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Wu X, Xiang D, Zhang W, Ma Y, Zhao G, Yin Z. Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes. Genes (Basel) 2024; 15:623. [PMID: 38790252 PMCID: PMC11120843 DOI: 10.3390/genes15050623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Genetic variation facilitates the evolution, environmental adaptability, and biodiversity of organisms. Danish Large White (LW) pigs have more desirable phenotypes compared with local Chinese pigs, which have difficulty adapting to the modern swine industry. However, the genome-wide mutational differences between these pig breeds are yet to be evaluated. Therefore, this study aimed to evaluate genomic variation and identify breed-specific SNPs in Danish LW pigs. Here, 43 LW, 15 Diqing Tibetan (DQZ), and 15 Diannan small-ear (DN) pigs whose genomes were re-sequenced with 5× depth were selected. This was followed by a conjoined analysis of our previous resequencing data of 24 Anqing six-end white (AQ) and six Asian wild (SS) pigs. In total, 39,158,378 SNPs and 13,143,989 insertion-deletions were obtained in all breeds. The variation number of LW pigs was the lowest, with 287,194 breed-specific and 1289 non-synonymous SNPs compared with Chinese breeds. Functional analysis of the breed-specific non-synonymous SNPs indicated that these mutations were mainly associated with the reproductive performance, feed intake, and feed conversion ratio of LW pigs. These findings provide a theoretical basis for genetic improvements in the Chinese swine industry.
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Affiliation(s)
- Xudong Wu
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Decai Xiang
- Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming 650224, China
| | - Wei Zhang
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Yu Ma
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zongjun Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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2
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Zhu S, Si J, Zhang H, Qi W, Zhang G, Yan X, Huang Y, Zhao M, Guo Y, Liang J, Lan G. Comparative Serum Proteome Analysis Indicates a Negative Correlation between a Higher Immune Level and Feed Efficiency in Pigs. Vet Sci 2023; 10:vetsci10050338. [PMID: 37235421 DOI: 10.3390/vetsci10050338] [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: 03/24/2023] [Revised: 04/27/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Identifying and verifying appropriate biomarkers is instrumental in improving the prediction of early-stage pig production performance while reducing the cost of breeding and production. The main factor that affects the production cost and environmental protection cost of the pig industry is the feed efficiency of pigs. This study aimed to detect the differentially expressed proteins in the early blood index determination serum between high-feed efficiency and low-feed efficiency pigs and to provide a basis for further identification of biomarkers using the isobaric tandem mass tag and parallel reaction monitoring approach. In total, 350 (age, 90 ± 2 d; body weight, 41.20 ± 4.60 kg) purebred Yorkshire pigs were included in the study, and their serum samples were obtained during the early blood index determination. The pigs were then arranged based on their feed efficiency; 24 pigs with extreme phenotypes were grouped as high-feed efficiency and low-feed efficiency, with 12 pigs in each group. A total of 1364 proteins were found in the serum, and 137 of them showed differential expression between the groups with high- and low-feed efficiency, with 44 of them being upregulated and 93 being downregulated. PRM (parallel reaction monitoring) was used to verify 10 randomly chosen differentially expressed proteins. The proteins that were differentially expressed were shown to be involved in nine pathways, including the immune system, digestive system, human diseases, metabolism, cellular processing, and genetic information processing, according to the KEGG and GO analyses. Moreover, all of the proteins enriched in the immune system were downregulated in the high-feed efficiency pigs, suggesting that a higher immune level may not be conducive to improving feed efficiency in pigs. This study provides insights into the important feed efficiency proteins and pathways in pigs, promoting the further development of protein biomarkers for predicting and improving porcine feed efficiency.
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Affiliation(s)
- Siran Zhu
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Jinglei Si
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
- Guangxi State Farms Yongxin Animal Husbandry Group Co., Ltd., Nanning 530004, China
| | - Huijie Zhang
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Wenjing Qi
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Guangjie Zhang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Xueyu Yan
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Ye Huang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Mingwei Zhao
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Yafen Guo
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
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Davoudi P, Do DN, Colombo SM, Rathgeber B, Miar Y. Application of Genetic, Genomic and Biological Pathways in Improvement of Swine Feed Efficiency. Front Genet 2022; 13:903733. [PMID: 35754793 PMCID: PMC9220306 DOI: 10.3389/fgene.2022.903733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/20/2022] [Indexed: 12/24/2022] Open
Abstract
Despite the significant improvement of feed efficiency (FE) in pigs over the past decades, feed costs remain a major challenge for producers profitability. Improving FE is a top priority for the global swine industry. A deeper understanding of the biology underlying FE is crucial for making progress in genetic improvement of FE traits. This review comprehensively discusses the topics related to the FE in pigs including: measurements, genetics, genomics, biological pathways and the advanced technologies and methods involved in FE improvement. We first provide an update of heritability for different FE indicators and then characterize the correlations of FE traits with other economically important traits. Moreover, we present the quantitative trait loci (QTL) and possible candidate genes associated with FE in pigs and outline the most important biological pathways related to the FE traits in pigs. Finally, we present possible ways to improve FE in swine including the implementation of genomic selection, new technologies for measuring the FE traits, and the potential use of genome editing and omics technologies.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
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Kaewsatuan P, Poompramun C, Kubota S, Yongsawatdigul J, Molee W, Uimari P, Molee A. Comparative proteomics revealed duodenal metabolic function associated with feed efficiency in slow-growing chicken. Poult Sci 2022; 101:101824. [PMID: 35395531 PMCID: PMC8987610 DOI: 10.1016/j.psj.2022.101824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/10/2022] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
The Korat chicken (KR), developed in Thailand, is a slow-growing breed developed as an alternative breed for Thai chicken producers. The growing interest in slow-growing chicken meat, due to its unique taste, distinct texture, health benefits, and higher broiler welfare have led to higher market demand for KR. However, its low feed efficiency (FE) has a significant negative impact on farm profitability. Understanding the molecular mechanism regulating FE allows for designing a suitable selection program and contributing to breeding more efficient chicken for poultry production. Thus, the objective of our study was to investigate the proteome differences and possible pathways associated with FE in male KR using a label-free quantitative proteomic approach. Seventy-five KR males were individually evaluated for FE, and duodenum samples from 6 animals (3 high-FE and 3 low-FE chickens) were collected at 10 wk of age for differential abundant proteins (DAPs), protein networks, functional enrichment, and pathway analyses. In this study, we found 40 DAPs significantly associated with FE pathways, including glycolysis/gluconeogenesis, peroxisome, oxidative phosphorylation, tight junction, and cysteine and methionine metabolism. Thus, variations in observed DAPs or genes related to DAPs could be interesting biomarker candidates for selection for higher feed utilization efficiency in chicken.
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Affiliation(s)
- Pramin Kaewsatuan
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Chotima Poompramun
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Satoshi Kubota
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Jirawat Yongsawatdigul
- School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Wittawat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Pekka Uimari
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, 00790, Finland
| | - Amonrat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
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Wu J, Ye Y, Quan J, Ding R, Wang X, Zhuang Z, Zhou S, Geng Q, Xu C, Hong L, Xu Z, Zheng E, Cai G, Wu Z, Yang J. Using nontargeted LC-MS metabolomics to identify the Association of Biomarkers in pig feces with feed efficiency. Porcine Health Manag 2021; 7:39. [PMID: 34078468 PMCID: PMC8170940 DOI: 10.1186/s40813-021-00219-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
Background Improving feed efficiency is economically and environmentally beneficial in the pig industry. A deeper understanding of feed efficiency is essential on many levels for its highly complex nature. The aim of this project is to explore the relationship between fecal metabolites and feed efficiency-related traits, thereby identifying metabolites that may assist in the screening of the feed efficiency of pigs. Results We performed fecal metabolomics analysis on 50 individuals selected from 225 Duroc x (Landrace x Yorkshire) (DLY) commercial pigs, 25 with an extremely high feed efficiency and 25 with an extremely low feed efficiency. A total of 6749 and 5644 m/z features were detected in positive and negative ionization modes by liquid chromatography-mass spectrometry (LC/MS). Regrettably, the PCA could not classify the the samples accurately. To improve the classification, OPLS-DA was introduced. However, the predictive ability of the OPLS-DA model did not perform well. Then, through weighted coexpression network analysis (WGCNA), we found that one module in each positive and negative mode was related to residual feed intake (RFI), and six and three metabolites were further identified. The nine metabolites were found to be involved in multiple metabolic pathways, including lipid metabolism (primary bile acid synthesis, linoleic acid metabolism), vitamin D, glucose metabolism, and others. Then, Lasso regression analysis was used to evaluate the importance of nine metabolites obtained by the annotation process. Conclusions Altogether, this study provides new insights for the subsequent evaluation of commercial pig feed efficiency through small molecule metabolites, but also provide a reference for the development of new feed additives. Supplementary Information The online version contains supplementary material available at 10.1186/s40813-021-00219-w.
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Affiliation(s)
- Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Qian Geng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642l, China. .,Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou, 510642, China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China.
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Pezeshkian Z, Mirhoseini SZ, Ghovvati S. Identification of hub genes involved in apparent metabolizable energy of chickens. Anim Biotechnol 2020; 33:242-249. [PMID: 32634039 DOI: 10.1080/10495398.2020.1784187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Feed efficiency is one of the most economically significant traits in a breeding program. Apparent metabolizable energy is the most used method to evaluate energy utilization for feed efficiency. The purpose of this study was to identify candidate genes of chickens with divergent apparent metabolizable energy by bioinformatics analysis. The gene expression profile of duodenal of the highest and lowest apparent metabolizable energy-ranked birds were analyzed. Differentially expressed genes were picked out using GEO2R tool. Gene ontology and pathway analysis were performed using bioinformatics tools. Cytoscape software was used to visualize protein-protein network. There were 201 DEGs, including 99 up-regulated genes enriched in metabolic pathways, Cellular senescence and Focal adhesion, and 102 down-regulated genes enriched in metabolic pathways, Regulation of actin cytoskeleton, Neuroactive ligand-receptor interaction, Calcium signaling pathway and Focal adhesion. Two important modules were detected and pathway enrichment analysis showed that they were mainly associated with Focal adhesion, Regulation of actin cytoskeleton and RNA transport. Fifteen hub genes were selected and among them, ITGA8, CDC42 and GSK3B might be the core genes related to apparent metabolizable energy of chickens. These hub genes can be used as biomarkers for apparent metabolizable energy and feed efficiency in breeding program of chickens.
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Affiliation(s)
- Zahra Pezeshkian
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Iran
| | | | - Shahrokh Ghovvati
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Iran
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Wang M, Yang S, Cai J, Yan R, Meng L, Long M, Zhang Y. Proteomic analysis using iTRAQ technology reveals the toxic effects of zearalenone on the leydig cells of rats. Food Chem Toxicol 2020; 141:111405. [PMID: 32389840 DOI: 10.1016/j.fct.2020.111405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 12/25/2022]
Abstract
Zearalenone (ZEA) is a mycotoxin that contaminates crops worldwide and is toxic to the reproductive systems of mammals, however, the toxicological mechanism by which ZEA affects germ cells is not fully understood. In this study, proteomic analysis using iTRAQ technology was adopted to determine the cellular response of Leydig cells of rats to ZEA exposure. The results were used to elucidate the mechanisms responsible for the toxicity of the ZEA towards germ cells. After 24 h of exposure to ZEA at a concentration of 30 μmol/L, a total of 128 differentially expressed proteins (DEPs) were identified. Of these, 70 DEPs were up-regulated and 58 DEPs were down-regulated. The DEPs associated with ZEA toxicology were then screened by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The results show that these DEPs are involved in a number of important ZEA toxicological pathways including apoptosis, immunotoxicity, DNA damage, and signaling pathways. The complex regulatory relationships between the DEPs and ZEA toxicological signaling pathways are also explicitly demonstrated in the form of a protein-protein interaction network. This study thus provides a theoretical molecular basis for understanding the toxicological mechanisms by which ZEA affects germ cells.
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Affiliation(s)
- Mingyang Wang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Shuhua Yang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Jing Cai
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Rong Yan
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Lingqi Meng
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Miao Long
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Yi Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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