1
|
Ma X, Zhang Q, La Y, Fu D, Jiang H, Bao P, Wu X, Chu M, Guo X, Yan P, Liang C. Differential Abundance of Brain Mitochondrial Proteins in Yak and Cattle: A Proteomics-Based Study. Front Vet Sci 2021; 8:663031. [PMID: 34532350 PMCID: PMC8438127 DOI: 10.3389/fvets.2021.663031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
The plateau adaptability and stress resistance of yaks are widely known based on their capacity to survive under severe habitat conditions. However, a few studies on brain mitochondria have characterized these adaptations at the protein level. We identified and quantified the brain mitochondrial proteins using isobaric tags for relative and absolute quantification (iTRAQ) and Proteomics. Western blotting was used to verify changes in the expression of target proteins. A total of 57 differentially abundant proteins (DAPs) were identified in the yak brain tissue. Gene Ontology (GO) analysis showed molecular functions of these DAPs including downregulated oxidoreductase activity but upregulated coenzyme binding. Significantly enriched biological processes were oxidation-reduction process (downregulated) and small molecule metabolic processes (upregulated). STRING protein interaction analysis indicated a complex interaction between dehydrogenase, transaminase, and ATP synthetase families. Reactome pathway analysis highlighted that the majority of DAPs participated in aerobic metabolic pathways such as metabolism, citric acid cycle, and respiratory electron transport. Immunoblotting confirmed that changes in FKBP4 and ATPAF2 expression were consistent with the results of mass spectrometry. We performed a high-throughput screening to identify DAPs in brain mitochondria between yak and cattle, which could explain the plateau adaptability of yaks.
Collapse
Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Qiang Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China.,State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Yongfu La
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Hiu Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China.,State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| |
Collapse
|
2
|
Zhang W, Gao X, Zhang Y, Zhao Y, Zhang J, Jia Y, Zhu B, Xu L, Zhang L, Gao H, Li J, Chen Y. Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle. BMC Genet 2018; 19:114. [PMID: 30572824 PMCID: PMC6302425 DOI: 10.1186/s12863-018-0705-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022] Open
Abstract
Background China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30 K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50 K). Results In principal component analysis (PCA) and neighbour-joining (NJ) tree analysis, samples of the same breeds were grouped together, leading to clear separation from other breeds. And Chinese indigenous cattle were clustered into two groups of southern and northern breeds, originated from Asian Bos indicus lineage and Eurasian Bos taurus lineage, respectively. In STRUCTURE K = 2, a clear transition occurred from the northern breeds to the southern breeds. Additionally, the northern breeds contained a smaller Eurasian taurine (62.5%) descent proportion than that reported previously (more than 90%). In STRUCTURE K = 3, a distinct descent was detected in the southern Chinese breeds, which could reflect a long-term selection history of Chinese indigenous cattle. The results from TreeMix and f3 statistic provided the evidence of an admixture history between southern breeds and northern breeds. Conclusions Consistent with the observed geographical distributions, Chinese indigenous cattle were divided into two genetic clusters, northern indigenous cattle and southern indigenous cattle. Three improved breeds in the northern area also exhibited northern indigenous ancestry. We found that the breeds distributed in the northern China showed more southern lineage introgression than previously reported. Central-located populations appeared to the admixture between southern and northern lineages, and introgression events from European cattle were observed in Luxi Cattle, Qinchuan Cattle and Jinnan Cattle. The study revealed the population structures and levels of admixture pattern among Chinese indigenous cattle, shedding light on the origin and evolutionary history of these breeds. Electronic supplementary material The online version of this article (10.1186/s12863-018-0705-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wengang Zhang
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue Gao
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yang Zhang
- Xinjiang Academy of Animal Science, Urumqi, 830011, China
| | - Yumin Zhao
- Jilin Academy of Animal Science, Changchun, 130124, China
| | | | - Yutang Jia
- Institute of Animal Husbandry and Veterinary Medicine, AnhuiAcademyof Agricultural Sciences, Hefei, 230031, China
| | - Bo Zhu
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lingyang Xu
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lupei Zhang
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Huijiang Gao
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Junya Li
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Yan Chen
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| |
Collapse
|
3
|
Yang Q, Zhang S, Li J, Wang X, Peng K, Lan X, Pan C. Development of a touch-down multiplex PCR method for simultaneously rapidly detecting three novel insertion/deletions (indels) within one gene: an example for goat GHR gene. Anim Biotechnol 2018; 30:366-371. [DOI: 10.1080/10495398.2018.1517770] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Qing Yang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Shaoli Zhang
- Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jie Li
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xinyu Wang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kun Peng
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chuanying Pan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| |
Collapse
|