. A total of 18,608 unigenes were assembled from the reads obtained from the skin of the white and black chickens. A total of 649 known genes were differentially expressed in the black versus white chickens, with 314 genes that were up regulated and 335 genes that were down-regulated, and a total of 162 novel genes were differentially expressed in the black versus white chickens, consisting of 73 genes that were up-regulated (including 4 highly expressed genes that were expressed exclusively in the skin of the black chickens) and 89 genes that were down-regulated. There were also a total of 8 known coat-color genes expressed in previous studies (ASIP, TYR, KIT, TYRP1, OCA2, KITLG, MITF and MC1R). In this study, 4 of which showed greater expression in the black chickens, and several were up-regulated, such as KIT, ASIP, TYR and OCA2. To our surprise, KITLG, MITF and MC1R showed no significant difference in expression between the black- and white-skinned chickens, and the expression of TYRP1 was not detected in either skin color. The expression of ASIP, TYR, KIT, TYRP1, OCA2, KITLG, MITF and MC1R was validated by real-time quantitative polymerase chain reaction (qPCR), and the results of the qPCR were consistent with the RNA-seq. This study provides several candidate genes that may be associated with the development of black versus white skin. More importantly, the fact that the MC1R gene showed no significant difference in expression between the black and white chickens is of particular interest for future studies that aim to elucidate its functional role in the regulation of skin color.
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16
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Liu N, Li H, Liu K, Yu J, Bu R, Cheng M, De W, Liu J, He G, Zhao J. Identification of skin-expressed genes possibly associated with wool growth regulation of Aohan fine wool sheep. BMC Genet 2014; 15:144. [PMID: 25511509 PMCID: PMC4272822 DOI: 10.1186/s12863-014-0144-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 12/03/2014] [Indexed: 11/25/2022] Open
Abstract
Background Sheep are valuable resources for the animal fibre industry. Therefore, identifying genes which regulate wool growth would offer strategies for improving the quality of fine wool. In this study, we employed Agilent sheep gene expression microarray and proteomic technology to compare the gene expression patterns of the body side (hair-rich) and groin (hairless) skins of Aohan fine wool sheep (a Chinese indigenous breed). Results Comparing the body side to the groin skins (S/G) of Aohan fine wool sheep, the microarray study revealed that 1494 probes were differentially expressed, including 602 more highly expressed and 892 less highly expressed probes. The microarray results were verified by means of quantitative PCR. Cluster analysis could distinguish the body side skin and the groin skin. Based on the Database for Annotation, Visualization and Integrated Discovery (DAVID), 38 of the differentially expressed genes were classified into four categories, namely regulation of receptor binding, multicellular organismal process, protein binding and macromolecular complex. Proteomic study revealed that 187 protein spots showed significant (p < 0.05) differences in their respective expression levels. Among them, 46 protein entries were further identified by MALDI-TOF/MS analyses. Conclusions Microarray analysis revealed thousands of differentially expressed genes, many of which were possibly associated with wool growth. Several potential gene families might participate in hair growth regulation. Proteomic analysis also indentified hundreds of differentially expressed proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0144-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nan Liu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Hegang Li
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.
| | - Kaidong Liu
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.
| | - Juanjuan Yu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Ran Bu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Ming Cheng
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.
| | - Wei De
- Nanjing Medical University, Nanjing, 210002, China.
| | - Jifeng Liu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Guangling He
- State key Laboratory of Hydroscience and Engineering, Beijing, 100084, China.
| | - Jinshan Zhao
- Qingdao Agricultural University, Qingdao, 266109, China. .,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China. .,China Agricultural University, Beijing, 100193, China.
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17
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Liu N, Li H, Liu K, Yu J, Cheng M, De W, Liu J, Shi S, He Y, Zhao J. Differential expression of genes and proteins associated with wool follicle cycling. Mol Biol Rep 2014; 41:5343-9. [PMID: 24847760 DOI: 10.1007/s11033-014-3405-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/06/2014] [Indexed: 01/31/2023]
Abstract
Sheep are valuable resources for the wool industry. Wool growth of Aohan fine wool sheep has cycled during different seasons in 1 year. Therefore, identifying genes that control wool growth cycling might lead to ways for improving the quality and yield of fine wool. In this study, we employed Agilent sheep gene expression microarray and proteomic technology to compare the gene expression patterns of the body side skins at August and December time points in Aohan fine wool sheep (a Chinese indigenous breed). Microarray study revealed that 2,223 transcripts were differentially expressed, including 1,162 up-regulated and 1,061 down-regulated transcripts, comparing body side skin at the August time point to the December one (A/D) in Aohan fine wool sheep. Then seven differentially expressed genes were selected to validated the reliability of the gene chip data. The majority of the genes possibly related to follicle development and wool growth could be assigned into the categories including regulation of receptor binding, extracellular region, protein binding and extracellular space. Proteomic study revealed that 84 protein spots showed significant differences in expression levels. Of the 84, 63 protein spots were upregulated and 21 were downregulated in A/D. Finally, 55 protein points were determined through MALDI-TOF/MS analyses. Furthermore, the regulation mechanism of hair follicle might resemble that of fetation.
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Affiliation(s)
- Nan Liu
- Qingdao Agricultural University, Qingdao, 266109, China,
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18
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Fan R, Xie J, Bai J, Wang H, Tian X, Bai R, Jia X, Yang L, Song Y, Herrid M, Gao W, He X, Yao J, Smith GW, Dong C. Skin transcriptome profiles associated with coat color in sheep. BMC Genomics 2013; 14:389. [PMID: 23758853 PMCID: PMC3689618 DOI: 10.1186/1471-2164-14-389] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/04/2013] [Indexed: 01/06/2023] Open
Abstract
Background Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color. Results There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category. Conclusion The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep.
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Affiliation(s)
- Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
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Miao X, Luo Q. Genome-wide transcriptome analysis between small-tail Han sheep and the Surabaya fur sheep using high-throughput RNA sequencing. Reproduction 2013; 145:587-96. [PMID: 23579189 DOI: 10.1530/rep-12-0507] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The small-tail Han sheep and the Surabaya fur sheep are two local breeds in north China, which are characterized by high-fecundity and low-prolificacy breed respectively. Significant genetic differences between these two breeds have provided increasing interests in the identification and utilization of major prolificacy genes in these sheep. High prolificacy is a complex trait, and it is difficult to comprehensively identify the candidate genes related to this trait using the single molecular biology technique. To understand the molecular mechanisms of fecundity and provide more information about high prolificacy candidate genes in high- and low-fecundity sheep, we explored the utility of next-generation sequencing technology in this work. A total of 1.8 Gb sequencing reads were obtained and resulted in more than 20 000 contigs that averaged ∼300 bp in length. Ten differentially expressed genes were further verified by quantitative real-time RT-PCR to confirm the reliability of RNA-seq results. Our work will provide a basis for the future research of the sheep reproduction.
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Affiliation(s)
- Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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