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Yin H, Feng Y, Wang Y, Jiang Q, Zhang J, Zhao J, Chen Y, Wang Y, Peng R, Wang Y, Zhao T, Zheng C, Xu L, Gao X, Gao H, Li J, Wang Z, Zhang L. Genome-Wide Scans for Selection Signatures in Ningxia Angus Cattle Reveal Genetic Variants Associated with Economic and Adaptive Traits. Animals (Basel) 2024; 15:58. [PMID: 39795001 PMCID: PMC11718920 DOI: 10.3390/ani15010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Revised: 12/26/2024] [Accepted: 12/27/2024] [Indexed: 01/13/2025] Open
Abstract
The genetic improvement of beef cattle breeds is crucial for the advancement of the beef cattle industry. Whole-genome resequencing technology has been widely applied in genetic breeding as well as research on selection signatures in beef cattle. In this study, 20× whole-genome resequencing was performed on 282 Angus cattle from the Ningxia region, and a high-quality dataset encompassing extensive genomic variations across the entire genome was constructed. The iHS test identified 495 selection signal regions, which included pregnancy-associated glycoprotein (PAG) family genes and immune-related genes such as UL16-binding protein 21 (ULBP21), CD1b molecule (CD1B), and tumor necrosis factor ligand superfamily member 11 (TNFSF11). A quantitative trait locus (QTL) enrichment analysis revealed that several economic traits, including longissimus muscle area, marbling score, carcass weight, average daily gain, and milk yield, were significantly enriched in cattle with these selection signatures. Although the enrichment of QTLs for health traits was low, immune-related genes may indirectly contribute to improvements in production performance. These findings show the genetic basis of economic and adaptive traits in Ningxia Angus cattle, providing a theoretical foundation and guidance for further genetic improvement and breeding strategies.
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Affiliation(s)
- Haiqi Yin
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Yuan Feng
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Yu Wang
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Qiufei Jiang
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Juan Zhang
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China;
| | - Jie Zhao
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Yafei Chen
- Yinchuan Animal Husbandry Technology Extension Service Center, Yinchuan 750021, China;
| | - Yaxuan Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Ruiqi Peng
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Yahui Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Tong Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Caihong Zheng
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Lingyang Xu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Xue Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Huijiang Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Junya Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Zezhao Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Lupei Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
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Shah AU, Hemida MG. The ex vivo infection model of the peripheral bovine mononuclear cells (PBMCs) and the bovine spleen cells with the bovine coronavirus (BCoV) induced a differential expression of the host cytokine genes profiles and modulates the virus replication. Virology 2024; 600:110259. [PMID: 39490206 DOI: 10.1016/j.virol.2024.110259] [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: 07/01/2024] [Revised: 10/02/2024] [Accepted: 10/14/2024] [Indexed: 11/05/2024]
Abstract
The adaptive immune response during BCoV infection of peripheral blood mononuclear cells (PBMCs), the bovine spleen cells, and their isolated T lymphocytes was not studied well. Our study confirmed successful BCoV infection in PBMCs and spleen T cells. The BCoV replication was evidenced by measuring genome copy numbers using real-time PCR and expression levels of BCoV spike and nucleocapsid proteins via western blot and immunofluorescence assays. In infected PBMCs, CD4 T-cell levels were 1.45-fold higher, and CD8 T-cell levels were 1.6-fold lower compared to sham-infected cells. Conversely, infected splenocytes showed a 0.88-fold decrease in CD4 T-cells and a 1.88-fold increase in CD8 T-cells. The cytokine gene expression analysis revealed that BCoV infection activated type I interferon and upregulated IL-6 expression in PBMCs and splenocytes. These findings demonstrate that BCoV successfully infects immune cells from PBMCs and spleen, inducing differential host cytokine gene expression that favors virus replication.
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Affiliation(s)
- Abid Ullah Shah
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, 11548NY, USA
| | - Maged Gomaa Hemida
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, 11548NY, USA.
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Zewdie G, Akalu M, Tolossa W, Belay H, Deresse G, Zekarias M, Tesfaye Y. A review of foot-and-mouth disease in Ethiopia: epidemiological aspects, economic implications, and control strategies. Virol J 2023; 20:299. [PMID: 38102688 PMCID: PMC10724896 DOI: 10.1186/s12985-023-02263-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a contagious viral disease that affects the livelihoods and productivity of livestock farmers in endemic regions. It can infect various domestic and wild animals with cloven hooves and is caused by a virus belonging to the genus Aphthovirus and family Picornaviridae, which has seven different serotypes: A, O, C, SAT1, SAT2, SAT3, and Asia-1. This paper aims to provide a comprehensive overview of the molecular epidemiology, economic impact, diagnosis, and control measures of FMD in Ethiopia in comparison with the global situation. The genetic and antigenic diversity of FMD viruses requires a thorough understanding for developing and applying effective control strategies in endemic areas. FMD has direct and indirect economic consequences on animal production. In Ethiopia, FMD outbreaks have led to millions of USD losses due to the restriction or rejection of livestock products in the international market. Therefore, in endemic areas, disease control depends on vaccinations to prevent animals from developing clinical disease. However, in Ethiopia, due to the presence of diverse antigenic serotypes of FMD viruses, regular and extensive molecular investigation of new field isolates is necessary to perform vaccine-matching studies to evaluate the protective potential of the vaccine strain in the country.
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Affiliation(s)
- Girma Zewdie
- National Veterinary Institute (NVI), P. O. Box: 19, Bishoftu, Ethiopia.
| | - Mirtneh Akalu
- National Veterinary Institute (NVI), P. O. Box: 19, Bishoftu, Ethiopia
- Koneru Lakshmaiah Education Foundation, Department of Biotechnology, Vaddeswaram, Guntur, Ap, 522502, India
| | | | - Hassen Belay
- Africa Union Pan African Veterinary Vaccine Center (AU-PANVAC), P. O. Box: 1746, Bishoftu, Ethiopia
| | - Getaw Deresse
- National Veterinary Institute (NVI), P. O. Box: 19, Bishoftu, Ethiopia
| | | | - Yeneneh Tesfaye
- National Veterinary Institute (NVI), P. O. Box: 19, Bishoftu, Ethiopia
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