1
|
González-Buenfil R, Vieyra-Sánchez S, Quinto-Cortés CD, Oppenheimer SJ, Pomat W, Laman M, Cervantes-Hernández MC, Barberena-Jonas C, Auckland K, Allen A, Allen S, Phipps ME, Huerta-Sanchez E, Ioannidis AG, Mentzer AJ, Moreno-Estrada A. Genetic Signatures of Positive Selection in Human Populations Adapted to High Altitude in Papua New Guinea. Genome Biol Evol 2024; 16:evae161. [PMID: 39173139 PMCID: PMC11339866 DOI: 10.1093/gbe/evae161] [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] [Accepted: 07/09/2024] [Indexed: 08/24/2024] Open
Abstract
Papua New Guinea (PNG) hosts distinct environments mainly represented by the ecoregions of the Highlands and Lowlands that display increased altitude and a predominance of pathogens, respectively. Since its initial peopling approximately 50,000 years ago, inhabitants of these ecoregions might have differentially adapted to the environmental pressures exerted by each of them. However, the genetic basis of adaptation in populations from these areas remains understudied. Here, we investigated signals of positive selection in 62 highlanders and 43 lowlanders across 14 locations in the main island of PNG using whole-genome genotype data from the Oceanian Genome Variation Project (OGVP) and searched for signals of positive selection through population differentiation and haplotype-based selection scans. Additionally, we performed archaic ancestry estimation to detect selection signals in highlanders within introgressed regions of the genome. Among highland populations we identified candidate genes representing known biomarkers for mountain sickness (SAA4, SAA1, PRDX1, LDHA) as well as candidate genes of the Notch signaling pathway (PSEN1, NUMB, RBPJ, MAML3), a novel proposed pathway for high altitude adaptation in multiple organisms. We also identified candidate genes involved in oxidative stress, inflammation, and angiogenesis, processes inducible by hypoxia, as well as in components of the eye lens and the immune response. In contrast, candidate genes in the lowlands are mainly related to the immune response (HLA-DQB1, HLA-DQA2, TAAR6, TAAR9, TAAR8, RNASE4, RNASE6, ANG). Moreover, we find two candidate regions to be also enriched with archaic introgressed segments, suggesting that archaic admixture has played a role in the local adaptation of PNG populations.
Collapse
Affiliation(s)
- Ram González-Buenfil
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Sofía Vieyra-Sánchez
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Consuelo D Quinto-Cortés
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | | | - William Pomat
- Vector-Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Moses Laman
- Vector-Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Mayté C Cervantes-Hernández
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Carmina Barberena-Jonas
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | | | - Angela Allen
- Department of Molecular Haematology, MRC Weatherall Institute of Molecular Medicine, Headley Way, Headington, Oxford, OX3 9DS, UK
| | - Stephen Allen
- Department of Clinical Sciences,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Emilia Huerta-Sanchez
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Alexander G Ioannidis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomedical Data Science, Stanford Medical School, Stanford, CA, USA
| | | | - Andrés Moreno-Estrada
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| |
Collapse
|
2
|
Wadood AA, Zhang X. The Omics Revolution in Understanding Chicken Reproduction: A Comprehensive Review. Curr Issues Mol Biol 2024; 46:6248-6266. [PMID: 38921044 PMCID: PMC11202932 DOI: 10.3390/cimb46060373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Omics approaches have significantly contributed to our understanding of several aspects of chicken reproduction. This review paper gives an overview of the use of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics to elucidate the mechanisms of chicken reproduction. Genomics has transformed the study of chicken reproduction by allowing the examination of the full genetic makeup of chickens, resulting in the discovery of genes associated with reproductive features and disorders. Transcriptomics has provided insights into the gene expression patterns and regulatory mechanisms involved in reproductive processes, allowing for a better knowledge of developmental stages and hormone regulation. Furthermore, proteomics has made it easier to identify and quantify the proteins involved in reproductive physiology to better understand the molecular mechanisms driving fertility, embryonic development, and egg quality. Metabolomics has emerged as a useful technique for understanding the metabolic pathways and biomarkers linked to reproductive performance, providing vital insights for enhancing breeding tactics and reproductive health. The integration of omics data has resulted in the identification of critical molecular pathways and biomarkers linked with chicken reproductive features, providing the opportunity for targeted genetic selection and improved reproductive management approaches. Furthermore, omics technologies have helped to create biomarkers for fertility and embryonic viability, providing the poultry sector with tools for effective breeding and reproductive health management. Finally, omics technologies have greatly improved our understanding of chicken reproduction by revealing the molecular complexities that underpin reproductive processes.
Collapse
Affiliation(s)
- Armughan Ahmed Wadood
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China;
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China;
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
3
|
Xue M, Yu R, Yang L, Xie F, Fang M, Tang Q. Metabolomics and transcriptomics of embryonic livers reveal hypoxia adaptation of Tibetan chickens. BMC Genomics 2024; 25:131. [PMID: 38302894 PMCID: PMC10832288 DOI: 10.1186/s12864-024-10030-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Exploring the hypoxia adaptation mechanism of Tibetan chicken is of great significance for revealing the survival law of Tibetan chicken and plateau animal husbandry production. To investigate the hypoxia adaptation of Tibetan chickens (TBCs), an integrative metabolomic-transcriptomic analysis of the liver on day 18 of embryonic development was performed. Dwarf laying chickens (DLCs), a lowland breed, were used as a control. RESULTS A total of 1,908 metabolites were identified in both TBCs and DLCs. Energy metabolism and amino acid metabolism related differentially regulated metabolites (DRMs) were significantly enriched under hypoxia. Important metabolic pathways including the TCA cycle and arginine and proline metabolism were screened; PCK1, SUCLA2, and CPS1 were found to be altered under hypoxic conditions. In addition, integrated analysis suggested potential differences in mitochondrial function, which may play a crucial role in the study of chicken oxygen adaptation. CONCLUSIONS These results suggest that hypoxia changed the gene expression and metabolic patterns of embryonic liver of TBCs compared to DLCs. Our study provides a basis for uncovering the molecular regulation mechanisms of hypoxia adaptation in TBCs with the potential application of hypoxia adaptation research for other animals living on the Qinghai-Tibet plateau, and may even contribute to the study of diseases caused by hypoxia.
Collapse
Affiliation(s)
- Mingming Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Runjie Yu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Lixian Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Fuyin Xie
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Qiguo Tang
- Development Center of Science and Technology, MARA, 100176, Beijing, China.
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China.
| |
Collapse
|
4
|
Cao Y, Zeng T, Han W, Ma X, Gu T, Chen L, Tian Y, Xu W, Yin J, Li G, Lu L, Gun S. Comparative analysis of liver transcriptome reveals adaptive responses to hypoxia environmental condition in Tibetan chicken. Anim Biosci 2024; 37:28-38. [PMID: 37641844 PMCID: PMC10766467 DOI: 10.5713/ab.23.0126] [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: 04/05/2023] [Revised: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown. METHODS RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]). RESULTS A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds. CONCLUSION This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals.
Collapse
Affiliation(s)
- Yongqing Cao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wei Han
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Xueying Ma
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy Agricultural and Animal Husbandry Sciences, Lhasa 850004,
China
| | - Tiantian Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Jianmei Yin
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Guohui Li
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Lizhi Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
| |
Collapse
|
5
|
Li S, Zhang X, Dong X, Guo R, Nan J, Yuan J, Schlebusch CM, Sheng Z. Genetic structure and characteristics of Tibetan chickens. Poult Sci 2023; 102:102767. [PMID: 37321029 PMCID: PMC10404676 DOI: 10.1016/j.psj.2023.102767] [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: 12/06/2022] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.
Collapse
Affiliation(s)
- Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaojian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Dong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiyang Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiuhong Nan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
6
|
Nan J, Yang S, Zhang X, Leng T, Zhuoma J, Zhuoma R, Yuan J, Pi J, Sheng Z, Li S. Identification of candidate genes related to highland adaptation from multiple Chinese local chicken breeds by whole genome sequencing analysis. Anim Genet 2023; 54:55-67. [PMID: 36305422 DOI: 10.1111/age.13268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 01/07/2023]
Abstract
Understanding the genetic mechanism of highland adaptation is of great importance for breeding improvement of Tibetan chickens (TBC). Some studies of TBC have identified some candidate genes and pathways from multiple subgroups, but the related genetic mechanisms remain largely unknown. Different genetic backgrounds and the independent genetic basis of highland adaptation make it difficult to identity the selective region of highland adaptation with all TBC samples. In this study, we conducted pre-analysis in a large-scale population to select a TBC subgroup with the purest and highest level of highland-specific lineage for the further analysis. Finally, the 37 samples from a TBC subgroup and 19 Lahsa White chickens were used to represent the highland group for further analysis with 80 samples from five Chinese local lowland breeds as controls. Population structure analysis revealed that highland adaptation significantly affected population stratification in Chinese local chicken breeds. Genome-wide selection signal analysis identified 201 candidate genes associated with highland adaptation of TBC, and these genes were significantly enriched in calcium signaling, vascular smooth muscle contraction and the cellular response to oxidative stress pathways. Additionally, we identified a narrow 1.76 kb region containing an overlapping region between HBZ and an active enhancer, and our identified region showed a highly significant signal. The highland group selected the haplotype with high activity to improve the oxygen-carrying capacity, thus being adapted to a hypoxic environment. We also found that STX2 was significantly selected in the highland group, thus potentially reducing the oxidative stress caused by hypoxia, and that STX2 exhibited the opposite effects on highland adaptation and reproductive traits. Our findings advance our understanding of extreme environment adaptation of highland chickens, and provide some variants and genes beneficial to TBC genetic breeding improvement.
Collapse
Affiliation(s)
- Jiuhong Nan
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sendong Yang
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Zhang
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tianze Leng
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Joan Zhuoma
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Neighborhood Committee Office, Xigaze City, China
| | - Rensang Zhuoma
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Luomai Township People's Government of Seni District, Naqu City, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Zheya Sheng
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shijun Li
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
7
|
Chen X, Zhang Y, Zhang W, Nie R, Bao H, Zhang B, Zhang H. Regulatory effects of circular RNA on hypoxia adaptation in chicken embryos. J Anim Sci 2023; 101:skad344. [PMID: 37788641 PMCID: PMC10629444 DOI: 10.1093/jas/skad344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/03/2023] [Indexed: 10/05/2023] Open
Abstract
The Tibetan chicken, a native breed of the Tibetan plateau, is adapted to the high-altitude and hypoxic environment of the plateau. As endogenous molecules, circular RNAs (circRNAs) have been shown to play an important role in the adaptation to hypoxic environments and regulation of angiogenesis. In this study, highland Tibetan and lowland Chahua chicken eggs were incubated in a hypoxic environment and the chorionic allantoic membrane was collected for Ribo-Zero RNA sequencing. A total of 1,414 circRNAs, mostly derived from exons, were identified. Of these, 93 differentially expressed circRNAs were detected between Tibetan and Chahua chickens. Combined with the differentially expressed miRNAs and mRNAs identified in our previous study, we identified four circRNAs (circBRD1, circPRDM2, circPTPRS, and circDENND4C). These circRNAs may act as competing endogenous RNA (ceRNA) to upregulate APOA1 expression by absorbing novel_miR_589, thereby regulating angiogenesis and affecting hypoxia adaptation in chicken embryos. The regulatory circRNAs/novel_miR_589/APOA1 axis provides valuable evidence for a better understanding of the specific functions and molecular mechanisms of circRNAs in plateau hypoxia adaptation in Tibetan chickens.
Collapse
Affiliation(s)
- Xuejiao Chen
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ying Zhang
- General Department of Agricultural Museum, China Agricultural Museum, Beijing 100026, China
| | - Wenhui Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ruixue Nie
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haigang Bao
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bo Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hao Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
8
|
Wei W, Zha C, Jiang A, Chao Z, Hou L, Liu H, Huang R, Wu W. A Combined Differential Proteome and Transcriptome Profiling of Fast- and Slow-Twitch Skeletal Muscle in Pigs. Foods 2022; 11:foods11182842. [PMID: 36140968 PMCID: PMC9497725 DOI: 10.3390/foods11182842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Skeletal muscle fiber types can contribute in part to affecting pork quality parameters. Biceps femoris (Bf) (fast muscle or white muscle) and Soleus (Sol) (slow muscle or red muscle) are two typical skeletal muscles characterized by obvious muscle fiber type differences in pigs. However, the critical proteins and potential regulatory mechanisms regulating porcine skeletal muscle fibers have yet to be clearly defined. In this study, the isobaric Tag for Relative and Absolute Quantification (iTRAQ)-based proteome was used to identify the key proteins affecting the skeletal muscle fiber types with Bf and Sol, by integrating the previous transcriptome data, while function enrichment analysis and a protein–protein interaction (PPI) network were utilized to explore the potential regulatory mechanisms of skeletal muscle fibers. A total of 126 differentially abundant proteins (DAPs) between the Bf and Sol were identified, and 12 genes were found to be overlapping between differentially expressed genes (DEGs) and DAPs, which are the critical proteins regulating the formation of skeletal muscle fibers. Functional enrichment and PPI analysis showed that the DAPs were mainly involved in the skeletal-muscle-associated structural proteins, mitochondria and energy metabolism, tricarboxylic acid cycle, fatty acid metabolism, and kinase activity, suggesting that PPI networks including DAPs are the main regulatory network affecting muscle fiber formation. Overall, these data provide valuable information for understanding the molecular mechanism underlying the formation and conversion of muscle fiber types, and provide potential markers for the evaluation of meat quality.
Collapse
Affiliation(s)
- Wei Wei
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengwan Zha
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiwen Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Liming Hou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruihua Huang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: ; Tel.: +86-25-84399762
| |
Collapse
|
9
|
Chen B, Li D, Ran B, Zhang P, Wang T. Key miRNAs and Genes in the High-Altitude Adaptation of Tibetan Chickens. Front Vet Sci 2022; 9:911685. [PMID: 35909692 PMCID: PMC9330022 DOI: 10.3389/fvets.2022.911685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Tibetan chickens living at high altitudes show specific physiological adaptations to the extreme environmental conditions. However, the regulated base of how chickens adapt to high-altitude habitats remains largely unknown. In this study, we sequenced 96 transcriptomes (including 48 miRNA and 48 mRNA transcriptomes of heart, liver, lung, and brain) and resequenced 12 whole genomes of Tibetan chickens and Peng'xian yellow chickens. We found that several miRNAs show the locally optimal plastic changes that occurred in miRNAs of chickens, such as miR-10c-5p, miR-144-3p, miR-3536, and miR-499-5p. These miRNAs could have effects on early adaption to the high-altitude environment of chickens. In addition, the genes under selection between Tibetan chickens and Peng'xian yellow chickens were mainly related to oxygen transport and oxidative stress. The I-kappa B kinase/NF-kappa B signaling pathway is widely found for high-altitude adaptation in Tibetan chickens. The candidate differentially expressed miRNAs and selected genes identified in this study may be useful in current breeding efforts to develop improved breeds for the highlands.
Collapse
Affiliation(s)
- Binlong Chen
- College of Animal Science, Xichang University, Xichang, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, China
- *Correspondence: Diyan Li
| | - Bo Ran
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Pu Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, China
- Tao Wang
| |
Collapse
|
10
|
Zhao P, Zhao F, Hu J, Wang J, Liu X, Zhao Z, Xi Q, Sun H, Li S, Luo Y. Physiology and Transcriptomics Analysis Reveal the Contribution of Lungs on High-Altitude Hypoxia Adaptation in Tibetan Sheep. Front Physiol 2022; 13:885444. [PMID: 35634140 PMCID: PMC9133604 DOI: 10.3389/fphys.2022.885444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/12/2022] [Indexed: 01/10/2023] Open
Abstract
The Tibetan sheep is an indigenous species on the Tibetan plateau with excellent adaptability to high-altitude hypoxia and is distributed at altitudes of 2500–5000 m. The high-altitude hypoxia adaptation of Tibetan sheep requires adaptive reshaping of multiple tissues and organs, especially the lungs. To reveal the mechanisms of adaptation at the tissue and molecular levels in the lungs of Tibetan sheep under hypoxic conditions at different altitudes, we performed light and electron microscopic observations, transcriptomic sequencing, and enzyme-linked immunosorbent assay studies on the lungs of Tibetan sheep from three altitudes (2500, 3500, and 4500 m). The results showed that in addition to continuous increase in pulmonary artery volume, thickness, and elastic fiber content with altitude, Tibetan sheep increase the hemoglobin concentration at an altitude of 3500 m, while they decrease the Hb concentration and increase the surface area of gas exchange and capacity of the blood at an altitude of 4500 m. Other than that, some important differentially expressed genes related to angiogenesis (FNDC1, HPSE, and E2F8), vasomotion and fibrogenesis (GJA4, FAP, COL1A1, COL1A2, COL3A1, and COL14A1), and gas transport (HBB, HBA1, APOLD1, and CHL1) were also identified; these discoveries at the molecular level explain to some extent the physiological findings. In conclusion, the lungs of Tibetan sheep adopt different strategies when adapting to different altitudes, and these findings are valuable for understanding the basis of survival of indigenous species on the Tibetan plateau.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Shaobin Li
- *Correspondence: Shaobin Li, ; Yuzhu Luo,
| | - Yuzhu Luo
- *Correspondence: Shaobin Li, ; Yuzhu Luo,
| |
Collapse
|
11
|
Notch Signaling and Cross-Talk in Hypoxia: A Candidate Pathway for High-Altitude Adaptation. Life (Basel) 2022; 12:life12030437. [PMID: 35330188 PMCID: PMC8954738 DOI: 10.3390/life12030437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 12/17/2022] Open
Abstract
Hypoxia triggers complex inter- and intracellular signals that regulate tissue oxygen (O2) homeostasis, adjusting convective O2 delivery and utilization (i.e., metabolism). Human populations have been exposed to high-altitude hypoxia for thousands of years and, in doing so, have undergone natural selection of multiple gene regions supporting adaptive traits. Some of the strongest selection signals identified in highland populations emanate from hypoxia-inducible factor (HIF) pathway genes. The HIF pathway is a master regulator of the cellular hypoxic response, but it is not the only regulatory pathway under positive selection. For instance, regions linked to the highly conserved Notch signaling pathway are also top targets, and this pathway is likely to play essential roles that confer hypoxia tolerance. Here, we explored the importance of the Notch pathway in mediating the cellular hypoxic response. We assessed transcriptional regulation of the Notch pathway, including close cross-talk with HIF signaling, and its involvement in the mediation of angiogenesis, cellular metabolism, inflammation, and oxidative stress, relating these functions to generational hypoxia adaptation.
Collapse
|
12
|
Li G, Zhao H, Guo D, Liu Z, Wang H, Sun Q, Liu Q, Xu B, Guo X. Distinct molecular impact patterns of abamectin on Apis mellifera ligustica and Apis cerana cerana. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113242. [PMID: 35104778 DOI: 10.1016/j.ecoenv.2022.113242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The effects of insecticides on bee health are a topic of intensive research. Although abamectin is toxic to bees, the molecular impact of abamectin needs to be clarified. Here, we found that Apis cerana cerana exhibited a higher mortality rate when exposed to abamectin than Apis mellifera ligustica. In addition, A. cerana cerana had markedly higher numbers of differentially expressed genes (DEGs), differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) than A. mellifera ligustica during exposure to abamectin. These results indicate that abamectin exposure exerts stronger effects on A. cerana cerana than on A. mellifera ligustica. In addition, six DEGs, two DEPs and two DEMs overlapped between the two bee species under abamectin exposure; however, some genes or proteins from the zinc finger protein, superoxide dismutase and peroxiredoxin families and the energy metabolism pathway were only unregulated in A. cerana cerana, which indicates a significant difference in the impact of abamectin on the two bee species. Despite these differences, several of the same gene families, such as heat shock proteins, cytochrome P450, odorant-binding proteins and cuticle proteins, and pathways, including the carbohydrate metabolism, immune system, lipid metabolism, amino acid metabolism, sensory system, locomotion and development pathways, were influenced by abamectin exposure in both A. cerana cerana and A. mellifera ligustica. Together, our results indicate that abamectin causes adverse effects on bees and thus poses a risk to bee populations and that abamectin exposure affects A. cerana cerana more strongly than A. mellifera ligustica. These findings improve our understanding of the behavioural and physiological effects of abamectin on bees.
Collapse
Affiliation(s)
- Guilin Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China; College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China; College of Life Sciences, Qufu Normal University, Qufu 273165, PR China
| | - Hang Zhao
- College of Life Sciences, Qufu Normal University, Qufu 273165, PR China
| | - Dezheng Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Zhenguo Liu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Hongfang Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Qingxin Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China.
| |
Collapse
|
13
|
Zhang P, Li Q, Wu Y, Zhang Y, Zhang B, Zhang H. Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs. Sci Rep 2022; 12:2844. [PMID: 35181733 PMCID: PMC8857214 DOI: 10.1038/s41598-022-06868-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.
Collapse
Affiliation(s)
- Pan Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Qinggang Li
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yijing Wu
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
14
|
Beer MA, Kane RA, Micheletti SJ, Kozakiewicz CP, Storfer A. Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change. Evol Appl 2022; 15:220-236. [PMID: 35233244 PMCID: PMC8867708 DOI: 10.1111/eva.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/27/2021] [Accepted: 10/18/2021] [Indexed: 11/28/2022] Open
Abstract
Understanding spatial patterns of genetic differentiation and local adaptation is critical in a period of rapid environmental change. Climate change and anthropogenic development have led to population declines and shifting geographic distributions in numerous species. The streamside salamander, Ambystoma barbouri, is an endemic amphibian with a small geographic range that predominantly inhabits small, ephemeral streams. As A. barbouri is listed as near-threatened by the IUCN, we describe range-wide patterns of genetic differentiation and adaptation to assess the species' potential to respond to environmental change. We use outlier scans and genetic-environment association analyses to identify genomic variation putatively underlying local adaptation across the species' geographic range. We find evidence for adaptation with a polygenic architecture and a set of candidate SNPs that identify genes putatively contributing to local adaptation. Our results build on earlier work that suggests that some A. barbouri populations are locally adapted despite evidence for asymmetric gene flow between the range core and periphery. Taken together, the body of work describing the evolutionary genetics of range limits in A. barbouri suggests that the species may be unlikely to respond naturally to environmental challenges through a range shift or in situ adaptation. We suggest that management efforts such as assisted migration may be necessary in future.
Collapse
Affiliation(s)
- Marc A. Beer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Rachael A. Kane
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | | | | | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| |
Collapse
|
15
|
Meng Y, Chen D, Qiu N, Mine Y, Keast R, Meng S, Zhu C. Comparative N-glycoproteomic analysis of Tibetan and lowland chicken fertilized eggs: Implications on proteins biofunction and species evolution. J Food Biochem 2021; 46:e14006. [PMID: 34859904 DOI: 10.1111/jfbc.14006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
The characterization and functionality of protein glycosylation among different related species are of common interest. Herein, non-standard quantification and N-glycosylation enrichment technology combined with ultra-high liquid chromatography-tandem mass spectrometry were used to establish detailed N-glycoproteomics of fertilized eggs, and quantitatively compared between Tibetan and lowland chicken. A total of 396N-glycosites from 143 glycoproteins were found. Specifically, compared with lowland chicken egg white, 32N-glycosites of 22 glycoproteins were up-regulated and 57N-glycosites of 25 glycoproteins were down-regulated in Tibetan chicken egg white. Also, 137N-glycosites in 72 glycoproteins showed much higher-degree glycosylation and 36N-glycosites in 15 glycoproteins displayed lower-degree glycosylation in Tibetan chicken egg yolk than those in lowland chicken egg yolk. Through bioinformatic analysis, these varied glycoproteins were highly associated with antifreeze activity, hypoxia adaptation, coagulation cascade, and binding/immunity activities, which may be related to plateau hypoxia and cold stress. PRACTICAL APPLICATIONS: These findings provide a new insight on the role of biological egg N-glycoproteins related to environmental adaptation and evolution, which may be further applied in improving egg processing and human health, by developing biomolecules for food and medical industry.
Collapse
Affiliation(s)
- Yaqi Meng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Diao Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Ning Qiu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yoshinori Mine
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Russell Keast
- CASS Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria, Australia
| | - Sichong Meng
- Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Chunxia Zhu
- Center of Stomatology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| |
Collapse
|
16
|
High-throughput sequencing revealed the expression profile and potential key molecules of the circular RNAs involved in the process of hypoxic adaptation in Tibetan chickens. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00848-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
17
|
Padmasekar M, Savai R, Seeger W, Pullamsetti SS. Exposomes to Exosomes: Exosomes as Tools to Study Epigenetic Adaptive Mechanisms in High-Altitude Humans. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8280. [PMID: 34444030 PMCID: PMC8392481 DOI: 10.3390/ijerph18168280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 12/29/2022]
Abstract
Humans on earth inhabit a wide range of environmental conditions and some environments are more challenging for human survival than others. However, many living beings, including humans, have developed adaptive mechanisms to live in such inhospitable, harsh environments. Among different difficult environments, high-altitude living is especially demanding because of diminished partial pressure of oxygen and resulting chronic hypobaric hypoxia. This results in poor blood oxygenation and reduces aerobic oxidative respiration in the mitochondria, leading to increased reactive oxygen species generation and activation of hypoxia-inducible gene expression. Genetic mechanisms in the adaptation to high altitude is well-studied, but there are only limited studies regarding the role of epigenetic mechanisms. The purpose of this review is to understand the epigenetic mechanisms behind high-altitude adaptive and maladaptive phenotypes. Hypobaric hypoxia is a form of cellular hypoxia, which is similar to the one suffered by critically-ill hypoxemia patients. Thus, understanding the adaptive epigenetic signals operating in in high-altitude adjusted indigenous populations may help in therapeutically modulating signaling pathways in hypoxemia patients by copying the most successful epigenotype. In addition, we have summarized the current information about exosomes in hypoxia research and prospects to use them as diagnostic tools to study the epigenome of high-altitude adapted healthy or maladapted individuals.
Collapse
Affiliation(s)
- Manju Padmasekar
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
| | - Rajkumar Savai
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
- Department of Internal Medicine, Justus-Liebig University Giessen, Member of the DZL, Member of CPI, 35392 Giessen, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, 60438 Frankfurt am Main, Germany
| | - Werner Seeger
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
- Department of Internal Medicine, Justus-Liebig University Giessen, Member of the DZL, Member of CPI, 35392 Giessen, Germany
| | - Soni Savai Pullamsetti
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
- Department of Internal Medicine, Justus-Liebig University Giessen, Member of the DZL, Member of CPI, 35392 Giessen, Germany
| |
Collapse
|
18
|
Zhang Y, Su W, Zhang B, Ling Y, Kim WK, Zhang H. Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens. J Anim Sci Biotechnol 2021; 12:60. [PMID: 33934713 PMCID: PMC8091548 DOI: 10.1186/s40104-021-00582-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play roles in the hypoxic adaptation of high-altitude animals, although their exact involvement remains unclear. RESULTS This study aimed to elucidate the global landscape of mRNAs, lncRNAs, and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs (ceRNAs) and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos. In total, 354 differentially expressed genes (DE genes), 389 differentially expressed lncRNAs (DE lncRNAs), and 73 differentially expressed miRNAs (DE miRNAs) were identified between Tibetan chickens (TC) and control Chahua chickens (CH). GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis (including blood vessel development and blood circulation) and energy metabolism (including glucose, carbohydrate, and lipid metabolism). The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions, which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens. CONCLUSIONS Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism. These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.
Collapse
Affiliation(s)
- Ying Zhang
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Woyu Su
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Yao Ling
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, 303 Poultry Science Building, Athens, GA, 30602, USA.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China.
| |
Collapse
|