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Galdino Andrade TE, Scavassini Peña M, Fiorotti J, de Souza Bin R, Rodrigues Caetano A, Connelley T, Ferreira de Miranda Santos IK. Graduate Student Literature Review: The DRB3 gene of the bovine major histocompatibility complex-Discovery, diversity, and distribution of alleles in commercial breeds of cattle and applications for development of vaccines. J Dairy Sci 2024; 107:11324-11341. [PMID: 39004123 DOI: 10.3168/jds.2023-24628] [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: 12/28/2023] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
The bovine major histocompatibility complex (MHC), also known as the bovine leukocyte antigen (BoLA) complex, is the genomic region that encodes the most important molecules for antigen presentation to initiate immune responses. The first evidence of MHC in bovines pointed to a locus containing 2 antigens, one detected by cytotoxic antiserum (MHC class I) and another studied by mixed lymphocyte culture tests (MHC class II). The most studied gene in the BoLA region is the highly polymorphic BoLA-DRB3, which encodes a β chain with a peptide groove domain involved in antigen presentation for T cells that will develop and co-stimulate cellular and humoral effector responses. The BoLA-DRB3 alleles have been associated with outcomes in infectious diseases such as mastitis, trypanosomiasis, and tick loads, and with production traits. To catalog these alleles, 2 nomenclature methods were proposed, and the current use of both systems makes it difficult to list, comprehend and apply these data effectively. In this review we have organized the knowledge available in all of the reports on the frequencies of BoLA-DRB3 alleles. It covers information from studies made in at least 26 countries on more than 30 breeds; studies are lacking in countries that are important producers of cattle livestock. We highlight practical applications of BoLA studies for identification of markers associated with resistance to infectious and parasitic diseases, increased production traits and T cell epitope mapping, in addition to genetic diversity and conservation studies of commercial and Creole and locally adapted breeds. Finally, we provide support for the need of studies to discover new BoLA alleles and uncover unknown roles of this locus in production traits.
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Affiliation(s)
| | - Maurício Scavassini Peña
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, Brazil, 14049-900
| | - Jéssica Fiorotti
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, Brazil, 14049-900
| | - Renan de Souza Bin
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, Brazil, 14049-900
| | | | - Timothy Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom, EH25 9RG
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Hamada R, Giovambattista G, Metwally S, Borjigin L, Polat Yamanaka M, Matsuura R, Ali AO, Mahmoud HYAH, Mohamed AEA, Kyaw Moe K, Takeshima SN, Wada S, Aida Y. First characterization of major histocompatibility complex class II DRB3 diversity in cattle breeds raised in Egypt. Gene 2024; 918:148491. [PMID: 38649062 DOI: 10.1016/j.gene.2024.148491] [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: 01/12/2024] [Revised: 03/12/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Genes encoding bovine leukocyte antigen (BoLA) enable the immune system to identify pathogens. Therefore, these genes have been used as genetic markers for infectious and autoimmune diseases as well as for immunological traits in cattle. Although BoLA polymorphisms have been reported in various cattle breeds worldwide, they have not been studied in cattle populations in Egypt. In this study, we characterized BoLA-DRB3 in two local Egyptian populations and one foreign population using polymerase chain reaction-sequence-based typing (PCR-SBT) method. Fifty-four previously reported BoLA-DRB3 alleles and eight new alleles (BoLA-DRB3*005:08, *015:07, *016:03, *017:04, *020:02:02, *021:03, *164:01, and *165:01) were identified. Alignment analysis of the eight new alleles revealed 90.7-98.9 %, and 83.1-97.8 % nucleotide and amino acid identities, respectively, with the BoLA-DRB3 cDNA clone NR-1. Interestingly, BoLA-DRB3 in Egyptian cattle showed a high degree of allelic diversity in native (na = 28, hE > 0.95), mixed (na = 61, hE > 0.96), and Holstein (na = 18, hE > 0.88) populations. BoLA-DRB3*002:01 (14.3 %), BoLA-DRB3*001:01 (8.5 %), and BoLA-DRB3*015:01 (20.2 %) were the most frequent alleles in native, mixed, and Holstein populations, respectively, indicating that the genetic profiles differed in each population. Based on the allele frequencies of BoLA-DRB3, genetic variation among Egyptian, Asian, African, and American breeds was examined using Nei's distances and principal component analysis. The results suggested that native and mixed cattle populations were most closely associated with African breeds in terms of their gene pool, whereas Holstein cattle were more distinct from the other breeds and were closely related to Holstein cattle populations from other countries.
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Affiliation(s)
- Rania Hamada
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Pathology and Clinical Pathology, Faculty of Veterinary Medicine, Damanhour University, Damanhour City, El Beheira 22511, Egypt
| | - Guillermo Giovambattista
- Facultad de Ciencias Veterinarias UNLP, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina; Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Samy Metwally
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Division of Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Damanhour University, Damanhour City, El Beheira 22511, Egypt
| | - Liushiqi Borjigin
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Meripet Polat Yamanaka
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryosuke Matsuura
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Alsagher O Ali
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena City, Qena 83523, Egypt
| | - Hassan Y A H Mahmoud
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena City, Qena 83523, Egypt
| | - Adel E A Mohamed
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena City, Qena 83523, Egypt
| | - Kyaw Kyaw Moe
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Pathology and Microbiology, University of Veterinary Science, Yezin, Nay Pyi Taw, Myanmar
| | - Shin-Nosuke Takeshima
- Department of Food and Nutrition, Faculty of Human Life, Jumonji University, 2-1-28 Sugasawa, Niiza, Saitama, Japan
| | - Satoshi Wada
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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Gou X, Tsunekawa A, Tsubo M, Peng F, Cheng Y. Abundant resources compensate for the uneven distribution of ungulates in desert grassland. FRONTIERS IN PLANT SCIENCE 2024; 15:1421998. [PMID: 39129765 PMCID: PMC11310146 DOI: 10.3389/fpls.2024.1421998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024]
Abstract
Introduction Strategically managing livestock grazing in arid regions optimizes land use and reduces the damage caused by overgrazing. Controlled grazing preserves the grassland ecosystem and fosters sustainability despite resource limitations. However, uneven resource distribution can lead to diverse grazing patterns and land degradation, particularly in undulating terrains. Methods In this study, we developed a herbivore foraging algorithm based on a resource selection function model to analyze foraging distribution patterns, predict the probability of foraging, and identify the determinants of foraging probability in cattle. The study area was a complex desert landscape encompassing dunes and interdunes. Data on cattle movements and resource distribution were collected and analyzed to model and predict foraging behavior. Results Our findings revealed that cattle prefer areas with abundant vegetation in proximity to water sources and avoid higher elevations. However, abundant resource availability mitigated these impacts and enhanced the role of water points, particularly during late grazing periods. The analysis showed that available resources primarily determine foraging distribution patterns and lessen the effects of landforms and water distance on patch foraging. Discussion The results suggest that thoughtful water source placement and the subdivision of pastures into areas with varied terrain are crucial for sustainable grazing management. By strategically managing these factors, land degradation can be minimized, and the ecological balance of grassland ecosystems can be maintained. Further research is needed to refine the model and explore its applicability in other arid regions.
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Affiliation(s)
- Xiaowei Gou
- Department of Grassland Resource and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing, China
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
| | | | - Mitsuru Tsubo
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Fei Peng
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Yunxiang Cheng
- Department of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Hamada R, Metwally S, Matsuura R, Borjigin L, Lo CW, Ali AO, Mohamed AEA, Wada S, Aida Y. BoLA-DRB3 Polymorphism Associated with Bovine Leukemia Virus Infection and Proviral Load in Holstein Cattle in Egypt. Pathogens 2023; 12:1451. [PMID: 38133334 PMCID: PMC10746042 DOI: 10.3390/pathogens12121451] [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: 11/24/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis, the most prevalent neoplastic disease of cattle worldwide. The immune response to BLV and disease susceptibility and resistance in cattle are strongly correlated with the bovine leukocyte antigen (BoLA)-DRB3 allelic polymorphism. BLV infection continues to spread in Egypt, in part because the relationships between BLV infection, proviral load in Egypt, and BoLA-DRB3 polymorphism are unknown. Here, we identified 18 previously reported alleles in 121 Holstein cows using a polymerase chain reaction sequence-based typing method. Furthermore, BoLA-DRB3 gene polymorphisms in these animals were investigated for their influence on viral infection. BoLA-DRB3*015:01 and BoLA-DRB3*010:01 were identified as susceptible and resistant alleles, respectively, for BLV infection in the tested Holsteins. In addition, BoLA-DRB3*012:01 was associated with low PVL in previous reports but high PVL in Holstein cattle in Egypt. This study is the first to demonstrate that the BoLA-DRB3 polymorphism confers resistance and susceptibility to PVL and infections of BLV in Holstein cattle in Egypt. Our results can be useful for the disease control and eradication of BLV through genetic selection.
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Affiliation(s)
- Rania Hamada
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (R.H.); (S.M.); (R.M.); (L.B.); (C.-W.L.)
- Department of Pathology and Clinical Pathology, Faculty of Veterinary Medicine, Damanhour University, Damanhour City 22511, Egypt
| | - Samy Metwally
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (R.H.); (S.M.); (R.M.); (L.B.); (C.-W.L.)
- Division of Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Damanhour University, Damanhour City 22511, Egypt
| | - Ryosuke Matsuura
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (R.H.); (S.M.); (R.M.); (L.B.); (C.-W.L.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Liushiqi Borjigin
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (R.H.); (S.M.); (R.M.); (L.B.); (C.-W.L.)
| | - Chieh-Wen Lo
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (R.H.); (S.M.); (R.M.); (L.B.); (C.-W.L.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Alsagher O. Ali
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena City 83523, Egypt; (A.O.A.); (A.E.A.M.)
| | - Adel E. A. Mohamed
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena City 83523, Egypt; (A.O.A.); (A.E.A.M.)
| | - Satoshi Wada
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (R.H.); (S.M.); (R.M.); (L.B.); (C.-W.L.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Dass G, Chopra A, Kandalkar Y, Vijay V, Choudhary A, Magotra A, Rajendran R. Cross-population genetic analysis revealed genetic variation and selection in the Ovar-DRB1 gene of Indian sheep breeds. Anim Biotechnol 2023; 34:2928-2939. [PMID: 36153754 DOI: 10.1080/10495398.2022.2125404] [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] [Indexed: 11/01/2022]
Abstract
In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of Ovar-DRB diversity across sheep breeds of India. Here, Ovar-DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN > dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.
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Affiliation(s)
- G R Gowane
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - S S Misra
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - Rani Alex
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Gopal Dass
- Animal Genetics & Breeding Division, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics & Breeding Division, ICAR-Arid Region Campus, Central Sheep & Wool Research Institute Bikaner, Avikanagar, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | - V Vijay
- Sonadi Seep Breeding Unit, NWPSI at Navaniya Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | | | - Ankit Magotra
- Animal Genetics & Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - R Rajendran
- Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Theni, India
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Ribeiro G, Baldi F, Cesar ASM, Alexandre PA, Peripolli E, Ferraz JBS, Fukumasu H. Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle. BMC Genomics 2022; 23:774. [PMID: 36434498 PMCID: PMC9700932 DOI: 10.1186/s12864-022-08958-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs. RESULTS The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10). CONCLUSION Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.
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Affiliation(s)
- Gabriela Ribeiro
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Fernando Baldi
- grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Aline S. M. Cesar
- grid.11899.380000 0004 1937 0722Escola Superior de Agricultura “Luiz de Queiroz”, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Pâmela A. Alexandre
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD 4067 Australia
| | - Elisa Peripolli
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - José B. S. Ferraz
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
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Suprovych TM, Salyha YT, Suprovych MP, Fedorovych EI, Fedorovych VV, Chornyj IO. Genetic Polymorphism of BoLA-DRB3.2 Locus in Ukrainian Cattle Breeds. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722040089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Thi DL, Vu SN, Lo CW, Dao TD, Bui VN, Ogawa H, Imai K, Sugiura K, Aida Y, Haga T. Association between BoLA-DRB3 polymorphism and bovine leukemia virus proviral load in Vietnamese Holstein Friesian cattle. HLA 2021; 99:105-112. [PMID: 34854239 DOI: 10.1111/tan.14503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/11/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022]
Abstract
Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis. Polymorphism in bovine leukocyte antigen (BoLA)-DRB3 allele can influence the host immune response to pathogens, including BLV. However, association between specific BoLA-DRB3 alleles and BLV proviral load (PVL), which is a useful index for estimating disease progression and transmission risk, in Vietnamese cattle are unknown. Here, association study of BoLA-DRB3 allele frequency between cattle with high or low PVL demonstrated BoLA-DRB3*12:01 associates with high PVL in Vietnamese Holstein-Friesian (HF) crossbred cattle. This is the first study to demonstrate that BoLA-DRB3 polymorphism confers susceptibility to BLV high PVL in HF crossbred kept in Vietnam. Our results may be useful in disease control and eradiation for BLV through genetic selection. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dung Le Thi
- Division of Infection Control and Disease Prevention, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Son Nguyen Vu
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam.,Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Chieh-Wen Lo
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tung Duy Dao
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan.,National Institute of Veterinary Research, Hanoi, Vietnam
| | - Vuong Nghia Bui
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan.,National Institute of Veterinary Research, Hanoi, Vietnam
| | - Haruko Ogawa
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan
| | - Kunitoshi Imai
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan
| | - Katsuaki Sugiura
- Laboratory of Environment Science for Sustainable Development, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Nippon Institute for Biological Science, Tokyo, Japan
| | - Yoko Aida
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeshi Haga
- Division of Infection Control and Disease Prevention, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Bai L, Borjigin L, Sato H, Takeshima SN, Asaji S, Ishizaki H, Kawashima K, Obuchi Y, Sunaga S, Ando A, Inoko H, Wada S, Aida Y. Kinetic Study of BLV Infectivity in BLV Susceptible and Resistant Cattle in Japan from 2017 to 2019. Pathogens 2021; 10:pathogens10101281. [PMID: 34684230 PMCID: PMC8537920 DOI: 10.3390/pathogens10101281] [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: 09/02/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/30/2022] Open
Abstract
Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis. Polymorphism in bovine lymphocyte antigen (BoLA)-DRB3 alleles is related to susceptibility to BLV proviral load (PVL), which is a useful index for estimating disease progression and transmission risk. However, whether differential BoLA-DRB3 affects BLV infectivity remains unknown. In a three-year follow-up investigation using a luminescence syncytium induction assay for evaluating BLV infectivity, we visualized and evaluated the kinetics of BLV infectivity in cattle with susceptible, resistant and neutral BoLA-DRB3 alleles which were selected from 179 cattle. Susceptible cattle showed stronger BLV infectivity than both resistant and neutral cattle. The order of intensity of BLV infectivity was as follows: susceptible cattle > neutral cattle > resistant cattle. BLV infectivity showed strong positive correlation with PVL at each testing point. BLV-infected susceptible cattle were found to be at higher risk of horizontal transmission, as they had strong infectivity and high PVL, whereas BLV-infected resistant cattle were low risk of BLV transmission owing to weak BLV infection and low PVL. Thus, this is the first study to demonstrate that the BoLA-DRB3 polymorphism is associated with BLV infection.
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Affiliation(s)
- Lanlan Bai
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (S.-N.T.); (S.W.)
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (H.S.)
| | - Liushiqi Borjigin
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (H.S.)
| | - Hirotaka Sato
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (H.S.)
| | - Shin-Nosuke Takeshima
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (S.-N.T.); (S.W.)
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (H.S.)
- Department of Food and Nutrition, Jumonji University, 2-1-28 Sugasawa, Niiza 352-8510, Saitama, Japan
| | - Sakurako Asaji
- GenoDive Pharma Inc., 4-14-1 Naka-cho, Atsugi 243-0018, Kanagawa, Japan; (S.A.); (A.A.); (H.I.)
| | - Hiroshi Ishizaki
- Grazing Animal Unit, Division of Grassland Farming, Institute of Livestock and Grassland Science, NARO, 768 Senbonmatsu, Nasushiobara 329-2793, Tochigi, Japan;
| | - Keiji Kawashima
- Tobu and General Agricultural Office Livestock Hygiene Division, Ota 373-0805, Gunma, Japan;
| | - Yuko Obuchi
- Department of Agriculture Dairy and Livestock Division, Maebashi 371-8570, Gunma, Japan; (Y.O.); (S.S.)
| | - Shinji Sunaga
- Department of Agriculture Dairy and Livestock Division, Maebashi 371-8570, Gunma, Japan; (Y.O.); (S.S.)
| | - Asako Ando
- GenoDive Pharma Inc., 4-14-1 Naka-cho, Atsugi 243-0018, Kanagawa, Japan; (S.A.); (A.A.); (H.I.)
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1119, Kanagasa, Japan
| | - Hidehito Inoko
- GenoDive Pharma Inc., 4-14-1 Naka-cho, Atsugi 243-0018, Kanagawa, Japan; (S.A.); (A.A.); (H.I.)
| | - Satoshi Wada
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (S.-N.T.); (S.W.)
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako 351-0198, Saitama, Japan; (L.B.); (H.S.)
- Department of Food and Nutrition, Jumonji University, 2-1-28 Sugasawa, Niiza 352-8510, Saitama, Japan
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: ; Tel.: +81-3-5841-5383
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10
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BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds. Sci Rep 2021; 11:17202. [PMID: 34433838 PMCID: PMC8387388 DOI: 10.1038/s41598-021-96330-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 08/02/2021] [Indexed: 11/08/2022] Open
Abstract
Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agro-ecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan's harsh environment.
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11
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Vasoya D, Oliveira PS, Muriel LA, Tzelos T, Vrettou C, Morrison WI, de Miranda Santos IKF, Connelley T. High throughput analysis of MHC-I and MHC-DR diversity of Brazilian cattle populations. HLA 2021; 98:93-113. [PMID: 34102036 DOI: 10.1111/tan.14339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 06/02/2021] [Indexed: 01/16/2023]
Abstract
The major histocompatibility complex (MHC) contains many genes that play key roles in initiating and regulating immune responses. This includes the polymorphic MHCI and MHCII genes that present epitopes to CD8+ and CD4+ T-cells, respectively. Consequently, the characterisation of the repertoire of MHC genes is an important component of improving our understanding of the genetic variation that determines the outcomes of immune responses. In cattle, MHC (BoLA) research has predominantly focused on Holstein-Friesian animals (as the most economically important breed globally), although the development of high-throughput approaches has allowed the BoLA-DRB3 repertoire to be studied in a greater variety of breeds. In a previous study we reported on the development of a MiSeq-based method to enable high-throughput and high-resolution analysis of bovine MHCI repertoires. Herein, we report on the expansion of this methodology to incorporate analysis of the BoLA-DRB3 and its application to analyse MHC diversity in a large cohort of cattle from Brazil (>500 animals), including representatives from the three major Bos indicus breeds present in Brazil - Guzerat, Gir and Nelore. This large-scale description of paired MHCI-DRB3 repertoires in Bos indicus cattle has identified a small number of novel DRB3 alleles, a large number of novel MHCI alleles and haplotypes, and provided novel insights into MHCI-MHCII association - further expanding our knowledge of bovine MHC diversity.
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Affiliation(s)
- Deepali Vasoya
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Priscila Silva Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Ribeirão Preto, São Paulo, Brazil
| | - Laura Agundez Muriel
- Translational Synthetic Biology Department, Mammalian genome editing and gene therapy, Parque de Investigación Biomédica, Carrer del Dr, Barcelona, Spain
| | - Thomas Tzelos
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Christina Vrettou
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - W Ivan Morrison
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Timothy Connelley
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
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12
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Oladosu OJ, Haruna IL, Hadebe SA, Zhou H, Hickford JGH. Nucleotide sequence variation of the major histocompatibility complex class II DQA1 gene in different cattle breeds from Nigeria and New Zealand. Vet Immunol Immunopathol 2021; 237:110273. [PMID: 34044268 DOI: 10.1016/j.vetimm.2021.110273] [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] [Received: 03/25/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
The major histocompatibility complex (MHC) plays a role in immune response. Among other activities, the bovine MHC genes (BoLA) trigger immune responses, including the activation of antibody-producing B-cells. In this study, White Fulani (n = 24), Red Bororo (n = 5) and Holstein-White × Fulani-cross (n = 11) cattle from Nigeria, and New Zealand Holstein-Friesian × Jersey-cross (n = 40) cattle were used to investigate variability in exon 2 of BoLA-DQA1. Ten alleles were identified using a PCR-Single Strand Conformation Polymorphism (SSCP) approach and their nucleotide sequences confirmed by DNA sequencing. A total of 12.60 % of all nucleotide positions analysed were revealed to be variable and two novel BoLA-DQA1 alleles are reported here for the first time.
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Affiliation(s)
- Oyekunle J Oladosu
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Ishaku L Haruna
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Sibusiso A Hadebe
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Huitong Zhou
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Jon G H Hickford
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand.
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13
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Suprovych TM, Suprovych MP, Mokhnachova NB, Biriukova OD, Strojanovska LV, Chepurna VA. Genetic variability and biodiversity of Ukrainian Gray cattle by the BoLA-DRB3 gene. REGULATORY MECHANISMS IN BIOSYSTEMS 2021. [DOI: 10.15421/022106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
At the current stage of genetic studies of cattle, more and more attention is being drawn to autochthonous breeds. Native cattle have a number of prominent phenotypic traits and have preserved unique genes and their combinations lost by modern commercial breeds, which would be valuable to use in selective programs. We surveyed polymorphism of the Ukrainian autochthonous Gray breed according to alleles of exon 2 of the BoLA-DRB3 gene. The uniqueness of the gene lies in the broad variability of its allele variants. Significant informativeness at DNA level is quite important for genetic studies. We surveyed allele polymorphism using the PCR-RLFP method on DNA isolated from 88 samples of blood of cows and 5 samples of sperm. We identified 28 alleles, of which 23 variants were nomenclature ones and 5 (jba, *jab, *jbb, *nad and *nda) were “without established nomenclature”, their share accounting for 8.9%. Four alleles *06, *12, *16 and *jba had a frequency above 5% and occupied 69.9% of the breed’s allele fund overall. The commonest allele was BoLA-DRB3.2*16 (44.1%). In total, we found 40 genotypes. Considering the significant dominance of variant *16, as expected, 5 genotypes with its inclusion occurred: *16/*16, *12/*16, *06/*16, *16/*24 and *jba/*16. It was present in the genotype of two out three studied animals. Parameters of heterozygosity, effective number of alleles, Shannon and Pielou indices indicate that Ukrainian Gray cattle are characterized by lowest level of genetic variability and biodiversity according to the BoLA-DRB3 gene compared with other breeds. Due to significant dominance of allele *16, the breed has no inbred motifs. We noted deviation toward increase in homozygosity without deviations from the norm of the distribution according to Hardy-Weinberg equilibrium. The obtained results will be used for genetic-populational programs with the purpose of improving the genetic potential of cattle breeds in terms of economically beneficial traits and diseases of cattle.
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14
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Giovambattista G, Takeshima SN, Moe KK, Pereira Rico JA, Polat M, Loza Vega A, Arce Cabrera ON, Aida Y. BoLA-DRB3 genetic diversity in Highland Creole cattle from Bolivia. HLA 2020; 96:688-696. [PMID: 33094557 DOI: 10.1111/tan.14120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 01/24/2023]
Abstract
The genetic diversity of the BoLA-DRB3 gene has been reported in different cattle breeds owing to its central role in the immune response. However, it is still unknown in hundreds of cattle breeds, especially native populations. Here, we studied BoLA-DRB3 genetic diversity in Highland Creole cattle (CrAl) from Western Bolivia, raised at altitudes between 3800 and 4200 m. DNAs from 48 CrAl cattle were genotyped for BoLA-DRB3 exon 2 alleles using polymerase chain reaction-sequence-based typing (PCR-SBT). The results were compared with 1341 previously reported data from Tropical Creole cattle and other breeds raised in the region. Twenty-three BoLA-DRB3 alleles were identified in CrAl, including the BoLA-DRB3*029:02 variant previously detected in other Creole cattle. Observed and expected heterozygosity were 0.87 and 0.93, respectively. Nucleotide diversity and the number of pairwise difference values were 0.078 and 19.46, respectively. The average number of nonsynonymous and synonymous substitutions were 0.037 and 0.097 for the entire BoLA-DRB3 exon 2, and 0.129 and 0.388 for the antigen-binding site, respectively. Venn analysis and the review of the IPD-MHC database and the literature showed that 2 of 64 alleles were only detected in CrAl, including BoLA-DRB3*029:01 previously reported in African cattle and *048:01 detected in Philippine cattle. Two additional alleles, BoLA-DRB3*007:02 and *029:02, were only present in CrAl and Lowland Creole cattle. Principal Component Analysis (PCA) showed that Bolivian Creole cattle breeds were closely located but they were distant from the Colombian Hartón del Valle Creole. FST analysis showed a low degree of genetic differentiation between Highland and Lowland Bolivian Creole cattle (FST = 0.015). The present results contribute to increasing our knowledge of BoLA-DRB3 genetic diversity in cattle breeds.
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Affiliation(s)
- Guillermo Giovambattista
- IGEVET-Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Shin-Nosuke Takeshima
- Department of Food and Nutrition, Faculty of Human Life, Jumonji University, Saitama, Japan.,Virus Infectious Diseases Unit, RIKEN, Saitama, Japan
| | - Kyaw Kyaw Moe
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hub, Saitama, Japan.,Department of Pathology and Microbiology, University of Veterinary Science, Yezin, Myanmar
| | - Juan A Pereira Rico
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - Meripet Polat
- Virus Infectious Diseases Unit, RIKEN, Saitama, Japan.,Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hub, Saitama, Japan
| | - Ariel Loza Vega
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - Orlando N Arce Cabrera
- Facultad de Ciencias Agrarias y Veterinarias, Universidad Técnica de Oruro, Oruro, Bolivia
| | - Yoko Aida
- Virus Infectious Diseases Unit, RIKEN, Saitama, Japan.,Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hub, Saitama, Japan
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15
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Morales JPA, López-Herrera A, Zuluaga JE. Association of BoLA DRB3 gene polymorphisms with BoHV-1 infection and zootechnical traits. Open Vet J 2020; 10:331-339. [PMID: 33282705 PMCID: PMC7703619 DOI: 10.4314/ovj.v10i3.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/20/2020] [Indexed: 01/06/2023] Open
Abstract
Background: The dairy sector is one of the leading in agricultural production sectors in the world and the bovine herpesvirus 1 (BoHV-1) is an important pathogen that causes great losses in most production systems. Moreover, BoLA DRB3 immunological gene presents different alleles related to protection against many pathogens. Methods: Serological diagnosis was carried out to determine the BoHV-1 infection and through PCR-RFLP 506 Holstein cows from several municipalities of Antioquia were genotyped for BoLA DRB3.2 gene polymorphisms. Results: Alleles 8, 16, 22, and 24 were the most common out of the 42 alleles found. By indirect ELISA technique, a 58.7% prevalence of BoHV-1 infection in this population was diagnosed and Odd ratios for found alleles were calculated by logistic regression; the only significant association was held for allele 37, which showed that it effects confers susceptibility to infection. On the other hand, by using generalized linear models, a significant association between BoLA DRB3.2 gene and milk and fat yield in primiparous and services per conception in multiparous was found, with the most favorable alleles being 11 and 28 in primiparous and 22 and 28 in multiparous; allele 37 was unfavorable only in primiparous. Conclusion: BoLA DRB3.2 gene polymorphisms have shown high variability and significant effects on Holstein cattle and their performance in production systems in Antioquia are at both sanitary or health and productive levels.
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Affiliation(s)
- Juan Pablo Arismendy Morales
- Biodiversity and Molecular Genetics Research Group "BIOGEM", Animal Production Department, Universidad Nacional de Colombia, Medellín, Colombia
| | - Albeiro López-Herrera
- Biodiversity and Molecular Genetics Research Group "BIOGEM", Animal Production Department, Universidad Nacional de Colombia, Medellín, Colombia
| | - Julián Echeverri Zuluaga
- Biodiversity and Molecular Genetics Research Group "BIOGEM", Animal Production Department, Universidad Nacional de Colombia, Medellín, Colombia
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16
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Giovambattista G, Moe KK, Polat M, Borjigin L, Hein ST, Moe HH, Takeshima SN, Aida Y. Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar. BMC Genet 2020; 21:95. [PMID: 32867670 PMCID: PMC7460757 DOI: 10.1186/s12863-020-00905-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/23/2020] [Indexed: 11/16/2022] Open
Abstract
Background Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations. Methods Blood samples (n = 294) were taken from two native breeds (Pyer Sein, n = 163 and Shwe Ni, n = 69) and a cattle crossbreed (Holstein-Friesian, n = 62) distributed across six regions of Myanmar (Bago, n = 38; Sagaing, n = 77; Mandalay, n = 46; Magway, n = 46; Kayin, n = 43; Yangon, n = 44). In addition, a database that included 2428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native from Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software. Results We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST = 0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis (PCA) and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations from Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations. Conclusion This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.
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Affiliation(s)
- Guillermo Giovambattista
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, B1900AVW, CC 296, La Plata, Argentina.
| | - Kyaw Kyaw Moe
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Pathology and Microbiology, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Meripet Polat
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Liushiqi Borjigin
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Si Thu Hein
- Department of Anatomy, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Hla Hla Moe
- Department of Genetics and Animal Breeding, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Shin-Nosuke Takeshima
- Department of Food and Nutrition, Faculty of Human Life, Jumonji University, 2-1-28 Sugasawa, Niiza-shi, Saitama, 352-8510, Japan
| | - Yoko Aida
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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17
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Lo CW, Borjigin L, Saito S, Fukunaga K, Saitou E, Okazaki K, Mizutani T, Wada S, Takeshima SN, Aida Y. BoLA-DRB3 Polymorphism is Associated with Differential Susceptibility to Bovine Leukemia Virus-Induced Lymphoma and Proviral Load. Viruses 2020; 12:v12030352. [PMID: 32235771 PMCID: PMC7150773 DOI: 10.3390/v12030352] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/11/2020] [Accepted: 03/20/2020] [Indexed: 12/22/2022] Open
Abstract
Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leucosis. However, less than 5% of BLV-infected cattle will develop lymphoma, suggesting that, in addition to viral infection, host genetic polymorphisms might play a role in disease susceptibility. Bovine leukocyte antigen (BoLA)-DRB3 is a highly polymorphic gene associated with BLV proviral load (PVL) susceptibility. Due to the fact that PVL is positively associated with disease progression, it is believed that controlling PVL can prevent lymphoma development. Thus, many studies have focused on the relationship between PVL and BoLA-DRB3. Despite this, there is little information regarding the relationship between lymphoma and BoLA-DRB3. Furthermore, whether or not PVL-associated BoLA-DRB3 is linked to lymphoma-associated BoLA-DRB3 has not been clarified. Here, we investigated whether or not lymphoma-associated BoLA-DRB3 is correlated with PVL-associated BoLA-DRB3. We demonstrate that two BoLA-DRB3 alleles were specifically associated with lymphoma resistance (*010:01 and *011:01), but no lymphoma-specific susceptibility alleles were found; furthermore, two other alleles, *002:01 and *012:01, were associated with PVL resistance and susceptibility, respectively. In contrast, lymphoma and PVL shared two resistance-associated (DRB3*014:01:01 and *009:02) BoLA-DRB3 alleles. Interestingly, we found that PVL associated alleles, but not lymphoma associated alleles, are related with the anti-BLV gp51 antibody production level in cows. Overall, our study is the first to demonstrate that the BoLA-DRB3 polymorphism confers differential susceptibility to BLV-induced lymphoma and PVL.
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Affiliation(s)
- Chieh-Wen Lo
- Laboratory of Global Animal Resource Science, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (L.B.); (S.S.); (S.-n.T.)
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Liushiqi Borjigin
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (L.B.); (S.S.); (S.-n.T.)
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Susumu Saito
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (L.B.); (S.S.); (S.-n.T.)
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan;
| | - Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan;
| | - Etsuko Saitou
- Hyogo Prefectural Awaji Meat Inspection Center, 49-18 Shitoorinagata, Minamiawaji, Hyogo 656-0152, Japan;
| | - Katsunori Okazaki
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan;
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan;
| | - Satoshi Wada
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Shin-nosuke Takeshima
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (L.B.); (S.S.); (S.-n.T.)
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
- Department of Food and Nutrition, Jumonji University, Niiza, Saitama 352-8510, Japan
| | - Yoko Aida
- Laboratory of Global Animal Resource Science, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (L.B.); (S.S.); (S.-n.T.)
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan;
- Correspondence:
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Sahoo NR, Kumar P, Khan MF, Mourya R, Ravikumar GVPPS, Tiwari AK. Sequence diversity of major histo-compatibility complex class II DQA1 in Indian Tharparkar cattle: novel alleles and in-silico analysis. HLA 2019; 93:451-461. [PMID: 30868742 DOI: 10.1111/tan.13521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/29/2023]
Abstract
Exon 2 of MHC class II gene codes for the first domain of the molecule that forms the peptide-binding groove and its polymorphism partly explains functional MHC diversity. A 850 bp DQA1 gene fragment spanning from intron I to exon III was typed by sequencing of 40 Tharparkar cattle of various agro-climatic zones of northern India along with 10 Tharparkar crossbreds. On analysis of nucleotide sequences, a total of 30 polymorphic sites (1 insertion and 29 SNPs) were identified in 14 MHC alleles leading to amino acid changes in 5 places in 249 bp (exon 2). Five new BoLa DQA1 alleles were identified and reported. The within group mean distance was highest in Tharparkar herd of Bikaner (0.045) and lowest (0.020) in that of Surathgarh (breeding tract) whereas, between groups mean distance was highest in Bikaner Tharparkar-Suratgarh Tharparkar pair. There was excess of nonsynonymous over synonymous nucleotide substitutions in the present study. The effects of these substitutions were predicted using I-Mutant and Panther online resources. The mean ratio of dN/dS was found to be >1.0 at 12 codons with two mutation hotspots at 13th codon (P = 0.002) and 64th codon (P = 0.01). The phylo-geographic analysis revealed that alleles 5, 7 and 13 formed a different cluster with alleles 7 and 13 grouped by the most frequent allele (BoLa-DQA*1401).
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Affiliation(s)
- Nihar R Sahoo
- Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Pushpendra Kumar
- Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Mohd F Khan
- Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Ranjeeta Mourya
- Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - G V P P S Ravikumar
- Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.,National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Ashok K Tiwari
- Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
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19
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The influence of BoLA-DRB3 alleles on incidence of clinical mastitis, cystic ovary disease and milk traits in Holstein Friesian cattle. Mol Biol Rep 2018; 45:917-923. [DOI: 10.1007/s11033-018-4238-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 07/04/2018] [Indexed: 11/25/2022]
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20
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Peters SO, Hussain T, Adenaike AS, Adeleke MA, De Donato M, Hazzard J, Babar ME, Imumorin IG. Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America. J Genomics 2018; 6:88-97. [PMID: 29928467 PMCID: PMC6004549 DOI: 10.7150/jgen.26491] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
Genetic polymorphisms and diversity of BoLA-DRB3.2 are essential because of DRB3 gene's function in innate immunity and its association with infectious diseases resistance or tolerance in cattle. The present study was aimed at assessing the level of genetic diversity of DRB3 in the exon 2 (BoLA-DRB3.2) region in African, American and Asian cattle breeds. Amplification of exon 2 in 174 cattle revealed 15 haplotypes. The breeds with the highest number of haplotypes were Brangus (10), Sokoto Gudali (10) and Dajal (9), while the lowest number of haplotypes were found in Holstein and Sahiwal with 4 haplotypes each. Medium Joining network obtained from haplotypic data showed that all haplotypes condensed around a centric area and each sequence (except in H-3, H-51 and H-106) representing almost a specific haplotype. The BoLA-DRB3.2 sequence analyses revealed a non-significant higher rate of non-synonymous (dN) compared to synonymous substitutions (dS). The ratio of dN/dS substitution across the breeds were observed to be greater than one suggesting that variation at the antigen-binding sites is under positive selection; thus increasing the chances of these breeds to respond to wide array of pathogenic attacks. An analysis of molecular variance revealed that 94.01 and 5.99% of the genetic variation was attributable to differences within and among populations, respectively. Generally, results obtained suggest that within breed genetic variation across breeds is higher than between breeds. This genetic information will be important for investigating the relationship between BoLADRB3.2 and diseases in various cattle breeds studied with attendant implication on designing breeding programs that will aim at selecting individual cattle that carry resistant alleles.
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Affiliation(s)
- Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA 30149.,Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Adeyemi S Adenaike
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Matthew A Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal (Westville Campus), P/Bag X54001, Durban 4000, South Africa
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Quretaro, Mexico
| | - Jordan Hazzard
- Department of Animal Science, Berry College, Mount Berry, GA 30149
| | - Masroor E Babar
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Ikhide G Imumorin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332.,African Institute for Bioscience Research and Training, Ibadan, Nigeria
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21
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Takeshima SN, Corbi-Botto C, Giovambattista G, Aida Y. Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations. BMC Genet 2018; 19:33. [PMID: 29788904 PMCID: PMC5964877 DOI: 10.1186/s12863-018-0618-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 04/30/2018] [Indexed: 11/17/2022] Open
Abstract
Background Bovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolution typing methods has been poor. Here, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 421 cattle (116 Bolivian Nellore, 110 Bolivian Gir, and 195 Peruvian Nellore-Brahman). Data from 1416 Taurine and Zebu samples were also included in the analysis. Results We identified 46 previously reported alleles and no novel variants. Of note, 1/3 of the alleles were detected only in Zebu cattle. Comparison of the degree of genetic variability at the population and sequence levels with genetic distance in the three above mentioned breeds and nine previously reported breeds revealed that Zebu breeds had a gene diversity score higher than 0.86, a nucleotide diversity score higher than 0.06, and a mean number of pairwise differences greater than 16, being similar to those estimated for other cattle breeds. A neutrality test revealed that only Nellore-Brahman cattle showed the even gene frequency distribution expected under a balanced selection scenario. The FST index and the exact G test showed significant differences across all cattle populations (FST = 0.057; p < 0.001). Neighbor-joining trees and principal component analysis identified two major clusters: one comprising mainly European Taurine breeds and a second comprising Zebu breeds. This is consistent with the historical and geographical origin of these breeds. Some of these differences may be explained by variation of amino acid motifs at antigen-binding sites. Conclusions The results presented herein show that the historical divergence between Taurine and Zebu cattle breeds is a result of origin, selection, and adaptation events, which would explain the observed differences in BoLA-DRB3 gene diversity between the two major bovine types. This allelic information will be important for investigating the relationship between the major histocompatibility complex and disease, and contribute to an ongoing effort to catalog bovine MHC allele frequencies according to breed and location. Electronic supplementary material The online version of this article (10.1186/s12863-018-0618-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shin-Nosuke Takeshima
- Nanomedical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate school of frontier sciences, The University of Tokyo, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Institute of Agriculture, Tokyo University of agriculture and technology, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Food and Nutrition Faculty of Human Life, Jumonji University, 2-1-28 Sugasawa, Niiza, Saitama, 352-8510, Japan
| | - Claudia Corbi-Botto
- IGEVET, CCT LA PLATA CONICET, FCV, UNLP, B1900AVW, CC 296, La Plata, Argentina
| | | | - Yoko Aida
- Nanomedical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Graduate school of frontier sciences, The University of Tokyo, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Institute of Agriculture, Tokyo University of agriculture and technology, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Department of global agricultural science, The University of Tokyo, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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22
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Identification of an Atypical Enzootic Bovine Leukosis in Japan by Using a Novel Classification of Bovine Leukemia Based on Immunophenotypic Analysis. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00067-17. [PMID: 28659325 DOI: 10.1128/cvi.00067-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022]
Abstract
Bovine leukemia is classified into two types: enzootic bovine leukosis (EBL) and sporadic bovine leukosis (SBL). EBL is caused by infection with bovine leukemia virus (BLV), which induces persistent lymphocytosis and B-cell lymphoma in cattle after a long latent period. Although it has been demonstrated that BLV-associated lymphoma occurs predominantly in adult cattle of >3 to 5 years, suspicious cases of EBL onset in juvenile cattle were recently reported in Japan. To investigate the current status of bovine leukemia in Japan, we performed immunophenotypic analysis of samples from 50 cattle that were clinically diagnosed as having bovine leukemia. We classified the samples into five groups on the basis of the analysis and found two different types of EBL: classic EBL (cEBL), which has the familiar phenotype commonly known as EBL, and polyclonal EBL (pEBL), which exhibited neoplastic proliferation of polyclonal B cells. Moreover, there were several atypical EBL cases even in cEBL, including an early onset of EBL in juvenile cattle. A comparison of the cell marker expressions among cEBL, pEBL, and B-cell-type SBL (B-SBL) revealed characteristic patterns in B-cell leukemia, and these patterns could be clearly differentiated from those of healthy phenotypes, whereas it was difficult to discriminate between cEBL, pEBL, and B-SBL only by the expression patterns of cell markers. This study identified novel characteristics of bovine leukemia that should contribute to a better understanding of the mechanism underlying tumor development in BLV infection.
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23
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Carignano HA, Beribe MJ, Caffaro ME, Amadio A, Nani JP, Gutierrez G, Alvarez I, Trono K, Miretti MM, Poli MA. BOLA-DRB3gene polymorphisms influence bovine leukaemia virus infection levels in Holstein and Holstein × Jersey crossbreed dairy cattle. Anim Genet 2017; 48:420-430. [DOI: 10.1111/age.12566] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2017] [Indexed: 12/11/2022]
Affiliation(s)
- H. A. Carignano
- Instituto de Genética; Centro de Investigaciones en Ciencias Veterinarias y Agronómicas - INTA; Hurlingham B1686 Argentina
| | - M. J. Beribe
- Estación Experimental Agropecuaria Pergamino - INTA; Pergamino B2700 Argentina
| | - M. E. Caffaro
- Instituto de Genética; Centro de Investigaciones en Ciencias Veterinarias y Agronómicas - INTA; Hurlingham B1686 Argentina
| | - A. Amadio
- Estación Experimental Agropecuaria Rafaela - INTA; Rafaela S2300 Santa Fe Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Ciudad Autónoma de Buenos Aires C1033AAJ Argentina
| | - J. P. Nani
- Estación Experimental Agropecuaria Rafaela - INTA; Rafaela S2300 Santa Fe Argentina
| | - G. Gutierrez
- Instituto de Virología; Centro de Investigaciones en Ciencias Veterinarias y Agronómicas - INTA; Hurlingham B1686 Argentina
| | - I. Alvarez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Ciudad Autónoma de Buenos Aires C1033AAJ Argentina
- Instituto de Virología; Centro de Investigaciones en Ciencias Veterinarias y Agronómicas - INTA; Hurlingham B1686 Argentina
| | - K. Trono
- Instituto de Virología; Centro de Investigaciones en Ciencias Veterinarias y Agronómicas - INTA; Hurlingham B1686 Argentina
| | - M. M. Miretti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Ciudad Autónoma de Buenos Aires C1033AAJ Argentina
- Grupo de Investigación en Genética Aplicada; Instituto de Biología Subtropical (GIGA - IBS); Universidad Nacional de Misiones; Posadas N3300 Argentina
| | - M. A. Poli
- Instituto de Genética; Centro de Investigaciones en Ciencias Veterinarias y Agronómicas - INTA; Hurlingham B1686 Argentina
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24
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Bai X, Zheng Z, Liu B, Ji X, Bai Y, Zhang W. Whole blood transcriptional profiling comparison between different milk yield of Chinese Holstein cows using RNA-seq data. BMC Genomics 2016; 17 Suppl 7:512. [PMID: 27557137 PMCID: PMC5001199 DOI: 10.1186/s12864-016-2901-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The objective of this research was to investigate the variation of gene expression in the blood transcriptome profile of Chinese Holstein cows associated to the milk yield traits. Results We used RNA-seq to generate the bovine transcriptome from the blood of 23 lactating Chinese Holstein cows with extremely high and low milk yield. A total of 100 differentially expressed genes (DEGs) (p < 0.05, FDR < 0.05) were revealed between the high and low groups. Gene ontology (GO) analysis demonstrated that the 100 DEGs were enriched in specific biological processes with regard to defense response, immune response, inflammatory response, icosanoid metabolic process, and fatty acid metabolic process (p < 0.05). The KEGG pathway analysis with 100 DEGs revealed that the most statistically-significant metabolic pathway was related with Toll-like receptor signaling pathway (p < 0.05). The expression level of four selected DEGs was analyzed by qRT-PCR, and the results indicated that the expression patterns were consistent with the deep sequencing results by RNA-Seq. Furthermore, alternative splicing analysis of 100 DEGs demonstrated that there were different splicing pattern between high and low yielders. The alternative 3’ splicing site was the major splicing pattern detected in high yielders. However, in low yielders the major type was exon skipping. Conclusion This study provides a non-invasive method to identify the DEGs in cattle blood using RNA-seq for milk yield. The revealed 100 DEGs between Holstein cows with extremely high and low milk yield, and immunological pathway are likely involved in milk yield trait. Finally, this study allowed us to explore associations between immune traits and production traits related to milk production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2901-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhuqing Zheng
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.,Institute of ATCG Nei Mongol Bio-Information, Hohhot, 010020, China
| | - Bin Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.,Institute of ATCG Nei Mongol Bio-Information, Hohhot, 010020, China.,Nei Mongol BioNew Technology Co.Ltd, Hohhot, 010018, China
| | - Xiaoyang Ji
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.,Institute of ATCG Nei Mongol Bio-Information, Hohhot, 010020, China
| | - Yongsheng Bai
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, U.S.A..
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China. .,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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25
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Takeshima SN, Giovambattista G, Okimoto N, Matsumoto Y, Rogberg-Muñoz A, Acosta TJ, Onuma M, Aida Y. Characterization of bovine MHC class II DRB3 diversity in South American Holstein cattle populations. ACTA ACUST UNITED AC 2015; 86:419-30. [PMID: 26514650 DOI: 10.1111/tan.12692] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/14/2015] [Accepted: 10/06/2015] [Indexed: 12/11/2022]
Abstract
Holstein cattle dominate the global milk production industry because of their outstanding milk production, however, this breed is susceptible to tropical endemic pathogens and suffers from heat stress and thus fewer Holstein populations are raised in tropical areas. The bovine major histocompatibility complex (BoLA)-DRB3 class II gene is used as a marker for disease and immunological traits, and its polymorphism has been studied extensively in Holstein cattle from temperate and cold regions. We studied the genetic diversity of the BoLA-DRB3 gene in South American Holstein populations to determine whether tropical populations have diverged from those bred in temperate and cold regions by selection and/or crossbreeding with local native breeds. We specifically studied Exon 2 of this gene from 855 South American Holstein individuals by a polymerase chain reaction (PCR) sequence-based typing method. We found a high degree of gene diversity at the allelic (Na > 20 and He > 0.87) and molecular (π > 0.080) levels, but a low degree of population structure (FST = 0.009215). A principal components analysis and tree showed that the Bolivian subtropical population had the largest genetic divergence compared with Holsteins bred in temperate or cold regions, and that this population was closely related to Bolivian Creole cattle. Our results suggest that Holstein genetic divergence can be explained by selection and/or gene introgression from local germplasms. This is the first examination of BoLA-DRB3 in Holsteins adapted to tropical environments, and contributes to an ongoing effort to catalog bovine MHC allele frequencies by breed and location.
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Affiliation(s)
- S-N Takeshima
- Viral Infectious Diseases Unit, RIKEN, Saitama, Japan
| | | | - N Okimoto
- Laboratory for Computational Molecular Design, Computational Biology Research Core, Quantitative Biology Center (QBiC), RIKEN, Hyogo, Japan
| | - Y Matsumoto
- Viral Infectious Diseases Unit, RIKEN, Saitama, Japan
| | - A Rogberg-Muñoz
- IGEVET, CCT LA PLATA CONICET, FCV, UNLP, La Plata, Argentina
| | - T J Acosta
- Field Center of Animal Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - M Onuma
- Viral Infectious Diseases Unit, RIKEN, Saitama, Japan
| | - Y Aida
- Viral Infectious Diseases Unit, RIKEN, Saitama, Japan
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26
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Kułaj D, Pokorska J, Ormian M, Dusza M. Short Communication: New alleles at the BoLA-DQA1 locus in Holstein–Fresian cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2015. [DOI: 10.4141/cjas-2014-147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Kułajaj, D., Pokorska, J., Ormian, M. and Dusza, M. 2015. Short Communication: New alleles at the BoLA-DQA1 locus in Holstein Fresian cattle. Can. J. Anim. Sci. 95: 161–164. The aim of the study was to analyze genetic polymorphism at locus BoLA-DQA1 in Polish Holstein-Friesian cattle, using next generation sequencing technology (Miseq sequencer – Illumina). In the studied cattle population we identified 14 alleles, of which three were determined for the first time (BoLA-DQA1*0106, BoLA-DQA1*3201, BoLA-DQA1*3301). The frequencies of these alleles were respectively: 0.0423, 0.0282, 0.0282. At locus BoLA-DQA1 the highest frequency was found for the BoLA-DQA1*10011 and BoLA-DQA1*0101 alleles and their frequencies were respectively: 0.3592 and 0.2606. The frequencies of other alleles identified in the studied population ranged from 0.0070 to 0.0704. The results obtained in this study indicate that the BoLA-DQA1 locus is highly polymorphic and new alleles are still identifiable.
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Affiliation(s)
- Dominika Kułaj
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - Joanna Pokorska
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - Marian Ormian
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - Magdalena Dusza
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
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27
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Wilson AB, Whittington CM, Bahr A. High intralocus variability and interlocus recombination promote immunological diversity in a minimal major histocompatibility system. BMC Evol Biol 2014; 14:273. [PMID: 25526691 PMCID: PMC4302578 DOI: 10.1186/s12862-014-0273-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/12/2014] [Indexed: 12/03/2022] Open
Abstract
Background The genes of the major histocompatibility complex (MHC/MH) have attracted considerable scientific interest due to their exceptional levels of variability and important function as part of the adaptive immune system. Despite a large number of studies on MH class II diversity of both model and non-model organisms, most research has focused on patterns of genetic variability at individual loci, failing to capture the functional diversity of the biologically active dimeric molecule. Here, we take a systematic approach to the study of MH variation, analyzing patterns of genetic variation at MH class IIα and IIβ loci of the seahorse, which together form the immunologically active peptide binding cleft of the MH class II molecule. Results The seahorse carries a minimal class II system, consisting of single copies of both MH class IIα and IIβ, which are physically linked and inherited in a Mendelian fashion. Both genes are ubiquitously expressed and detectible in the brood pouch of male seahorses throughout pregnancy. Genetic variability of the two genes is high, dominated by non-synonymous variation concentrated in their peptide-binding regions. Coding variation outside these regions is negligible, a pattern thought to be driven by intra- and interlocus recombination. Despite the tight physical linkage of MH IIα and IIβ loci, recombination has produced novel composite alleles, increasing functional diversity at sites responsible for antigen recognition. Conclusions Antigen recognition by the adaptive immune system of the seahorse is enhanced by high variability at both MH class IIα and IIβ loci. Strong positive selection on sites involved in pathogen recognition, coupled with high levels of intra- and interlocus recombination, produce a patchwork pattern of genetic variation driven by genetic hitchhiking. Studies focusing on variation at individual MH loci may unintentionally overlook an important component of ecologically relevant variation.
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Affiliation(s)
- Anthony B Wilson
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Department of Biology, Brooklyn College and The Graduate Center, City University of New York, 2900 Bedford Avenue, Brooklyn, New York, 11210, USA. .,Department of Biology, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York, 11210, USA.
| | - Camilla M Whittington
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,School of Biological Sciences, University of Sydney, Heydon-Laurence Building A08, Sydney, NSW, 2006, Australia.
| | - Angela Bahr
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
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28
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Takeshima SN, Miyasaka T, Matsumoto Y, Xue G, Diaz VDLB, Rogberg-Muñoz A, Giovambattista G, Ortiz M, Oltra J, Kanemaki M, Onuma M, Aida Y. Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class II BoLA-DRB3 allele. ACTA ACUST UNITED AC 2014; 85:35-44. [PMID: 25430590 DOI: 10.1111/tan.12481] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 10/14/2014] [Accepted: 10/28/2014] [Indexed: 11/30/2022]
Abstract
Bovine leukocyte antigens (BoLAs) are used extensively as markers for bovine disease and immunological traits. In this study, we estimated BoLA-DRB3 allele frequencies using 888 cattle from 10 groups, including seven cattle breeds and three crossbreeds: 99 Red Angus, 100 Black Angus, 81 Chilean Wagyu, 49 Hereford, 95 Hereford × Angus, 71 Hereford × Jersey, 20 Hereford × Overo Colorado, 113 Holstein, 136 Overo Colorado, and 124 Overo Negro cattle. Forty-six BoLA-DRB3 alleles were identified, and each group had between 12 and 29 different BoLA-DRB3 alleles. Overo Negro had the highest number of alleles (29); this breed is considered in Chile to be an 'Old type' European Holstein Friesian descendant. By contrast, we detected 21 alleles in Holstein cattle, which are considered to be a 'Present type' Holstein Friesian cattle. Chilean cattle groups and four Japanese breeds were compared by neighbor-joining trees and a principal component analysis (PCA). The phylogenetic tree showed that Red Angus and Black Angus cattle were in the same clade, crossbreeds were closely related to their parent breeds, and Holstein cattle from Chile were closely related to Holstein cattle in Japan. Overall, the tree provided a thorough description of breed history. It also showed that the Overo Negro breed was closely related to the Holstein breed, consistent with historical data indicating that Overo Negro is an 'Old type' Holstein Friesian cattle. This allelic information will be important for investigating the relationship between major histocompatibility complex (MHC) and disease.
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Affiliation(s)
- S-N Takeshima
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
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Goodswen SJ, Kennedy PJ, Ellis JT. Discovering a vaccine against neosporosis using computers: is it feasible? Trends Parasitol 2014; 30:401-11. [PMID: 25028089 DOI: 10.1016/j.pt.2014.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 12/31/2022]
Abstract
A vaccine is urgently needed to prevent cattle neosporosis. This infectious disease is caused by the parasite Neospora caninum, a complex biological system with multifaceted life cycles. An in silico vaccine discovery approach attempts to transform digital abstractions of this system into adequate knowledge to predict candidates. Researchers need current information to implement such an approach, such as understanding evasion mechanisms of the immune system, type of immune response to elicit, availability of data and prediction programs, and statistical models to analyze predictions. Taken together, an in silico approach involves assembly of an intricate jigsaw of interdisciplinary and interdependent knowledge. In this review, we focus on the approach influencing vaccine development against Neospora caninum, which can be generalized to other pathogenic apicomplexans.
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Affiliation(s)
- Stephen J Goodswen
- School of Medical and Molecular Biosciences at the University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
| | - Paul J Kennedy
- School of Software, Faculty of Engineering and Information Technology and the Centre for Quantum Computation and Intelligent Systems at the University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
| | - John T Ellis
- School of Medical and Molecular Biosciences at the University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia.
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The great diversity of major histocompatibility complex class II genes in Philippine native cattle. Meta Gene 2014; 2:176-90. [PMID: 25606401 PMCID: PMC4287811 DOI: 10.1016/j.mgene.2013.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/28/2013] [Accepted: 12/04/2013] [Indexed: 11/21/2022] Open
Abstract
Bovine leukocyte antigens (BoLA) are extensively used as markers for bovine disease and immunological traits. However, none of the BoLA genes in Southeast Asian breeds have been characterized by polymerase chain reaction (PCR)-sequence-based typing (SBT). Therefore, we sequenced exon 2 of the BoLA class II DRB3 gene from 1120 individual cows belonging to the Holstein, Sahiwal, Simbrah, Jersey, Brahman, and Philippine native breeds using PCR-SBT. Several cross-breeds were also examined. BoLA-DRB3 PCR-SBT identified 78 previously reported alleles and five novel alleles. The number of BoLA-DRB3 alleles identified in each breed from the Philippines was higher (71 in Philippine native cattle, 58 in Brahman, 46 in Holstein × Sahiwal, and 57 in Philippine native × Brahman) than that identified in breeds from other countries (e.g., 23 alleles in Japanese Black and 35 in Bolivian Yacumeño cattle). A phylogenetic tree based on the DA distance calculated from the BoLA-DRB3 allele frequency showed that Philippine native cattle from different Philippine islands are closely related, and all of them are closely similar to Philippine Brahman cattle but not to native Japanese and Latin American breeds. Furthermore, the BoLA-DRB3 allele frequency in Philippine native cattle from Luzon Island, located in the Northern Philippines was different from that in cattle from Iloilo, Bohol, and Leyte Islands, which are located in the Southern Philippines. Therefore, we conclude that Philippine native cattle can be divided into two populations, North and South areas. Moreover, a neutrality test revealed that Philippine native cattle from Leyte showed significantly greater genetic diversity, which may be maintained by balancing selection. This study shows that Asian breeds have high levels of BoLA-DRB3 polymorphism. This finding, especially the identification of five novel BoLA-DRB3 alleles, will be helpful for future SBT studies of BoLA-DRB3 alleles in East Asian cattle.
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Giovambattista G, Takeshima SN, Ripoli MV, Matsumoto Y, Franco LAA, Saito H, Onuma M, Aida Y. Characterization of bovine MHC DRB3 diversity in Latin American Creole cattle breeds. Gene 2013; 519:150-8. [DOI: 10.1016/j.gene.2013.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/30/2012] [Accepted: 01/04/2013] [Indexed: 01/23/2023]
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Gowane GR, Sharma AK, Sankar M, Narayanan K, Das B, Subramaniam S, Pattnaik B. Association of BoLA DRB3 alleles with variability in immune response among the crossbred cattle vaccinated for foot-and-mouth disease (FMD). Res Vet Sci 2013; 95:156-63. [PMID: 23541924 DOI: 10.1016/j.rvsc.2013.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 02/23/2013] [Accepted: 03/03/2013] [Indexed: 12/20/2022]
Abstract
Polymorphism of bovine leukocyte antigen (BoLA) DRB3 gene is being intensively investigated for potential association with economically important diseases of cattle. Accordingly, we investigated the association of DRB3 Exon 2 polymorphism as evidenced by the variation in the binding pockets with variability in immune response to inactivated trivalent (O, A and Asia1) foot and mouth disease virus (FMDV) vaccine in a closed population of crossbred cattle. Antibody titer of ≥ 1.8 was set as the cut off value to distinguish the protected (≥ 1.8) and unprotected (<1.8) animals. Eleven different alleles of over 3% frequency were detected in the population. We found that DRB3 alleles 0201, 0801 and 1501 always ranked high for protective immune response whereas alleles 0701, 1103 and 1101 consistently ranked low for unprotected immune response for all the three serotypes. Rank correlation of DRB3 alleles among the three serotypes was positive, high in magnitude and statistically significant (P<0.05). Logistic regression analysis revealed that odds of protection from the vaccine were highest for all the three serotypes if allele (∗)1501 was present and strengthened the results of allele ranking. Predicted amino acid substitution in the peptide binding pockets revealed that all the important sites had high Wu-Kabat index. Similarly, specific residues in pockets were crucial for immune response to FMD vaccine. There were specific substitutions in un-protected alleles such as absence of acidic amino acids substituted by basic amino acid at β71, presence of non-polar cysteine or basic histidine at β30 and presence of polar tyrosine at β37. From the observations, we hypothesize that the substitutions lead to unique conformational changes in the protein products of the studied alleles that would associate with the protective or unprotective antibody response to FMDV vaccine. The knowledge has potential implications in future selection programs if integrated with the complete BoLA haplotype details and production traits of the herd.
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Affiliation(s)
- G R Gowane
- Central Sheep & Wool Research Institute, Avikanagar via Jaipur, Rajasthan 304 501, India.
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Heatley SL, Pietra G, Lin J, Widjaja JML, Harpur CM, Lester S, Rossjohn J, Szer J, Schwarer A, Bradstock K, Bardy PG, Mingari MC, Moretta L, Sullivan LC, Brooks AG. Polymorphism in human cytomegalovirus UL40 impacts on recognition of human leukocyte antigen-E (HLA-E) by natural killer cells. J Biol Chem 2013; 288:8679-8690. [PMID: 23335510 PMCID: PMC3605686 DOI: 10.1074/jbc.m112.409672] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 12/20/2012] [Indexed: 11/06/2022] Open
Abstract
Natural killer (NK) cell recognition of the nonclassical human leukocyte antigen (HLA) molecule HLA-E is dependent on the presentation of a nonamer peptide derived from the leader sequence of other HLA molecules to CD94-NKG2 receptors. However, human cytomegalovirus can manipulate this central innate interaction through the provision of a "mimic" of the HLA-encoded peptide derived from the immunomodulatory glycoprotein UL40. Here, we analyzed UL40 sequences isolated from 32 hematopoietic stem cell transplantation recipients experiencing cytomegalovirus reactivation. The UL40 protein showed a "polymorphic hot spot" within the region that encodes the HLA leader sequence mimic. Although all sequences that were identical to those encoded within HLA-I genes permitted the interaction between HLA-E and CD94-NKG2 receptors, other UL40 polymorphisms reduced the affinity of the interaction between HLA-E and CD94-NKG2 receptors. Furthermore, functional studies using NK cell clones expressing either the inhibitory receptor CD94-NKG2A or the activating receptor CD94-NKG2C identified UL40-encoded peptides that were capable of inhibiting target cell lysis via interaction with CD94-NKG2A, yet had little capacity to activate NK cells through CD94-NKG2C. The data suggest that UL40 polymorphisms may aid evasion of NK cell immunosurveillance by modulating the affinity of the interaction with CD94-NKG2 receptors.
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Affiliation(s)
- Susan L Heatley
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gabriella Pietra
- Department of Experimental Medicine, University of Genova, Genova 16132, Italy
| | - Jie Lin
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jacqueline M L Widjaja
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christopher M Harpur
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sue Lester
- Department of Rheumatology, The Queen Elizabeth Hospital, South Australia 5011, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Jeff Szer
- Department of Clinical Haematology and Bone Marrow Transplant Service, Royal Melbourne Hospital, Victoria 3050, Australia
| | - Anthony Schwarer
- Malignant Haematology and Stem Cell Transplantation Service, The Alfred Hospital, Victoria 3004, Australia
| | - Kenneth Bradstock
- Department of Haematology, Westmead Hospital, New South Wales 2145, Australia
| | - Peter G Bardy
- Director of Cancer Services, Royal Adelaide Hospital, South Australia 5000, Australia
| | - Maria Cristina Mingari
- Department of Experimental Medicine, University of Genova, Genova 16132, Italy; IRCCS AOU San Martino-IST, Genova 16132, Italy
| | | | - Lucy C Sullivan
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia.
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Miyasaka T, Takeshima SN, Jimba M, Matsumoto Y, Kobayashi N, Matsuhashi T, Sentsui H, Aida Y. Identification of bovine leukocyte antigen class II haplotypes associated with variations in bovine leukemia virus proviral load in Japanese Black cattle. ACTA ACUST UNITED AC 2012; 81:72-82. [DOI: 10.1111/tan.12041] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 09/29/2012] [Accepted: 11/09/2012] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Y. Matsumoto
- Viral Infectious Diseases Unit; RIKEN; Wako; Saitama; Japan
| | - N. Kobayashi
- Gifu Prefectural Livestock Research Institute; Gifu; Japan
| | - T. Matsuhashi
- Gifu Prefectural Livestock Research Institute; Gifu; Japan
| | - H. Sentsui
- School of Veterinary Medicine; Nihon University; Fujisawa; Kanagawa; Japan
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Larruskain A, Minguijón E, Garcia-Etxebarria K, Arostegui I, Moreno B, Juste RA, Jugo BM. Amino acid signatures in the Ovar-DRB1 peptide-binding pockets are associated with Ovine Pulmonary Adenocarcinoma susceptibility/resistance. Biochem Biophys Res Commun 2012; 428:463-8. [DOI: 10.1016/j.bbrc.2012.10.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 10/24/2012] [Indexed: 10/27/2022]
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Morse K, Norimine J, Hope JC, Brown WC. Breadth of the CD4+ T cell response to Anaplasma marginale VirB9-1, VirB9-2 and VirB10 and MHC class II DR and DQ restriction elements. Immunogenetics 2012; 64:507-23. [PMID: 22361828 PMCID: PMC3372765 DOI: 10.1007/s00251-012-0606-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/04/2012] [Indexed: 01/11/2023]
Abstract
MHC class II molecules influence antigen-specific CD4+ T lymphocyte responses primed by immunization and infection. CD4+ T cell responses are important for controlling infection by many bacterial pathogens including Anaplasma marginale and are observed in cattle immunized with the protective A. marginale outer membrane (OM) vaccine. Immunogenic proteins that comprise the protective OM vaccine include type IV secretion system (T4SS) proteins VirB9-1, VirB9-2 and VirB10, candidates for inclusion in a multiepitope vaccine. Our goal was to determine the breadth of the VirB9-1, VirB9-2 and VirB10 T cell response and MHC class II restriction elements in six cattle with different MHC class II haplotypes defined by DRB3, DQA and DQB allele combinations for each animal. Overlapping peptides spanning each T4SS protein were tested in T cell proliferation assays with autologous antigen-presenting cells (APC) and artificial APC expressing combinations of bovine DR and DQ molecules. Twenty immunostimulatory peptides were identified; three representing two or more epitopes in VirB9-1, ten representing eight or more epitopes in VirB9-2 and seven representing seven or more epitopes in VirB10. Of the eight DRA/DRB3 molecules, four presented 15 peptides, which was biased as DRA/DRB3*1201 presented ten and DRA/DRB3*1101 presented four peptides. Four DQA/DQB molecules composed of two intrahaplotype and two interhaplotype pairs presented seven peptides, of which five were uniquely presented by DQ molecules. In addition, three functional mixed isotype (DQA/DRB3) restriction elements were identified. The immunogenicity and broad MHC class II presentation of multiple VirB9-1, VirB9-2 and VirB10 peptide epitopes justify their testing as a multiepitope vaccine against A. marginale.
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Affiliation(s)
- Kaitlyn Morse
- Program in Vector-Borne Diseases, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman WA 99164-7040
| | - Junzo Norimine
- Program in Vector-Borne Diseases, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman WA 99164-7040
| | - Jayne C. Hope
- Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Wendy C. Brown
- Program in Vector-Borne Diseases, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman WA 99164-7040
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Behl JD, Verma NK, Tyagi N, Mishra P, Behl R, Joshi BK. The major histocompatibility complex in bovines: a review. ISRN VETERINARY SCIENCE 2012; 2012:872710. [PMID: 23738132 PMCID: PMC3658703 DOI: 10.5402/2012/872710] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 03/29/2012] [Indexed: 11/23/2022]
Abstract
Productivity in dairy cattle and buffaloes depends on the genetic factors governing the production of milk and milk constituents as well as genetic factors controlling disease resistance or susceptibility. The immune system is the adaptive defense system that has evolved in vertebrates to protect them from invading pathogens and also carcinomas. It is remarkable in the sense that it is able to generate an enormous variety of cells and biomolecules which interact with each other in numerous ways to form a complex network that helps to recognize, counteract, and eliminate the apparently limitless number of foreign invading pathogens/molecules. The major histocompatibility complex which is found to occur in all mammalian species plays a central role in the development of the immune system. It is an important candidate gene involved in susceptibility/resistance to various diseases. It is associated with intercellular recognition and with self/nonself discrimination. It plays major role in determining whether transplanted tissue will be accepted as self or rejected as foreign.
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Affiliation(s)
- Jyotsna Dhingra Behl
- Animal Genetics Division, National Bureau of Animal Genetics Resources, P.O. Box 129, GT Bypass Road, Haryana, Karnal 132001, India
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Miyasaka T, Takeshima SN, Sentsui H, Aida Y. Identification and diversity of bovine major histocompatibility complex class II haplotypes in Japanese Black and Holstein cattle in Japan. J Dairy Sci 2012; 95:420-31. [PMID: 22192221 DOI: 10.3168/jds.2011-4621] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022]
Abstract
Bovine leukocyte antigen (BoLA), the major histocompatibility complex of cattle, is one of the most polymorphic gene clusters. We genotyped a population of 109 Japanese Black and 39 Holstein cattle to analyze their BoLA class II haplotypes, BoLA-DRB3 locus, 5 BoLA-DQA loci, and 5 BoLA-DQB loci. We identified 26 previously reported DRB3 alleles, 22 previously reported and 3 new DQA alleles, and 24 previously reported and 6 new DQB alleles. A dendrogram was constructed based on the predicted amino acid sequences of the α1 or β1 domains encoded by BoLA-DQA or -DQB alleles, which revealed that DQA alleles were clustered into 5 loci, whereas DQB alleles could not be clearly assigned to specific DQB loci. The BoLA-DRB3-DQA-DQB haplotypes were sorted by sequential analytical processes, and 42 distinct haplotypes, including 11 previously published haplotypes and 31 novel haplotypes, were defined. Strong linkage disequilibrium was present in the BoLA genes. We also compared DRB3-DQA1 haplotype frequencies between 507 Japanese Black and 143 Holstein cattle. Thirty-nine DRB3-DQA1 haplotypes were identified, including 29 haplotypes from Japanese Black and 22 haplotypes from Holstein cattle. The majority of the haplotypes could be identified in both breeds, although several haplotypes were identified in only a single breed. This is the first report presenting a detailed study of the BoLA class II haplotype in Japanese Black and Holstein cattle in Japan.
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Affiliation(s)
- T Miyasaka
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
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