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An L, Pan Y, Yuan M, Wen Z, Qiao L, Wang W, Liu J, Li B, Liu W. Full-Length Transcriptome and Gene Expression Analysis of Different Ovis aries Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis. Animals (Basel) 2023; 14:7. [PMID: 38200738 PMCID: PMC10777924 DOI: 10.3390/ani14010007] [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: 10/19/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Sheep have historically been bred globally as a vital food source. To explore the transcriptome of adipose tissue and investigate key genes regulating adipose metabolism in sheep, adipose tissue samples were obtained from F1 Dorper × Hu sheep. High-throughput sequencing libraries for second- and third-generation sequencing were constructed using extracted total RNA. Functional annotation of differentially expressed genes and isoforms facilitated the identification of key regulatory genes and isoforms associated with sheep fat metabolism. SMRT-seq generated 919,259 high-accuracy cDNA sequences after filtering. Full-length sequences were corrected using RNA-seq sequences, and 699,680 high-quality full-length non-chimeric (FLNC) reads were obtained. Upon evaluating the ratio of total lengths based on FLNC sequencing, it was determined that 36,909 out of 56,316 multiple-exon isoforms met the criteria for full-length status. This indicates the identification of 330,375 full-length FLNC transcripts among the 370,114 multiple-exon FLNC transcripts. By comparing the reference genomes, 60,276 loci and 111,302 isoforms were identified. In addition, 43,423 new genes and 44,563 new isoforms were identified. The results identified 185 (3198), 394 (3592), and 83 (3286) differentially expressed genes (transcripts) between tail and subcutaneous, tail and visceral, and subcutaneous and visceral adipose tissues, respectively. Functional annotation and pathway analysis revealed the following observations. (1) Among the differentially expressed genes (DEGs) of TF and SF tissues, the downregulation of ACADL, ACSL6, and NC_056060.1.2536 was observed in SF, while FFAR4 exhibited upregulation. (2) Among the DEGs of TF and VF tissues, expressions of ACADL, ACSL6, COL1A1, COL1A2, and SCD were downregulated in VF, with upregulation of FFAR4. (3) Among SF and VF expressions of COL1A1, COL1A2, and NC_056060.1.2536 were downregulated in VF. Specific differentially expressed genes (ACADL, ACSL6, COL1A1, COL1A2, FFAR4, NC_056060.1.2536, and SCD) and transcripts (NC_056066.1.1866.16 and NC_056066.1.1866.22) were identified as relevant to fat metabolism. These results provide a dataset for further verification of the regulatory pathway associated with fat metabolism in sheep.
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Affiliation(s)
- Lixia An
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
- School of Food & Environment, Jinzhong College of Information, Jinzhong 030801, China
| | - Yangyang Pan
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Mengjiao Yuan
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Zhonghao Wen
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Liying Qiao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Weiwei Wang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Jianhua Liu
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Baojun Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
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Uyanga VA, Bello SF, Qian X, Chao N, Li H, Zhao J, Wang X, Jiao H, Onagbesan OM, Lin H. Transcriptomics analysis unveils key potential genes associated with brain development and feeding behavior in the hypothalamus of L-citrulline-fed broiler chickens. Poult Sci 2023; 102:103136. [PMID: 37844531 PMCID: PMC10585647 DOI: 10.1016/j.psj.2023.103136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
High ambient temperature is a major environmental stressor affecting poultry production, especially in the tropical and subtropical regions of the world. Nutritional interventions have been adopted to combat thermal stress in poultry, including the use of amino acids. L-citrulline is a nonessential amino acid that is involved in nitric oxide generation and thermoregulation, however, the molecular mechanisms behind L-citrulline's regulation of body temperature are still unascertained. This study investigated the global gene expression in the hypothalamus of chickens fed either basal diet or L-citrulline-supplemented diets under different housing temperatures. Ross 308 broilers were fed with basal diet (CON) or 1% L-citrulline diet (LCT) from day-old, and later subjected to 2 environmental temperatures in a 2 by 2 factorial arrangement as follows; basal diet-fed chickens housed at 24°C (CON-TN); L-citrulline diet-fed chickens housed at 24°C (LCT-TN); basal diet-fed chickens housed at 35°C (CON-HS), and L-citrulline diet-fed chickens housed at 35°C (LCT-HS) from 22 to 42 d of age. At 42-days old, hypothalamic tissues were collected for mRNA analyses and RNA sequencing. A total of 1,019 million raw reads were generated and about 82.59 to 82.96% were uniquely mapped to genes. The gene ontology (GO) term between the CON-TN and LCT-TN groups revealed significant enrichments of pathways such as central nervous system development, and Wnt signaling pathway. On the other hand, GO terms between the CON-HS and LCT-HS groups revealed enrichments in the regulation of corticosteroid release, regulation of feeding behavior, and regulation of inflammatory response. Several potential candidate genes were identified to be responsible for central nervous system development (EMX2, WFIKKN2, SLC6A4 Wnt10a, and PHOX2B), and regulation of feed intake (NPY, AgRP, GAL, POMC, and NMU) in chickens. Therefore, this study unveils that L-citrulline can influence transcripts associated with brain development, feeding behavior, energy metabolism, and thermoregulation in chickens raised under different ambient temperatures.
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Affiliation(s)
- Victoria Anthony Uyanga
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China; Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Xin Qian
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Ning Chao
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Haifang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Jingpeng Zhao
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Xiaojuan Wang
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Hongchao Jiao
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China
| | - Okanlawon M Onagbesan
- Department of Animal Physiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Hai Lin
- Department of Animal Science, College of Animal Science and Veterinary Medicine, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control, Shandong Agricultural University, Tai'an City, Shandong Province 271018, China.
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3
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Juiputta J, Chankitisakul V, Boonkum W. Appropriate Genetic Approaches for Heat Tolerance and Maintaining Good Productivity in Tropical Poultry Production: A Review. Vet Sci 2023; 10:591. [PMID: 37888543 PMCID: PMC10611393 DOI: 10.3390/vetsci10100591] [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: 08/14/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Heat stress is a major environmental threat to poultry production systems, especially in tropical areas. The effects of heat stress have been discovered in several areas, including reduced growth rate, reduced egg production, low feed efficiency, impaired immunological responses, changes in intestinal microflora, metabolic changes, and deterioration of meat quality. Although several methods have been used to address the heat stress problem, it persists. The answer to this problem can be remedied sustainably if genetic improvement approaches are available. Therefore, the purpose of this review article was to present the application of different approaches to genetic improvement in poultry in the hope that users will find suitable solutions for their poultry population and be able to plan future poultry breeding programs.
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Affiliation(s)
- Jiraporn Juiputta
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
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Luna-Ramirez RI, Limesand SW, Goyal R, Pendleton AL, Rincón G, Zeng X, Luna-Nevárez G, Reyna-Granados JR, Luna-Nevárez P. Blood Transcriptomic Analyses Reveal Functional Pathways Associated with Thermotolerance in Pregnant Ewes Exposed to Environmental Heat Stress. Genes (Basel) 2023; 14:1590. [PMID: 37628641 PMCID: PMC10454332 DOI: 10.3390/genes14081590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Environmental heat stress triggers a series of compensatory mechanisms in sheep that are dependent on their genetic regulation of thermotolerance. Our objective was to identify genes and regulatory pathways associated with thermotolerance in ewes exposed to heat stress. We performed next-generation RNA sequencing on blood collected from 16 pregnant ewes, which were grouped as tolerant and non-tolerant to heat stress according to a physiological indicator. Additional samples were collected to measure complete blood count. A total of 358 differentially expressed genes were identified after applying selection criteria. Gene expression analysis detected 46 GO terms and 52 KEGG functional pathways. The top-three signaling pathways were p53, RIG-I-like receptor and FoxO, which suggested gene participation in biological processes such as apoptosis, cell signaling and immune response to external stressors. Network analysis revealed ATM, ISG15, IRF7, MDM4, DHX58 and TGFβR1 as over-expressed genes with high regulatory potential. A co-expression network involving the immune-related genes ISG15, IRF7 and DXH58 was detected in lymphocytes and monocytes, which was consistent with hematological findings. In conclusion, transcriptomic analysis revealed a non-viral immune mechanism involving apoptosis, which is induced by external stressors and appears to play an important role in the molecular regulation of heat stress tolerance in ewes.
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Affiliation(s)
- Rosa I. Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sean W. Limesand
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Ravi Goyal
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Alexander L. Pendleton
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Xi Zeng
- Zoetis Inc., VMRD Genetics R&D, Kalamazoo, MI 49007, USA
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Javier R. Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
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Rybalka E, Kourakis S, Bonsett CA, Moghadaszadeh B, Beggs AH, Timpani CA. Adenylosuccinic Acid: An Orphan Drug with Untapped Potential. Pharmaceuticals (Basel) 2023; 16:822. [PMID: 37375769 PMCID: PMC10304260 DOI: 10.3390/ph16060822] [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: 05/09/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Adenylosuccinic acid (ASA) is an orphan drug that was once investigated for clinical application in Duchenne muscular dystrophy (DMD). Endogenous ASA participates in purine recycling and energy homeostasis but might also be crucial for averting inflammation and other forms of cellular stress during intense energy demand and maintaining tissue biomass and glucose disposal. This article documents the known biological functions of ASA and explores its potential application for the treatment of neuromuscular and other chronic diseases.
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Affiliation(s)
- Emma Rybalka
- Institute for Health and Sport (IHeS), Victoria University, Melbourne, VIC 8001, Australia; (S.K.); (C.A.T.)
- Inherited and Acquired Myopathy Program, Australian Institute for Musculoskeletal Science (AIMSS), St Albans, VIC 3021, Australia
- Department of Medicine—Western Health, Melbourne Medical School, The University of Melbourne, St Albans, VIC 3021, Australia
- Division of Neuropaediatrics and Developmental Medicine, University Children’s Hospital of Basel (UKBB), 4056 Basel, Switzerland
| | - Stephanie Kourakis
- Institute for Health and Sport (IHeS), Victoria University, Melbourne, VIC 8001, Australia; (S.K.); (C.A.T.)
- Inherited and Acquired Myopathy Program, Australian Institute for Musculoskeletal Science (AIMSS), St Albans, VIC 3021, Australia
| | - Charles A. Bonsett
- Dystrophy Concepts Incorporated, Indianapolis, IN 46226, USA;
- School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Behzad Moghadaszadeh
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (B.M.); (A.H.B.)
| | - Alan H. Beggs
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (B.M.); (A.H.B.)
| | - Cara A. Timpani
- Institute for Health and Sport (IHeS), Victoria University, Melbourne, VIC 8001, Australia; (S.K.); (C.A.T.)
- Inherited and Acquired Myopathy Program, Australian Institute for Musculoskeletal Science (AIMSS), St Albans, VIC 3021, Australia
- Department of Medicine—Western Health, Melbourne Medical School, The University of Melbourne, St Albans, VIC 3021, Australia
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6
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Sumasgutner P, Cunningham SJ, Hegemann A, Amar A, Watson H, Nilsson JF, Andersson MN, Isaksson C. Interactive effects of rising temperatures and urbanisation on birds across different climate zones: A mechanistic perspective. GLOBAL CHANGE BIOLOGY 2023; 29:2399-2420. [PMID: 36911976 PMCID: PMC10947105 DOI: 10.1111/gcb.16645] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 05/28/2023]
Abstract
Climate change and urbanisation are among the most pervasive and rapidly growing threats to biodiversity worldwide. However, their impacts are usually considered in isolation, and interactions are rarely examined. Predicting species' responses to the combined effects of climate change and urbanisation, therefore, represents a pressing challenge in global change biology. Birds are important model taxa for exploring the impacts of both climate change and urbanisation, and their behaviour and physiology have been well studied in urban and non-urban systems. This understanding should allow interactive effects of rising temperatures and urbanisation to be inferred, yet considerations of these interactions are almost entirely lacking from empirical research. Here, we synthesise our current understanding of the potential mechanisms that could affect how species respond to the combined effects of rising temperatures and urbanisation, with a focus on avian taxa. We discuss potential interactive effects to motivate future in-depth research on this critically important, yet overlooked, aspect of global change biology. Increased temperatures are a pronounced consequence of both urbanisation (through the urban heat island effect) and climate change. The biological impact of this warming in urban and non-urban systems will likely differ in magnitude and direction when interacting with other factors that typically vary between these habitats, such as resource availability (e.g. water, food and microsites) and pollution levels. Furthermore, the nature of such interactions may differ for cities situated in different climate types, for example, tropical, arid, temperate, continental and polar. Within this article, we highlight the potential for interactive effects of climate and urban drivers on the mechanistic responses of birds, identify knowledge gaps and propose promising future research avenues. A deeper understanding of the behavioural and physiological mechanisms mediating species' responses to urbanisation and rising temperatures will provide novel insights into ecology and evolution under global change and may help better predict future population responses.
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Affiliation(s)
- Petra Sumasgutner
- Konrad Lorenz Research Centre, Core Facility for Behavior and Cognition, Department of Behavioral & Cognitive BiologyUniversity of ViennaViennaAustria
- FitzPatrick Institute of African Ornithology, DSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
| | - Susan J. Cunningham
- FitzPatrick Institute of African Ornithology, DSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
| | | | - Arjun Amar
- FitzPatrick Institute of African Ornithology, DSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
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Hosseinzadeh S, Hasanpur K. Gene expression networks and functionally enriched pathways involved in the response of domestic chicken to acute heat stress. Front Genet 2023; 14:1102136. [PMID: 37205120 PMCID: PMC10185895 DOI: 10.3389/fgene.2023.1102136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Heat stress in poultry houses, especially in warm areas, is one of the main environmental factors that restrict the growth of broilers or laying performance of layers, suppresses the immune system, and deteriorates egg quality and feed conversion ratio. The molecular mechanisms underlying the response of chicken to acute heat stress (AHS) have not been comprehensively elucidated. Therefore, the main object of the current work was to investigate the liver gene expression profile of chickens under AHS in comparison with their corresponding control groups, using four RNA-seq datasets. The meta-analysis, GO and KEGG pathway enrichment, WGCNA, machine-learning, and eGWAS analyses were performed. The results revealed 77 meta-genes that were mainly related to protein biosynthesis, protein folding, and protein transport between cellular organelles. In other words, under AHS, the expression of genes involving in the structure of rough reticulum membrane and in the process of protein folding was adversely influenced. In addition, genes related to biological processes such as "response to unfolded proteins," "response to reticulum stress" and "ERAD pathway" were differentially regulated. We introduce here a couple of genes such as HSPA5, SSR1, SDF2L1, and SEC23B, as the most significantly differentiated under AHS, which could be used as bio-signatures of AHS. Besides the mentioned genes, the main findings of the current work may shed light to the identification of the effects of AHS on gene expression profiling of domestic chicken as well as the adaptive response of chicken to environmental stresses.
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8
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Yasukochi Y, Shin S, Wakabayashi H, Maeda T. Transcriptomic Changes in Young Japanese Males After Exposure to Acute Hypobaric Hypoxia. Front Genet 2020; 11:559074. [PMID: 33101380 PMCID: PMC7506118 DOI: 10.3389/fgene.2020.559074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/14/2020] [Indexed: 12/27/2022] Open
Abstract
After the genomic era, the development of high-throughput sequencing technologies has allowed us to advance our understanding of genetic variants responsible for adaptation to high altitude in humans. However, transcriptomic characteristics associated with phenotypic plasticity conferring tolerance to acute hypobaric hypoxic stress remain unclear. To elucidate the effects of hypobaric hypoxic stress on transcriptional variability, we aimed to describe transcriptomic profiles in response to acute hypobaric hypoxia in humans. In a hypobaric hypoxic chamber, young Japanese males were exposed to a barometric pressure of 493 mmHg (hypobaric hypoxia) for 75 min after resting for 30 min at the pressure of 760 mmHg (normobaric normoxia) at 28°C. Saliva samples of the subjects were collected before and after hypobaric hypoxia exposure, to be used for RNA sequencing. Differential gene expression analysis identified 30 significantly upregulated genes and some of these genes may be involved in biological processes influencing hematological or immunological responses to hypobaric hypoxic stress. We also confirmed the absence of any significant transcriptional fluctuations in the analysis of basal transcriptomic profiles under no-stimulus conditions, suggesting that the 30 genes were actually upregulated by hypobaric hypoxia exposure. In conclusion, our findings showed that the transcriptional profiles of Japanese individuals can be rapidly changed as a result of acute hypobaric hypoxia, and this change may influence the phenotypic plasticity of lowland individuals for acclimatization to a hypobaric hypoxic environment. Therefore, the results obtained in this study shed light on the transcriptional mechanisms underlying high-altitude acclimatization in humans.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Organization for the Promotion of Regional Innovation, Mie University, Tsu, Japan
| | - Sora Shin
- Graduate School of Design, Kyushu University, Fukuoka, Japan
| | | | - Takafumi Maeda
- Department of Human Science, Faculty of Design, Kyushu University, Fukuoka, Japan.,Physiological Anthropology Research Center, Faculty of Design, Kyushu University, Fukuoka, Japan
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9
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Te Pas MFW, Borg R, Buddiger NJH, Wood BJ, Rebel JMJ, van Krimpen MM, Calus MPL, Park JE, Schokker D. Regulating appetite in broilers for improving body and muscle development - A review. J Anim Physiol Anim Nutr (Berl) 2020; 104:1819-1834. [PMID: 32592266 PMCID: PMC7754290 DOI: 10.1111/jpn.13407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022]
Abstract
Appetite is the desire for feed and water and the voluntary intake of feed and is an important regulator of livestock productivity and animal health. Economic traits such as growth rate and muscle development (meat deposition) in broilers are directly correlated to appetite. Factors that may influence appetite include environmental factors, such as stress and temperature variation, and animal‐specific factors, such as learning period, eating capacity and preferences. Feed preferences have been reported to be determined in early life, and this period is important in broilers due to their fast growth and relatively short growth trajectories. This may be of importance when contemplating the use of more circular and sustainable feeds and the optimization of appetite for these feeds. The objective of this review was to review the biological mechanisms underlying appetite using data from human, animal and bird models and to consider the option for modulating appetite particularly as it relates to broiler chickens.
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Affiliation(s)
- Marinus F W Te Pas
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | | | | | - Benjamin J Wood
- Hendrix Genetics North America Office, Kitchener, ON, Canada
| | - Johanna M J Rebel
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | - Marinus M van Krimpen
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | - Mario P L Calus
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | - Jong-Eun Park
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju, Korea
| | - Dirkjan Schokker
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
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Identification of genes related to effects of stress on immune function in the spleen in a chicken stress model using transcriptome analysis. Mol Immunol 2020; 124:180-189. [PMID: 32592984 DOI: 10.1016/j.molimm.2020.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/10/2020] [Accepted: 06/01/2020] [Indexed: 01/09/2023]
Abstract
Stress is a physiological manifestation of the body's defense against adverse effects of external environment, but the molecular regulatory mechanism of stress effects on immune function of poultry has not been fully clarified. In this study, 7-day-old Chinese local breed Gushi cocks were used as model animal, and the stress model was successfully constructed by adding corticosterone (CORT) 30 mg/kg basic diet for 7 days. The spleen transcriptomes of the control group (B_S group) and the stress model group (C_S group) was determined by high-throughput mRNA sequencing (RNA-Seq) technology, and a total of 269 significantly differentially expressed genes (SDEGs) were obtained (Padj < 0.05, |FC| ≥ 2 and FPKM > 1). Compared with B_S group, there were 140 significantly up-regulated genes and 129 significantly down-regulated genes in C_S group. The immune/stress-related Gene Ontology (GO) terms included positive regulation of T cell mediated immunity, chemokine-mediated signaling pathway, T cell mediated immunity and so on. The SDEGs such as IL8L1, HSPA8, HSPA2, RSAD2, CCR8L and DMB1 were involved in these GO terms. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the SDEGs participated in many immune-related signaling pathways. The immune-related genes HSPA2, HSPA8, HSP90AA1, HSPH1 and HERPUD1 were enriched in Protein processing in endoplasmic reticulum pathway, IL8L1, CXCL13L2, CCR6, LEPR, CCR9 and CCR8L were enriched in Cytokine-cytokine receptor interaction pathway. The protein-protein interactions (PPI) analysis showed HSPA8, HSPA2 and IL8L1 as key core nodes had 7 interactions and may play important roles in the regulation of CORT-induced stress effects on immune function. The data onto this study enriched the genomic study of stress effects on immune function, and provided unique insights into the molecular mechanism of stress effects on immune function, and the genes identified in this study can be candidates for future research on stress response.
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11
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Kumar H, Iskender AU, Srikanth K, Kim H, Zhunushov AT, Chooq H, Jang GW, Lim Y, Song KD, Park JE. Transcriptome of Chicken Liver Tissues Reveals the Candidate Genes and Pathways Responsible for Adaptation into Two Different Climatic Conditions. Animals (Basel) 2019; 9:ani9121076. [PMID: 31816986 PMCID: PMC6940799 DOI: 10.3390/ani9121076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing was used to profile the liver transcriptome of a Korean commercial chicken (Hanhyup) at two different environments (Korea and Kyrgyzstan) to investigate their role during acclimatization into different climatic conditions. Ten samples from each location were analyzed to identify candidate genes that respond to environmental changes such as altitude, humidity, temperature, etc. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches. At a false discovery rate (FDR) <0.05 and fold change (FC) ≥2, we found 315 genes were DE. Out of 315 DE genes, 174 and 141 were up- and down-regulated respectively in the Kyrgyz environment. Gene ontology (GO) enrichment analysis showed that the differentially expressed genes (DEGs) were associated with energy metabolism such as pyruvate and lactate metabolic processes, and glycerol catabolic process. Similarly, KEGG pathway analysis indicated pyruvate metabolism, glycolysis/gluconeogenesis, biosynthesis, citrate cycles were differentially enriched in the Kyrgyz environment. DEGs like TSKU, VTG1, SGK, CDK2, etc. in such pathways are highly involved in the adaptation of organisms into diverse climatic conditions. Our investigation may serve as a resource for the chicken industry, especially in exporting Hanhyup chicken from Korea to other countries.
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Affiliation(s)
- Himansu Kumar
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
| | - Asankadyr U. Iskender
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
- Institute of Biotechnology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan;
| | - Krishnamoorthy Srikanth
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
| | - Hana Kim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
| | - Asankadyr T. Zhunushov
- Institute of Biotechnology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan;
| | - Hyojun Chooq
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
| | - Gul Won Jang
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
| | - Youngjo Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
| | - Ki Duk Song
- The Animal Molecular Genetics and Breeding Center, Department of Animal Biotechnology, JeonBuk National University, Jeonju 54896, Korea;
| | - Jong Eun Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju 55365, Korea; (H.K.); (A.U.I.); (K.S.); (H.K.); (H.C.); (G.W.J.); (Y.L.)
- Correspondence:
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Srikanth K, Kumar H, Park W, Byun M, Lim D, Kemp S, Te Pas MFW, Kim JM, Park JE. Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response. Front Genet 2019; 10:993. [PMID: 31681427 PMCID: PMC6798392 DOI: 10.3389/fgene.2019.00993] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/18/2019] [Indexed: 12/30/2022] Open
Abstract
Heat stress (HS) negatively affects chicken performance. Agricultural expansion will happen in regions that experience high ambient temperatures, where fast-growing commercial chickens are vulnerable. Indigenous chickens of such regions, due to generations of exposure to environmental challenges, might have higher thermal tolerance. In this study, two indigenous chicken ecotypes, from the hot and humid Mombasa (lowland) and the colder Naivasha (highland) regions, were used to investigate the effects of acute (5 h, 35°C) and chronic (3 days of 35°C for 8 h/day) HS on the cardiac and skeletal muscle, through RNA sequencing. The rectal temperature gain and the number of differentially expressed genes (DEGs) [False Discovery Rate (FDR) < 0.05] were two times higher in the acute stage than in the chronic stage in both ecotypes, suggesting that cyclic exposure to HS can lead to adaptation. A tissue- and stage-specific difference in response to HS was observed, with peroxisome proliferator-activated-receptor (PPAR) signaling and mitogen-activate protein kinase (MAPK) signaling pathways, enriched in heart and skeletal muscle, respectively, and the p53 pathway enriched only in the acute stage in both tissues. The acute and chronic stage DEGs were integrated by a region-specific gene coexpression network (GCN), and genes with the highest number of connections (hub genes) were identified. The hub genes in the lowland network were CCNB2, Crb2, CHST9, SESN1, and NR4A3, while COMMD4, TTC32, H1F0, ACYP1, and RPS28 were the hub genes in the highland network. Pathway analysis of genes in the GCN showed that p53 and PPAR signaling pathways were enriched in both low and highland networks, while MAPK signaling and protein processing in endoplasmic reticulum were enriched only in the gene network of highland chickens. This shows that to dissipate the accumulated heat, to reduce heat induced apoptosis, and to promote DNA damage repair, the ecotypes activated or suppressed different genes, indicating the differences in thermal tolerance and HS response mechanisms between the ecotypes. This study provides information on the HS response of chickens, adapted to two different agro climatic environments, extending our understanding of the mechanisms of HS response and the effect of adaptation in counteracting HS.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Himansu Kumar
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Mijeong Byun
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Steve Kemp
- Animal Biosciences, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Marinus F W Te Pas
- Wageningen UR Livestock Research, Animal Breeding and Genomics, Wageningen, Netherlands
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
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E GX, Basang WD, Zhu YB. Whole-genome analysis identifying candidate genes of altitude adaptive ecological thresholds in yak populations. J Anim Breed Genet 2019; 136:371-377. [PMID: 31062447 DOI: 10.1111/jbg.12403] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/30/2022]
Abstract
The domestic yak (Bos grunniens) is an iconic symbol of animal husbandry on the Qinghai-Tibet Plateau. Long-term domestication and natural selection have led to a wide distribution of yak, forming many ecological populations to adapt to the local ecological environment. High altitude is closely related to oxygen density, and it is an important environmental ecological factor for biological survival and livestock production. The aim of the present study was to perform a preliminary analysis to identify the candidate genes of altitude distribution adapted ecological thresholds in yak using next-generation sequence technology. A total of 15,762,829 SNPs were obtained from 29 yaks with high- and low-altitude distribution by genome-wide sequencing. According to the results of the selective sweep analysis with FST and ZHp, 21 candidate genes were identified. 14 genes (serine/threonine protein kinase TNNI3K, TEN1, DYM, ITPR1, ZC4H2, KNTC1, ADGRB3, CLYBL, TANGO6, ASCC3, KLHL3, PDE4D, DEPDC1B and AGBL4) were grouped into 32 Gene Ontology terms, and four genes (RPS6KA6, ITPR1, GNAO1 and PDE4D) annotated in 35 pathways, including seven environmental information processing and one environmental adaptation. Therefore, the novel candidate genes found in the current study do not only support new theories about high-altitude adaptation, but also further explain the molecular mechanisms of altitude adaptation threshold in yaks.
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Affiliation(s)
- Guang-Xin E
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wang-Dui Basang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Sciences (TAAAS)), Lhasa, China.,Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yan-Bin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
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