1
|
Yan F, Wang Y, Wei M, Zhang J, Ye Y, Duan M, Chamba Y, Shang P. Exploring the role of the CapG gene in hypoxia adaptation in Tibetan pigs. Front Genet 2024; 15:1339683. [PMID: 38680426 PMCID: PMC11045884 DOI: 10.3389/fgene.2024.1339683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction: The CapG gene, which is an actin-binding protein, is prevalent in eukaryotic cells and is abundantly present in various pathways associated with plateau hypoxia adaptation. Tibetan pigs, which have inhabited high altitudes for extended periods, provide an excellent research population for investigating plateau hypoxia adaptation. Results: This study focused on Tibetan pigs and Yorkshire pigs residing in Nyingchi, Tibet. The blood physiological data of Tibetan pigs were found to be significantly higher than those of Yorkshire pigs, including RBC, HGB, HCT, MCH, and MCHC. The SNP analysis of the CapG gene identified six sites with mutations only present in Tibetan pigs. Notably, the transcription factors at sites C-489T, C-274T, and A-212G were found to be altered, and these sites are known to be associated with hypoxia adaptation and blood oxygen transportation. The mRNA expression of the CapG gene exhibited highly significant differences in several tissues, with the target proteins predominantly higher in the Yorkshire pig compared to the Tibetan pig. Specifically, a notable difference was observed in the lung tissues. Immunohistochemistry analysis revealed high expression levels of CapG proteins in the lung tissues of both Tibetan and Yorkshire pigs, primarily localized in the cytoplasm and cell membrane. Conclusion: The CapG gene plays a significant role in regulating hypoxia adaptation in Tibetan pigs. This study provides a theoretical basis for the conservation and utilization of Tibetan pig resources, the breeding of highland breeds, epidemic prevention and control, and holds great importance for the development of the highland livestock economy.
Collapse
Affiliation(s)
- Feifei Yan
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Yu Wang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Mingbang Wei
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Jian Zhang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Yourong Ye
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| |
Collapse
|
2
|
Chen B, Liu X, Wu S, Hou J, Shang P, Chamba Y, Mehmood K, Fouad D, Li Y, Zhang H. Inhalation of ammonia promotes apoptosis and induces autophagy in hepatocytes via Bax/BCl-2 and m-TOR/ATG5/LC-3bII axes. Sci Total Environ 2024; 912:169036. [PMID: 38061639 DOI: 10.1016/j.scitotenv.2023.169036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/20/2023] [Accepted: 11/30/2023] [Indexed: 01/18/2024]
Abstract
Ammonia (NH3) is an irritating gas and atmospheric pollutant that endangers the health of humans and animals by stimulating respiratory tract's mucosa and causing liver damage. However, physiological role of ammonia gas in hepatotoxicity remains unclear. To investigate the hepatotoxic effects of inhaled ammonia gas, experiments were conducted using mouse model exposed to 100 ppm of ammonia gas for 21 days. The exposed mice exhibited signs of depression, emaciation, and reduced growth. This study revealed that inhalation of ammonia led to significant decrease in water (P < 0.0001) and food intake (P < 0.05), resulting in slower growth. Histopathological analysis showed that ammonia stress alters the microstructure of the liver by enlarging the gap between hepatic lobule and fibrosis. Moreover, ammonia-induced stress significantly reduces the expression of the anti-apoptotic protein BCl-2 (P < 0.001), while elevates the mRNA expression of the pro-apoptotic gene Bax (P < 0.001). Furthermore, ammonia inhalation significantly increases the protein expression of LC-3bII (P < 0.05) and the mRNA expression of autophagy-related gene 5 (ATG5) (P < 0.05) and p62 (P < 0.05) while remarkably decreases the mRNA expression of mammalian target of rapamycin (m-TOR) (P < 0.05). In conclusion, this study demonstrates that inhalation of ammonia gas causes liver damage and suggests autophagy happening via m-TOR/p62/LC-3bII and pro-apoptosis effect mediated by Bax/BCl-2 in the liver damage caused by ammonia inhalation. Our study provides a new perspective on ammonia-induced hepatotoxicity.
Collapse
Affiliation(s)
- Bohan Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoqing Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Shouyan Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Junhong Hou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi 860000, China
| | - Yangzom Chamba
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi 860000, China
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Dalia Fouad
- Department of Zoology, College of Science, King Saud University, PO Box 22452, Riyadh 11495, Saudi Arabia
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
3
|
Chang X, Xiao Y, Cheng L, Gu X, Yang L, Chamba Y, Zhang J, Geng F. Quantitative Proteomic Analysis of Yorkshire Pig Liver Reveals Its Response to High Altitude. J Agric Food Chem 2023; 71:7618-7629. [PMID: 37140090 DOI: 10.1021/acs.jafc.3c01724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In this study, the protein profiles in the livers of Shannan Yorkshire pigs (SNY), Linzhi Yorkshire pigs (LZY), and Jiuzhaigou Yorkshire pigs (JZY) were comparatively analyzed using quantitative proteomics. A total of 6804 proteins were identified, of which 6471 were quantified and 774 differentially expressed proteins (DEPs) were screened. The higher level of energy metabolism in LZY livers was in response to the critical altitude environment compared to that in JZY, while the high-altitude environment suppressed energy output in SNY livers. Several key antioxidant enzymes were locally regulated in Yorkshire pig liver to balance antioxidant levels in a high-altitude, low-oxygen environment. In addition, ribosomal proteins were differentially expressed in Yorkshire pig livers in response to different altitudinal environments. These findings provide clues to the adaptation of the Yorkshire pig liver to the three altitudinal environments and the molecular links that exist between them.
Collapse
Affiliation(s)
- Xinping Chang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Yu Xiao
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Lei Cheng
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Xuedong Gu
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Lin Yang
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Yangzom Chamba
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| |
Collapse
|
4
|
Shang P, Dong S, Han Y, Bo S, Ye Y, Duan M, Chamba Y. Environmental exposure to swine farms reshapes human gut microbiota. Chemosphere 2022; 307:135558. [PMID: 35780983 DOI: 10.1016/j.chemosphere.2022.135558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The gut microbiota can change to varying degrees because of changes in the environment. In the present study, we performed microbial amplicon sequencing on the feces of people who had long-term exposure to swine farms (F) and that of people living in normal environments (S) to investigate the impact of the environment on the human gut microbiota. A total of 1,283,503 high-quality ordered sequences were obtained, which provided different levels of microbial classification and statistics. We found that different environments did not alter the richness and diversity of the microbial communities in participants, but caused significant changes in the proportion of some bacteria. The main bacterial phyla found in group F participants were Firmicutes (69.44-89.03%), Actinobacteria (1.7-18.95%), and Bacteroidetes (1.17-22.35%); those found in group S participants were Firmicutes (49.93-95.04%), Bacteroidetes (0.62-39.59%), and Proteobacteria (0.98-11.95%). Additionally, because of changes in phylum proportions, the Bugbase phenotypic classification predicted an increase in the proportion of Gram-positive bacteria in group F and an increase in the proportion of Gram-negative bacteria in group S. In conclusion, our findings suggest that human exposure to swine farms can reshape the gut microbiota, resulting in changes in the microbial abundances. This change can potentially reduce the odds of developing bowel disease and contribute to the prevention of intestinal diseases, providing a theoretical basis for improving human health.
Collapse
Affiliation(s)
- Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Shixiong Dong
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yuqing Han
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Suxue Bo
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yourong Ye
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China.
| |
Collapse
|
5
|
Yan F, Xu S, Chang Z, Nazar M, Chamba Y, Shang P. Seroprevalence and Risk Factors Investigations of Parvovirus Disease in Tibetan Pigs: First Report from Tibet. Vet Sci 2022; 9:576. [PMID: 36288189 PMCID: PMC9610086 DOI: 10.3390/vetsci9100576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023] Open
Abstract
Porcine parvovirus (PPV) disease is a worldwide spread animal disease with high infection rate and serious impact on meat economy causing significant losses in livestock production. The purpose of this paper is to investigate and analyze the regional seroprevalence of PPV in Tibetan pigs in Tibet and evaluate risk factors related to the disease. A total of 356 serum samples of Tibetan pigs were collected from four counties and districts in Tibet, and anti-PPV antibodies were detected by using a commercial competitive ELISA. Our results show a seroprevalence of 91.01% (324 serum samples were found to be positive for anti-PPV antibodies). The positive rate among different district was 100%, 96.55%, 93.68% and 72.83%, respectively in the Mainling County, in Bayi district, Nang County and Bomê County. We found significant differences between different age and gender groups; particularly female animals show a seroprevalence of 96.03% while the males only 83.46%. From the perspective of the growth stage, our results indicate that subadults show a seroprevalence significative higher than other age groups (100%). This study describes for the first time the PPV seroprevalence among Tibetan pigs characterizing risk factors involved in its transmission and providing information to be taken into account for eventual surveillance or eradication plans.
Collapse
Affiliation(s)
- Feifei Yan
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
| | - Shijun Xu
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Zhenyu Chang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Mudassar Nazar
- University of Agriculture Faisalabad, Burewala 61010, Pakistan
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| |
Collapse
|
6
|
Shang P, Zhang B, Li P, Ahmed Z, Hu X, Chamba Y, Zhang H. Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs. Animals (Basel) 2022; 12:ani12151919. [PMID: 35953907 PMCID: PMC9367445 DOI: 10.3390/ani12151919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/29/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Elevated environments such as plateaus are often classified as low oxygen environments. The hypoxic adaptation mechanisms utilized by organisms in these conditions are not well understood. To address this, the differentially expressed genes (DEGs) involved in hypoxia adaptation were assessed using two pig breeds (Tibetan pig [TP] and Yorkshire sow [YY]). Genes related to lung tissue responses to hypoxia were assessed using transcriptomic (using RNA-seq) and proteomic (using iTRAQ) analysis. A total of 1021 DEGs were screened out. In the iTRAQ omics data, a total of 22,100 peptides were obtained and 4518 proteins were found after filtering. A total of 271 differentially expressed proteins [DEPs] were screened using the conditions of p < 0.05; FC ≤ 0.833; and FC ≥ 1.2. A total of 14 DEGs at the mRNA and protein levels were identified and found to be associated with regulation of the inflammatory response; blood particles; and MAPK cascade response regulation. Among the DEGs, six were associated with hypoxia adaptation function (mitochondria and glycolysis) in pigs. The results of this study identify novel candidate genes involved in porcine hypoxia adaptation mechanisms.
Collapse
Affiliation(s)
- Peng Shang
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
- Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Bo Zhang
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
| | - Pan Li
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot 12350, Pakistan;
| | - Xiaoxiang Hu
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
| | - Yangzom Chamba
- Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
- Correspondence: (Y.C.); (H.Z.)
| | - Hao Zhang
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
- Correspondence: (Y.C.); (H.Z.)
| |
Collapse
|
7
|
Shang P, Wei M, Duan M, Yan F, Chamba Y. Healthy Gut Microbiome Composition Enhances Disease Resistance and Fat Deposition in Tibetan Pigs. Front Microbiol 2022; 13:965292. [PMID: 35928149 PMCID: PMC9343729 DOI: 10.3389/fmicb.2022.965292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 01/10/2023] Open
Abstract
The gut microbiota is involved in a range of physiological processes in animals, and modulating the microbiome composition is considered a novel target for identifying animal traits. Tibetan pigs show better fat deposition and disease resistance compared to Yorkshire pigs. However, studies investigating the correlation between favorable characteristics in Tibetan pigs and the gut microbial community remain scarce. In the current study, 1,249,822 high-quality sequences were obtained by amplicon sequencing of the colon contents of Tibetan and Yorkshire pigs. We found that at the boundary level, the abundance and relative abundance of colon bacterial community in Tibetan pigs were higher than that in Yorkshire pigs (P > 0.05). Phylum level, Firmicutes were the dominant colonic microflora of Tibetan and Yorkshire pigs, and the ratio of Firmicutes to Bacteroides in Tibetan pigs was slightly higher than in Yorkshire pigs. Actinobacteria and Spirobacteria were significantly higher in Tibetan pigs than in Yorkshire pigs (P < 0.05). At the genus level, the relative abundance of Bifidobacterium, Lactobacillus, and Bacteriologist, which are related to disease resistance, was significantly higher than that in Yorkshire pigs in Yorkshire pigs. In conclusion, the composition and abundance of colonic intestinal microflora in Tibetan pigs were closely related to their superior traits. Bifidobacteria, Ruminococcaceae, and Family-XIII-AD3011-Group are conducive to improving disease resistance in Tibetan pigs. Lactobacillus and Solobacterium were observed to be the main bacterial communities involved in fat deposition in Tibetan pigs. This study will provide a new reference for the development and utilization of Tibetan pigs in future.
Collapse
Affiliation(s)
- Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Mingbang Wei
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Feifei Yan
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
- *Correspondence: Yangzom Chamba,
| |
Collapse
|
8
|
Gong X, Zheng M, Zhang J, Ye Y, Duan M, Chamba Y, Wang Z, Shang P. Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs. Front Vet Sci 2022; 9:919904. [PMID: 35754534 PMCID: PMC9218471 DOI: 10.3389/fvets.2022.919904] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Fat deposition traits are one of the key factors in pig production and breeding. The fat deposition capacity of pigs mainly affects the quality of pork and pig productivity. The aim of this study was to analyze the differential expression of mRNA levels in dorsal adipose tissue of Tibetan and York pigs at different growth stages using transcriptomic data to estimate key genes that regulate fat deposition in pigs. The results showed that a total of 32,747 positively expressed genes were present in the dorsal adipose tissue of the two breeds. Differentially expressed gene (DEG) screening of multiple combinations between the two breeds yielded 324 DEGS. Gene ontology (GO) biofunctional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGS were mainly involved in lipid metabolic pathways, steroid biosynthetic pathways and lipid biosynthetic processes, sterol biosynthetic processes, brown adipocyte differentiation, and other pathways related to lipid deposition and metabolism. The results showed that ACACA, SLC2A4 and THRSP genes positively regulated the lipid deposition ability and CHPT1 gene negatively regulated the lipid deposition ability in pigs. The results of this experiment suggest a theoretical basis for further studies on the regulatory mechanisms of fat deposition in pigs.
Collapse
Affiliation(s)
- Xinglong Gong
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Min Zheng
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Jian Zhang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Yourong Ye
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Mengqi Duan
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Zhongbin Wang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Peng Shang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| |
Collapse
|
9
|
Fu Y, Hao X, Shang P, Chamba Y, Zhang B, Zhang H. Functional Identification of Porcine DLK1 during Muscle Development. Animals (Basel) 2022; 12:ani12121523. [PMID: 35739860 PMCID: PMC9219491 DOI: 10.3390/ani12121523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Skeletal muscle is the largest tissue and serves as a protein reservoir and energy reservoir in the human and animal body. It also serves as the main metabolic activity site. The formation of skeletal muscle mainly depends on the differentiation and fusion of myocytes and other complex ordered processes; each step is regulated by various factors. In this study, we investigated the expression profiles, functional identification, and regulatory pathways of Delta-like 1 homolog (DLK1) in pigs and myocytes. We found that DLK1 was highly expressed in the muscle tissues of pigs. DLK1 promoted myocyte proliferation, migration, differentiation, fusion, and muscular hypertrophy, but suppressed muscle degradation. DLK1 also inhibited the Notch signaling pathway by regulating the expression of key factors in the pathway, thereby producing a phenotype in which DLK1 promotes muscle development. These findings provide valuable information to improve our understanding of the functional mechanisms of DLK1 that underly myogenesis to accelerate the process of animal genetic improvement. Abstract DLK1 is paternally expressed and is involved in metabolism switching, stem cell maintenance, cell proliferation, and differentiation. Porcine DLK1 was identified in our previous study as a candidate gene that regulates muscle development. In the present study, we characterized DLK1 expression in pigs, and the results showed that DLK1 was highly expressed in the muscles of pigs. In-vitro cellular tests showed that DLK1 promoted myoblast proliferation, migration, and muscular hypertrophy, and at the same time inhibited muscle degradation. The expression of myogenic and fusion markers and the formation of multinucleated myotubes were both upregulated in myoblasts with DLK1 overexpression. DLK1 levels in cultured myocytes were negatively correlated with the expression of key factors in the Notch pathway, suggesting that the suppression of Notch signaling pathways may mediate these processes. Collectively, our results suggest a biological function of DLK1 as an enhancer of muscle development by the inhibition of Notch pathways.
Collapse
Affiliation(s)
- Yu Fu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
| | - Xin Hao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Y.C.)
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Y.C.)
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
- Correspondence: (B.Z.); (H.Z.); Tel.: +86-010-62734852 (H.Z.)
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
- Correspondence: (B.Z.); (H.Z.); Tel.: +86-010-62734852 (H.Z.)
| |
Collapse
|
10
|
Wei M, Ye Y, Ali MM, Chamba Y, Tang J, Shang P. Effect of Fluoride on Cytotoxicity Involved in Mitochondrial Dysfunction: A Review of Mechanism. Front Vet Sci 2022; 9:850771. [PMID: 35518640 PMCID: PMC9062983 DOI: 10.3389/fvets.2022.850771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
Fluoride is commonly found in the soil and water environment and may act as chronic poison. A large amount of fluoride deposition causes serious harm to the ecological environment and human health. Mitochondrial dysfunction is a shared feature of fluorosis, and numerous studies reported this phenomenon in different model systems. More and more evidence shows that the functions of mitochondria play an extremely influential role in the organs and tissues after fluorosis. Fluoride invades into cells and mainly damages mitochondria, resulting in decreased activity of mitochondrial related enzymes, weakening of protein expression, damage of respiratory chain, excessive fission, disturbance of fusion, disorder of calcium regulation, resulting in the decrease of intracellular ATP and the accumulation of Reactive oxygen species. At the same time, the decrease of mitochondrial membrane potential leads to the release of Cyt c, causing a series of caspase cascade reactions and resulting in apoptosis. This article mainly reviews the mechanism of cytotoxicity related to mitochondrial dysfunction after fluorosis. A series of mitochondrial dysfunction caused by fluorosis, such as mitochondrial dynamics, mitochondrial Reactive oxygen species, mitochondrial fission, mitochondrial respiratory chain, mitochondrial autophagy apoptosis, mitochondrial fusion disturbance, mitochondrial calcium regulation are emphasized, and the mechanism of the effect of fluoride on cytotoxicity related to mitochondrial dysfunction are further explored.
Collapse
Affiliation(s)
- Mingbang Wei
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Yourong Ye
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Muhammad Muddassir Ali
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Jia Tang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, China
| |
Collapse
|
11
|
Zhao P, Zheng X, Yu Y, Hou Z, Diao C, Wang H, Kang H, Ning C, Li J, Feng W, Wang W, Liu GE, Li B, Smith J, Chamba Y, Liu JF. Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation. Genomics Proteomics Bioinformatics 2021; 19:772-786. [PMID: 33631433 PMCID: PMC9170766 DOI: 10.1016/j.gpb.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/05/2019] [Accepted: 11/29/2019] [Indexed: 11/29/2022]
Abstract
A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. In this study, we developed a tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues, further improving the genome annotation of the corresponding protein-coding genes. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellularlocations and potential functions for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.
Collapse
Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haifei Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huimin Kang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junhui Li
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
12
|
Zhao P, Du H, Jiang L, Zheng X, Feng W, Diao C, Zhou L, Liu GE, Zhang H, Chamba Y, Zhang Q, Li B, Liu JF. PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene. Genome Biol Evol 2021; 12:1751-1764. [PMID: 33151306 PMCID: PMC7643367 DOI: 10.1093/gbe/evaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/22/2022] Open
Abstract
Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single-nucleotide polymorphism information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5–0.2 Ma and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO, and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.
Collapse
Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Maryland
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yangzom Chamba
- College of Animal Science and Technology, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Qin Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, PR China
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
13
|
Shang P, Li W, Tan Z, Zhang J, Dong S, Wang K, Chamba Y. Population Genetic Analysis of Ten Geographically Isolated Tibetan Pig Populations. Animals (Basel) 2020; 10:ani10081297. [PMID: 32751240 PMCID: PMC7460208 DOI: 10.3390/ani10081297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed in this study. Population genetic analyses, including Principal Component Analysis (PCA), phylogenic tree, genetic differentiation, deleterious variant, contribution to meta-population genetic diversity and selective sweep were performed. Limited genetic differentiation was identified among these Tibetan pig populations. Most deleterious variants were low-frequency mutations and population specific. Contribution to the meta-population was largest in the TT population, based on gene and allelic diversity. Genes under selection were involved in hypoxia adaptation, hard palate development, facial appearance, and perception of smell. Abstract Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed. Population genetic analyses revealed limited genetic differentiation among the Tibetan pig populations. Evidence from deleterious variant analysis indicated that population-specific deleterious variants were the major component of all mutational loci. Contribution to the meta-population was largest in the TT (Qinghai-Tibet Plateau) population, based on gene diversity or allelic diversity. Selective sweep analysis revealed numerous genes, including RXFP1, FZD1, OR1F1, TBX19, MSTN, ESR1, MC1R, HIF3A, and EGLN2 which are involved in lung development, hard palate development, coat color, hormone metabolism, facial appearance, and perception of smell. These findings increase our understanding of the origins and domestication of the Tibetan pig, and help optimize the strategy for their conservation.
Collapse
Affiliation(s)
- Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Wenting Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450001, China;
| | - Zhankun Tan
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Jian Zhang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Shixiong Dong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450001, China;
- Correspondence: or (K.W.); (Y.C.)
| | - Yangzom Chamba
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
- Correspondence: or (K.W.); (Y.C.)
| |
Collapse
|
14
|
Zhang B, Ban D, Gou X, Zhang Y, Yang L, Chamba Y, Zhang H. Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia. J Anim Sci Biotechnol 2019; 10:25. [PMID: 30867905 PMCID: PMC6397503 DOI: 10.1186/s40104-019-0316-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude. However, the genetic and epigenetic mechanisms of hypoxic adaptation in animals remain unclear. Methods Whole-genome DNA methylation data were generated for heart tissues of Tibetan pigs grown in the highland (TH, n = 4) and lowland (TL, n = 4), as well as Yorkshire pigs grown in the highland (YH, n = 4) and lowland (YL, n = 4), using methylated DNA immunoprecipitation sequencing. Results We obtained 480 million reads and detected 280679, 287224, 259066, and 332078 methylation enrichment peaks in TH, YH, TL, and YL, respectively. Pairwise TH vs. YH, TL vs. YL, TH vs. TL, and YH vs. YL comparisons revealed 6829, 11997, 2828, and 1286 differentially methylated regions (DMRs), respectively. These DMRs contained 384, 619, 192, and 92 differentially methylated genes (DMGs), respectively. DMGs that were enriched in the hypoxia-inducible factor 1 signaling pathway and pathways involved in cancer and hypoxia-related processes were considered to be important candidate genes for high-altitude adaptation in Tibetan pigs. Conclusions This study elucidates the molecular and epigenetic mechanisms involved in hypoxic adaptation in pigs and may help further understand human hypoxia-related diseases.
Collapse
Affiliation(s)
- Bo Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Dongmei Ban
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiao Gou
- 2College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Yawen Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Lin Yang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yangzom Chamba
- 3College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 860000 Tibet China
| | - Hao Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
15
|
Shang P, Wang Z, Chamba Y, Zhang B, Zhang H, Wu C. A comparison of prenatal muscle transcriptome and proteome profiles between pigs with divergent growth phenotypes. J Cell Biochem 2018; 120:5277-5286. [PMID: 30302803 DOI: 10.1002/jcb.27802] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The growth of pigs is an important economic trait that involves multiple genes and coordinated regulatory mechanisms. The growth rate and potential of skeletal muscles are largely decided by embryonic myofiber development. Tibetan pig (TP) that is a mini-type breed has a divergent phenotype in growth rate and adult body weight with Wujin pig (WJ) and large White pig (LW). In the current study, the transcriptome (using RNA-seq) and proteome (using the isobaric tag for relative and absolute quantification [iTRAQ]) data from the prenatal muscle tissues were analyzed to identify the genes related to postnatal growth rate and growth potential in pigs. In the RNA-seq experiment, 19 626 genes were detected in the embryonic muscle tissues, and 3626 unique differentially expressed genes (DEGs) were identified in TP in comparison to that in LW and WJ. In the iTRAQ experiment, 2474 proteins were detected, and 735 unique differentially expressed proteins (DEPs) were identified in TP in comparison to that in LW and WJ. Combining the DEGs and DEPs, 209 genes were found to be differentially expressed, consistently at both the messenger RNA and protein levels, between TP and the other two breeds; these are mainly involved in 2-oxocarboxylic acid metabolism, citrate cycle, and biosynthesis of amino acids. Of these, 20 genes that were related to myoblast differentiation and muscle fiber formation might have important roles in determining the postnatal growth rate and potential body weight in pigs. Our results provide new candidate genes and insights into the molecular mechanisms involved muscle growth traits in pigs.
Collapse
Affiliation(s)
- Peng Shang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.,Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
| | - Zhixiu Wang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.,Department of Animal Genetics and Breeding, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yangzom Chamba
- Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
| | - Bo Zhang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hao Zhang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Changxin Wu
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| |
Collapse
|
16
|
Zhang H, Rehman MU, Li K, Luo H, Lan Y, Nabi F, Zhang L, Iqbal MK, Zhu S, Javed MT, Chamba Y, Li JK. Epidemiologic Survey of Japanese Encephalitis Virus Infection, Tibet, China, 2015. Emerg Infect Dis 2018; 23:1023-1024. [PMID: 28518046 PMCID: PMC5443422 DOI: 10.3201/eid2306.152115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We investigated Japanese encephalitis virus (JEV) prevalence in high-altitude regions of Tibet, China, by using standard assays to test mosquitoes, pigs, and humans. Results confirmed that JEV has spread to these areas. Disease prevention and control strategies should be used along with surveillance to limit spread of JEV in high-altitude regions of Tibet.
Collapse
|
17
|
Zhang B, Chamba Y, Shang P, Wang Z, Ma J, Wang L, Zhang H. Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in high-altitude adaptation in the Tibetan pig. Sci Rep 2017. [PMID: 28623314 PMCID: PMC5473931 DOI: 10.1038/s41598-017-03976-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tibetan pigs that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from lowland pigs, and have adapted well to extreme conditions. However, the mechanisms involved in regulating gene expression at high altitude in these animals are not fully understood. In this study, we obtained transcriptomic and proteomic data from the heart tissues of Tibetan and Yorkshire pigs raised in the highlands (TH and YH) and lowlands (TL and YL) via RNA-seq and iTRAQ (isobaric tags for relative and absolute quantitation) analyses, respectively. Comparative analyses of TH vs. YH, TH vs.TL, TL vs. YL, and YH vs. YL yielded 299, 169, 242, and 368 differentially expressed genes (DEGs), and 473, 297, 394, and 297 differentially expressed proteins (DEPs), respectively. By functional annotation of these DEGs and DEPs, genes that were enriched in the HIF-1 signaling pathway (NPPA, ERK2, ENO3, and EGLN3), VEGF signaling pathway (ERK2, A2M, FGF1, CTGF, and DPP4), and hypoxia-related processes (CRYAB, EGLN3, TGFB2, DPP4, and ACE) were identified as important candidate genes for high-altitude adaptation in the Tibetan pig. This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in pigs, and furthers our understanding of human hypoxic diseases.
Collapse
Affiliation(s)
- Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Peng Shang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.,Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Zhixiu Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Jun Ma
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Liyuang Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.
| |
Collapse
|
18
|
Wang Z, Shang P, Li Q, Wang L, Chamba Y, Zhang B, Zhang H, Wu C. iTRAQ-based proteomic analysis reveals key proteins affecting muscle growth and lipid deposition in pigs. Sci Rep 2017; 7:46717. [PMID: 28436483 PMCID: PMC5402282 DOI: 10.1038/srep46717] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/23/2017] [Indexed: 02/06/2023] Open
Abstract
Growth rate and meat quality, two economically important traits in pigs, are controlled by multiple genes and biological pathways. In the present study, we performed a proteomic analysis of longissimus dorsi muscle from six-month-old pigs from two Chinese native mini-type breeds (TP and DSP) and two introduced western breeds (YY and LL) using isobaric tag for relative and absolute quantification (iTRAQ). In total, 4,815 peptides corresponding to 969 proteins were detected. Comparison of expression patterns between TP-DSP and YY-LL revealed 288 differentially expressed proteins (DEPs), of which 169 were up-regulated and 119 were down-regulated. Functional annotation suggested that 28 DEPs were related to muscle growth and 15 to lipid deposition. Protein interaction network predictions indicated that differences in muscle growth and muscle fibre between TP-DSP and YY-LL groups were regulated by ALDOC, ENO3, PGK1, PGK2, TNNT1, TNNT3, TPM1, TPM2, TPM3, MYL3, MYH4, and TNNC2, whereas differences in lipid deposition ability were regulated by LPL, APOA1, APOC3, ACADM, FABP3, ACADVL, ACAA2, ACAT1, HADH, and PECI. Twelve DEPs were analysed using parallel reaction monitoring to confirm the reliability of the iTRAQ analysis. Our findings provide new insights into key proteins involved in muscle growth and lipid deposition in the pig.
Collapse
Affiliation(s)
- Zhixiu Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Peng Shang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China.,College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 100086, China
| | - Qinggang Li
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Liyuan Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 100086, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| |
Collapse
|
19
|
Wang Z, Li Q, Chamba Y, Zhang B, Shang P, Zhang H, Wu C. Correction: Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue. PLoS One 2017; 12:e0172930. [PMID: 28225810 PMCID: PMC5321414 DOI: 10.1371/journal.pone.0172930] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0141138.].
Collapse
|
20
|
Li K, Lan Y, Luo H, Zhang H, Liu D, Zhang L, Gui R, Wang L, Shahzad M, Sizhu S, Li J, Chamba Y. Prevalence, Associated Risk Factors, and Phylogenetic Analysis of Toxocara vitulorum Infection in Yaks on the Qinghai Tibetan Plateau, China. Korean J Parasitol 2016; 54:645-652. [PMID: 27853122 PMCID: PMC5127537 DOI: 10.3347/kjp.2016.54.5.645] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/11/2016] [Accepted: 09/12/2016] [Indexed: 11/23/2022]
Abstract
Toxocara vitulorum has been rarely reported in yaks at high altitudes and remote areas of Sichuan Province of Tibetan Plateau of China. The current study was designed to investigate the prevalence, associated risk factors, and phylogenetic characteristics of T. vitulorum in yak calves on the Qinghai Tibetan plateau. Fecal samples were collected from 891 yak calves and were examined for the presence of T. vitulorum eggs by the McMaster technique. A multivariable logistic regression model was employed to explore variables potentially associated with exposure to T. vitulorum infection. T. vitulorum specimens were collected from the feces of yaks in Hongyuan of Sichuan Province, China. DNA was extracted from ascaris. After PCR amplification, the sequencing of ND1 gene was carried out and phylogenetic analyses was performed by MEGA 6.0 software. The results showed that 64 (20.1%; 95% CI 15.8-24.9%), 75 (17.2; 13.8-21.1), 29 (40.9; 29.3-53.2), and 5 (7.6; 2.5-16.8) yak calves were detected out to excrete T. vitulorum eggs in yak calve feces in Qinghai, Tibet, Sichuan, and Gansu, respectively. The present study revealed that high infection and mortality by T. vitulorum is wildly spread on the Qinghai Tibetan plateau, China by fecal examination. Geographical origin, ages, and fecal consistencies are the risk factors associated with T. vitulorum prevalence by logistic regression analysis. Molecular detection and phylogenetic analysis of ND1 gene of T. vitulorum indicated that T. vitulorum in the yak calves on the Qinghai Tibetan plateau are homologous to preveiously studies reported.
Collapse
Affiliation(s)
- Kun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yanfang Lan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Houqiang Luo
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Hui Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Dongyu Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Lihong Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Rui Gui
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Lei Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Muhammad Shahzad
- University College of Veterinary & Animal Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Suolang Sizhu
- Laboratory of Detection and Monitoring of Highland Animal Disease, Tibet Agriculture and Animal Husbandry College, Linzhi 860000 Tibet, People's Republic of China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Laboratory of Detection and Monitoring of Highland Animal Disease, Tibet Agriculture and Animal Husbandry College, Linzhi 860000 Tibet, People's Republic of China
| | - Yangzom Chamba
- Laboratory of Detection and Monitoring of Highland Animal Disease, Tibet Agriculture and Animal Husbandry College, Linzhi 860000 Tibet, People's Republic of China
| |
Collapse
|
21
|
Wang Z, Li Q, Chamba Y, Zhang B, Shang P, Zhang H, Wu C. Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue. PLoS One 2015; 10:e0141138. [PMID: 26505482 PMCID: PMC4624711 DOI: 10.1371/journal.pone.0141138] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/04/2015] [Indexed: 01/25/2023] Open
Abstract
Transcriptome profiles established using high-throughput sequencing can be effectively used for screening genome-wide differentially expressed genes (DEGs). RNA sequences (from RNA-seq) and microRNA sequences (from miRNA-seq) from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small-ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. We obtained 27.18 G clean data through the RNA-seq and detected that 18,208 genes were positively expressed and 14,633 of them were co-expressed in the muscle tissues of the four samples. In all, 315 DEGs were found between the Chinese pig group and the introduced pig group, 240 of which were enriched with functional annotations from the David database and significantly enriched in 27 Gene Ontology (GO) terms that were mainly associated with muscle fiber contraction, cadmium ion binding, response to organic substance and contractile fiber part. Based on functional annotation, we identified 85 DEGs related to growth traits that were mainly involved in muscle tissue development, muscle system process, regulation of cell development, and growth factor binding, and 27 DEGs related to lipid deposition that were mainly involved in lipid metabolic process and fatty acid biosynthetic process. With miRNA-seq, we obtained 23.78 M reads and 320 positively expressed miRNAs from muscle tissues, including 271 known pig miRNAs and 49 novel miRNAs. In those 271 known miRNAs, 20 were higher and 10 lower expressed in DSP-TP than in LL-YY. The target genes of the 30 miRNAs were mainly participated in MAPK, GnRH, insulin and Calcium signaling pathway and others involved cell development, growth and proliferation, etc. Combining the DEGs and the differentially expressed (DE) miRNAs, we drafted a network of 46 genes and 18 miRNAs for regulating muscle growth and a network of 15 genes and 16 miRNAs for regulating lipid deposition. We identified that CAV2, MYOZ2, FRZB, miR-29b, miR-122, miR-145-5p and miR-let-7c, etc, were key genes or miRNAs regulating muscle growth, and FASN, SCD, ADORA1, miR-4332, miR-182, miR-92b-3p, miR-let-7a and miR-let-7e, etc, were key genes or miRNAs regulating lipid deposition. The quantitative expressions of eight DEGs and seven DE miRNAs measured with real-time PCR certified that the results of differential expression genes or miRNAs were reliable. Thus, 18,208 genes and 320 miRNAs were positively expressed in porcine longissimus dorsi muscle. We obtained 85 genes and 18 miRNAs related to muscle growth and 27 genes and 16 miRNAs related to lipid deposition, which provided new insights into molecular mechanism of the economical traits in pig.
Collapse
Affiliation(s)
- Zhixiu Wang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
| | - Qinggang Li
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, People’s Republic of China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, People’s Republic of China
| | - Bo Zhang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
| | - Peng Shang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
| | - Hao Zhang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
- * E-mail:
| | - Changxin Wu
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
| |
Collapse
|
22
|
Zhang H, Wang XT, Chamba Y, Ling Y, Wu CX. Influences of hypoxia on hatching performance in chickens with different genetic adaptation to high altitude. Poult Sci 2008; 87:2112-6. [PMID: 18809874 DOI: 10.3382/ps.2008-00122] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The experiments were conducted to assess how hatching performance is affected by chicken breeds and environment of high altitude and to analyze the vital factor of the low hatchability at a 2,900-m altitude. Eggs of Tibetan and Dwarf chickens were incubated at conditions of normobaric normoxia, normobaric hypoxia, hypobaric hypoxia, and supplemental O2 at high altitude (hypobaric normoxia) during the whole incubation or at 0 to 7, 8 to 14, and 15 to 22 d of incubation, respectively. The results showed that the Tibetan chickens had greater hatchability (79.72%), lower water loss (12.90%), greater relative embryo weight (38.08%), and relative chick weight (68.41%) compared with the Dwarf chickens (31.69, 15.79, 30.71, and 65.21%, respectively) when both of them were incubated at a 2,900-m altitude. The hatchability was 71.60% in Tibetan chicken and 36.23% in Dwarf chicken under the normobaric hypoxia condition. The hatchability of chicken was efficiently increased with supplemental O2. The previous results indicated that the O2 deficit is the main factor resulting in the low hatchability and the poor chick quality of the lowland chicken breed when incubated at a 2,900-m altitude. Breeding chickens for adaptability to hypoxia and supplemental O2 is a good way to improve the hatchability and chick quality at that altitude.
Collapse
Affiliation(s)
- H Zhang
- College of Animal Science and Technology, China Agricultural University, Bejing, China 100193
| | | | | | | | | |
Collapse
|
23
|
Zhang H, Wu CX, Chamba Y, Ling Y, Tang XH. [Cardiac enzymes related to high-altitude hypoxic adaptation in Tibetan chicken]. Zhongguo Ying Yong Sheng Li Xue Za Zhi 2008; 24:233-236. [PMID: 21141535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
AIM The purpose of this experiment was to investigate the cardiac physiological characteristics for adaptation to high-altitude hypoxia in chickens. METHODS Tibetan, Dwarf Recessive White and Shouguang chickens were fed at low-and high-altitude, and measurements were made in heart weights, lactic acid (LA), lactate dehydrogenase (LDH), and succinate dehydrogenase (SDH) at the age of 10 weeks. RESULTS The results showed that Tibetan chickens at high-altitude had lower heart weight and LA content, and similar LDH activity, and higher SDH activity when compared to Dwarf Recessive White and Shouguang chickens. CONCLUSION It was concluded that the cardiac mechanisms of high-altitude hypoxic adaptation in Tibetan chickens were increasing neither heart weight, nor level of anaerobic metabolism, but the higher SDH activity was significant to the adaptation. The SDH was a symbol enzyme for hypoxic adaptation in Tibetan chicken.
Collapse
Affiliation(s)
- Hao Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
| | | | | | | | | |
Collapse
|
24
|
Abstract
Tibetan chickens, a unique chicken breed native to high altitude, have good adaptation to hypoxia. The experiment was conducted to determine the adaptive blood characteristics in Tibetan chickens. Fertile eggs from Tibetan and Dwarf Recessive White chickens were incubated, and the chicks were reared until 10 wk of age at low altitude (100 m) and high altitude (2,900 m). At 1 d and 2, 6, and 10 wk of age, the hematological characteristics, blood gas value, and blood volume were measured. Tibetan chickens had more red blood cells (RBC), smaller mean cell volume, lower pH and partial pressure of oxygen, and higher partial pressure of carbon dioxide at high altitude and had lower blood volume, erythrocyte volume, and plasma volume at low and high altitude than Dwarf Recessive White chickens. Tibetan chickens reared at high altitude retained a high level of RBC and a stable level of hematocrit from younger to older, but Dwarf Recessive White chickens reared at high altitude presented an increase in RBC and hematocrit values. It was concluded the adaptation was achieved in Tibetan chickens by increase in RBC and blood oxygen affinity, decrease in mean cell volume, and reducing susceptivity to hypocapnia.
Collapse
Affiliation(s)
- H Zhang
- College of Animal Science and Technology, China Agricultural University, Bejing, China 100094
| | | | | | | |
Collapse
|
25
|
Zhang H, Wu CX, Chamba Y, Zhao CJ, Li XW, Ling Y. [Polymorphisms of three major genes for reproductive traits in Tibet pigs]. Yi Chuan 2007; 29:939-44. [PMID: 17681921 DOI: 10.1360/yc-007-0939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tibet pig is a special Chinese indigenous pig breed, which could survive in high-altitude areas of Tibet. In the present study, the genotypes of ESR, FSHbeta, and PRLR gene, the three known major genes of reproductive traits, were identified in 202 Tibet pig individuals. The results showed that the predominant genotypes of ESR, FSHbeta, and PRLR gene were BB, AB and AA, respectively. The genotype frequencies of the three genes were in Hardy-Weinberg equilibrium. The frequencies of desired alleles of the three genes were higher than those of other alleles, which indicated that Tibet pig had a good potential for improving reproductive traits.
Collapse
Affiliation(s)
- Hao Zhang
- College of Animal Science and Technology, China Agricultural University, Bejing 100094, China.
| | | | | | | | | | | |
Collapse
|