1
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Gu Z. Male yaks adapt to heat stress with enhancement of immunomodulation, anti-oxidation, and blood oxygen delivery. J Therm Biol 2024; 123:103879. [PMID: 38906049 DOI: 10.1016/j.jtherbio.2024.103879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/21/2024] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Yaks adapt to extremely low temperatures, but they are more susceptible to heat stress (HS). The adaptive mechanisms with crucial plasma protein markers regulating the response to HS remain elusive. In this study, data-independent acquisition proteomics were used to evaluate the thermal adaptability under chronic HS and thermal-neutral conditions. As a result, yaks increased body temperatures and respiratory rates in response to HS. Eight differential proteins mainly related to vasodilatation were decreased by HS, but another four proteins associated with blood oxygen delivery were presented at higher levels. Complement and coagulation cascades pathway was activated by HS, and more proteins were upregulated to protect against inflammation and oxidative stress by higher levels of antioxidant proteins. It is likely that yaks react to HS with enhancement of immunomodulation, anti-oxidation, and blood oxygen delivery, which is conducive to taking appropriate environment and nutrition management strategies to get healthy and high-performing yaks in low-altitude regions during summer.
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Affiliation(s)
- Zhaobing Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China; Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Kunming, 650201, China.
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2
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Wang W, Dong Y, Guo W, Zhang X, Degen AA, Bi S, Ding L, Chen X, Long R. Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management. Front Microbiol 2024; 15:1301258. [PMID: 38348184 PMCID: PMC10860762 DOI: 10.3389/fmicb.2024.1301258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.
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Affiliation(s)
- Weiwei Wang
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuntao Dong
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Wei Guo
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiao Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - A. Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sisi Bi
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Luming Ding
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Chen
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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3
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Yang S, Liu J, Gu Z, Liu P, Lan Q. Physiological and Metabolic Adaptation to Heat Stress at Different Altitudes in Yaks. Metabolites 2022; 12:1082. [PMID: 36355165 PMCID: PMC9699490 DOI: 10.3390/metabo12111082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 10/29/2023] Open
Abstract
Yaks have strong adaptability to extremely cold and hypoxic conditions but are susceptible to high ambient temperature when yaks are raised in low-altitude areas during the high-temperature season. Twenty-four adult male yaks with similar weights and ages were randomly divided into TN (Thermoneutral, altitude = 3464 m), LHS (Light heat stress, altitude = 1960 m), and MHS (Medium heat stress, altitude = 906 m) groups to evaluate adaptation strategies to HS. Non-targeted and targeted metabolomics were applied to investigate the effects of different extents of HS on yaks. LHS- and MHS-yaks showed higher rectal temperatures and respiratory rates than TN-yaks. MHS-yaks had higher levels of red blood cells (RBCs), hemoglobin (Hb), whole blood relative index of middle shear at a shear rate of 5 S-1 (WMS), whole blood relative index of high shear at a shear rate of 200 S-1 (WHS), Casson viscosity (CV), middle shear flow resistance at a shear rate of 5 S-1 (MSFR), and high shear flow resistance at a shear rate of 200 S-1 (HSFR) as compared to TN- and LHS-yaks. Differential metabolites and metabolic pathways, including fatty acid metabolism, lipid metabolism, glucose metabolism, and amino acid metabolism, were altered by HS. Metabolites in the glucose metabolism pathway in LHS- and MHS-yaks were lower than those in TN-yaks. However, LHS-yaks showed higher levels of metabolites in the HIF-1 signaling pathway compared to TN- and MHS-yaks. Most of the tricarboxylic acid cycle (TCA) intermediates and fatty acids were significantly decreased in MHS-yaks compared to the other two groups. As a whole, yaks raised at a low altitude (25.6 °C) suffered from severe HS, but they adapted to HS with vasodilatation for dissipating heat and the increased antioxidants and metabolite levels of energy substrates.
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Affiliation(s)
- Shuli Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Jinfeng Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhaobing Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Kunming 650201, China
| | - Ping Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Qin Lan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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4
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Ncube KT, Dzomba EF, Rosen BD, Schroeder SG, Van Tassell CP, Muchadeyi FC. Differential gene expression and identification of growth-related genes in the pituitary gland of South African goats. Front Genet 2022; 13:811193. [PMID: 36072660 PMCID: PMC9442344 DOI: 10.3389/fgene.2022.811193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Growth and carcass quality are economically important traits in goat production. This study investigated differentially expressed genes from the caprine pituitary gland transcriptome of South African indigenous goat breeds of varying growth performances and carcass quality parameters. Tissues were harvested from the pituitary gland of three South African Boer goats and three village ecotype goats all raised under similar conditions simulating intensive commercial production systems. Three additional tissues were harvested from village ecotype goats that were raised extensively on village farms. Between breed differences were investigated by comparing differential gene expression among three South African Boer and three village goats that were both raised under intensive commercial production system at a research farm. Within-breed differences were investigated by comparing differential gene expression among three village goats raised under extensive conditions (on-farm in Pella, S.A. village farming community) and three village goats raised under intensive commercial production system (at ARC research farm in Pretoria, South Africa. Total RNA was isolated from the pituitary gland of 36-week-old animals (n = 9) and sequenced individually in triplicates. An average of 28,298,512 trimmed, and quality-controlled reads/animal were mapped to the goat genome (Capra_hircus.ARS1.94) using HiSat2 software. Transcript assembly and quantification yielded 104 differentially expressed genes for village goats raised under extensive system and 62 for village goats raised under the intensive production system at the false discovery rate (FRD) of ≤0.05 and a fold change of ≥2. Growth-related genes such as POU3F4 and TSHZ1 were highly expressed within breeds raised under both production systems. Conversely, growth-related genes such as FGFR2 and SMPX genes were highly expressed between breeds raised under similar production systems. Ballgown analysis revealed a high expression of GH1 and IGF1 in the intensively raised compared to extensively raised goats. Both genes were also highly expressed in the village goats when compared to the Boer. The differential gene expression data provided insights into genes and molecular mechanisms associated with growth and growth development in goats.
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Affiliation(s)
- Keabetswe T. Ncube
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- Discipline of Genetics, School of Life Sciences, University of Kwa-Zulu Natal, Scottsville, South Africa
| | - Edgar F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of Kwa-Zulu Natal, Scottsville, South Africa
| | - Ben D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Stephen G. Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Curt P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Farai. C. Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- *Correspondence: Farai. C. Muchadeyi,
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5
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Wang H, Wang L, Luo X, Guan J, Zhang X, Zhang L, Xiang Y. Molecular cloning, expression and anti-tumor function analysis of yak IFITM2 gene. Int J Biol Macromol 2022; 209:405-412. [PMID: 35381283 DOI: 10.1016/j.ijbiomac.2022.03.212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
IFITM2 is interferon-induced transmembrane protein 2, which plays an extremely key role in anti-tumor and anti-virus diseases. In this study, the 602 bp cDNA sequence of the yak (Bos grunniens) IFITM2 (BgIFITM2) gene was obtained. Moreover, the prokaryotic expression vector of BgIFITM2 protein was constructed and expressed successfully, with a molecular weight of 33.680 kDa. The proliferation activities and migration abilities of HepG2 cells were significantly inhibited after treatment with BgIFITM2 protein (0.1 and 1 μg/mL) (P < 0.05). The expressions of B cell lymphoma-2 (BCL2)/BCL2-associated X (BAX) and molecular target of rapamycin (mTOR) genes were significantly decreased, but the expressions of BAX gene were significantly increased after treatment with BgIFITM2 protein (0.1 and 1 μg/mL) (P < 0.05). The expression of BAX protein was also significantly increased after treatment with 1 μg/mL BgIFITM2 protein (P < 0.05). Finally, the addition of BgIFITM2 protein attenuated the formation of tumor lesions in mice, and the pathological damage of the lung was less than that in the model group. The expression of Ki67 protein in the model group was significantly higher than that in the control group (P < 0.05), but the expression of Ki67 protein in the BgIFITM2 group was significantly lower than that in the model group (P < 0.05). Taken together, BgIFITM2 protein could inhibit the proliferative activity of HepG2 cells by regulating apoptosis-related genes, and reduce the invasiveness of HepG2 cells in mice lung tissue. These results facilitate further studies on the function of BgIFITM2 protein.
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Affiliation(s)
- Haipeng Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, PR China
| | - Li Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, PR China.
| | - Xiaolin Luo
- Sichuan Academy of Grassland Sciences, Chengdu 611731, PR China
| | - Jiuqiang Guan
- Sichuan Academy of Grassland Sciences, Chengdu 611731, PR China
| | - Xiangfei Zhang
- Sichuan Academy of Grassland Sciences, Chengdu 611731, PR China
| | - Ling Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, PR China
| | - Yi Xiang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, PR China
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6
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Wang H, Wang L, Li J, Fu F, Zheng Y, Zhang L. Molecular characterization, expression and functional analysis of yak IFITM3 gene. Int J Biol Macromol 2021; 184:349-357. [PMID: 34119542 DOI: 10.1016/j.ijbiomac.2021.06.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/18/2023]
Abstract
IFITM3 is interferon-induced transmembrane 3, which plays an extremely key role in anti-proliferation, anti-virus and anti-tumor diseases. In this study, the yak (Bos grunniens) IFITM3 (BgIFITM3) gene contained a 5'-untranslated region (UTR) (25 bp), a coding region (441 bp), and a 3'-UTR (115 bp). The expression of BgIFITM3 gene in liver was significantly higher than that in heart, spleen, lung and kidney (P < 0.01). BgIFITM3 protein was localized on the yak hepatocyte plasma membrane, and its expression was significantly different between 1 day and 15 months of age (P < 0.05). Moreover, the prokaryotic expression vector of BgIFITM3 protein was constructed and expressed successfully, with a molecular weight of 19.5 kDa. The activities of yak hepatocyte were significantly inhibited after treating with BgIFITM3 protein (10 and 20 μg/mL) (P < 0.01). The expression levels of ERBB-2, IRS-1, PI3KR-1, AKT-1 and MAPK-3 were significantly lower after treating with 20 μg/mL BgIFITM3 protein (P < 0.05). Besides, the activities of HepG2 cells were significantly inhibited after treating with BgIFITM3 protein (1, 10 and 20 μg/mL) (P < 0.05). While, the cloning ability and migration ability of HepG2 cells were significantly inhibited after treating with 10 μg/mL BgIFITM3 protein (P < 0.05). Finally, the mitochondria of HepG2 cells was concentrated, cristae widened, and the double film density of mitochondria was increased after treating with 10 μg/mL BgIFITM3 protein. After 10 μg/mL BgIFITM3 protein treating, the expression levels of VDAC-2, VDAC-3 and p53 genes were significantly increased, but the expression level of GPX-4 gene was significantly decreased (P < 0.01). Taken together, the BgIFITM3 protein could inhibit the proliferations of yak hepatocyte and HepG2 cells by regulating the PI3K/Akt pathway or ferroptosis-related genes, respectively. These results benefit for further study of the function of BgIFITM3 protein.
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Affiliation(s)
- Haipeng Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, China
| | - Li Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, China.
| | - Juan Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, China
| | - Fang Fu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, China
| | - Yao Zheng
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, China
| | - Ling Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, China
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7
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Liu YX, Ma XM, Xiong L, Wu XY, Liang CN, Bao PJ, Yu QL, Yan P. Effects of Intensive Fattening With Total Mixed Rations on Carcass Characteristics, Meat Quality, and Meat Chemical Composition of Yak and Mechanism Based on Serum and Transcriptomic Profiles. Front Vet Sci 2021; 7:599418. [PMID: 33553278 PMCID: PMC7859351 DOI: 10.3389/fvets.2020.599418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
The objective of this study was to investigate the effects of intensive fattening with total mixed rations (TMR) on carcass characteristics, meat quality, and chemical composition of the yak meat. Theoretical data has been provided for evaluating the quality of yak meat during natural grazing and short-term fattening. Based on the analysis, we found that in fattening yak, the carcass weight (CWT) was increased by 106.43%, whereas the cooking loss, tenderness, and drop loss were significantly improved due to higher intramuscular fat content and lower moisture (P < 0.05). Protein, fat, calcium, and amino acids were also much higher (P < 0.01) in fattening yak compared with the grazing yak. The levels of albumin (ALB), lactate dehydrogenase (LDH), triglyceride (TRIG), and amylase (AMYL) in serum indicated better nutritional status for fattening yaks. The transcriptomics analysis showed that the high expression of ACSL1 and ACACB genes improved the synthesis and deposition of fat in fattening yak, whereas the regulation of SLC7A8, ATP1A4, ATP1A1, SLC3A2, and CPA3 gene expression weakened the proteolysis. These results indicated that fattening with TMR improves the yield and quality of the yak meat.
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Affiliation(s)
- Yi-Xuan Liu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Xiao-Ming 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
| | - Lin Xiong
- 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
| | - Xiao-Yun 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
| | - Chun-Nian 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
| | - Peng-Jia 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
| | - Qun-Li Yu
- College of Food Science and Engineering, Gansu Agricultural University, 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
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8
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Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J. Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application. Genome Biol Evol 2020; 12:2211-2230. [PMID: 32970804 PMCID: PMC7846157 DOI: 10.1093/gbe/evaa200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1,479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune-related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune-related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.
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Affiliation(s)
- Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Feichen Shen
- Department of Human Genetics, Medical School, University of Michigan
| | | | - Yang Song
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jeffrey M Kidd
- Department of Human Genetics, Medical School, University of Michigan
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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9
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Guang-Xin E, Yang BG, Zhu YB, Duang XH, Basang WD, Luo XL, An TW. Genome-wide selective sweep analysis of the high-altitude adaptability of yaks by using the copy number variant. 3 Biotech 2020; 10:259. [PMID: 32432020 DOI: 10.1007/s13205-020-02254-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022] Open
Abstract
The domestic yak (Bos grunniens) from the Qinghai-Tibet Plateau is an important animal model in high-altitude adaptation studies. Here, we performed the genome-wide selective sweep analysis to identify the candidate copy number variation (CNV) for the high-altitude adaptation of yaks. A total of 531 autosomal CNVs were determined from 29 yak genome-wide resequencing data (15 high- and 14 low-altitude distributions) by using a CNV caller with a CNV identification interval > 5 kb, CNV silhouette score > 0.7, and minimum allele frequency > 0.05. Most high-frequency CNVs were located at the exonic (44.63%) and intergenic (46.52%) regions. In accordance with the results of the selective sweep analysis, 7 candidate CNVs were identified from the interaction of the top 20 CNVs with highest divergence from the F ST and V ST between the low (LA) and high (HA) altitudes. Five genes (i.e., GRIK4, IFNLR1, LOC102275985, GRHL3, and LOC102275713) were also annotated from the seven candidate CNVs and their upstream and downstream ranges at 300 kb. GRIK4, IFNLR1, and LOC102275985 were enriched in five known signal pathways, namely, glutamatergic synapse, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and olfactory transduction. These pathways are involved in the environmental adaptability and various physiological functions of animals, especially the physiological regulation under a hypoxic environment. The results of this study advanced the understanding of CNV as an important genomic structure variant type that contributes to HA adaptation and helped further explain the molecular mechanisms underlying the altitude adaptability of yaks.
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Affiliation(s)
- E Guang-Xin
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Bai-Gao Yang
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Yan-Bin Zhu
- 2State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Sciences (TAAAS)), Lhasa, 850002 China
| | - Xing-Hai Duang
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Wang-Dui Basang
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Xiao-Lin Luo
- 3Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
| | - Tian-Wu An
- 3Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
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Hao D, Wang X, Thomsen B, Kadarmideen HN, Wang X, Lan X, Huang Y, Qi X, Chen H. Copy Number Variations and Expression Levels of Guanylate-Binding Protein 6 Gene Associated with Growth Traits of Chinese Cattle. Animals (Basel) 2020; 10:E566. [PMID: 32230930 PMCID: PMC7222342 DOI: 10.3390/ani10040566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 11/16/2022] Open
Abstract
Association studies have indicated profound effects of copy number variations (CNVs) on various phenotypes in different species. In this study, we identified the CNV distributions and expression levels of guanylate-binding protein 6 (GBP6) associated with the growth traits of Chinese cattle. The results showed that the phenotypic values of body size and weight of Xianan (XN) cattle were higher than those of Nanyang (NY) cattle. The medium CNV types were mostly identified in the XN and NY breeds, but their CNV distributions were significantly different (adjusted p < 0.05). The association analysis revealed that the body weight, cannon circumference and chest circumference of XN cattle had significantly different values in different CNV types (p < 0.05), with CNV gain types (Log22-ΔΔCt > 0.5) displaying superior phenotypic values. We also found that transcription levels varied in different tissues (p < 0.001) and the CNV gain types showed the highest relative gene expression levels in the muscle tissue, consistent with the highest phenotypic values of body weight and cannon circumference among the three CNV types. Consequently, our results suggested that CNV gain types of GBP6 could be used as the candidate markers in the cattle-breeding program for growth traits.
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Affiliation(s)
- Dan Hao
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark;
| | - Xiao Wang
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (X.W.); (H.N.K.)
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark;
| | - Haja N. Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (X.W.); (H.N.K.)
| | - Xiaogang Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
| | - Xinglei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang 463700, Henan, China;
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
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Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak. Animals (Basel) 2019; 9:ani9121008. [PMID: 31766342 PMCID: PMC6940794 DOI: 10.3390/ani9121008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss- or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects. Abstract Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.
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