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Agina OA, Shaari MR, Isa NMM, Ajat M, Zamri-Saad M, Hamzah H. Identification of novel bovine leukocyte antigen alleles and association of BoLA-DRB3.2*020:02:01 with resistance to Theileria orientalis infection in crossbred Kedah-Kelantan cattle: a pilot study. Trop Anim Health Prod 2024; 56:277. [PMID: 39316238 DOI: 10.1007/s11250-024-04138-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024]
Abstract
The bovine leukocyte antigen (BoLA) gene is a significant genetic part of the immune system and has been used as a disease marker in cattle. In this study, we detected Theileria orientalis, T. sinensis, Anaplasma marginale, Anaplasma platys, Candidatus Mycoplasma haemobos and Trypanosoma evansi by PCR amplification and sequencing of the amplicons. The allelic association of the BoLA-DRB3.2 gene with blood pathogen disease resistance and susceptibility in 87 Kedah-Kelantan x Brahman (KKB) and 38 Bali cattle was determined by Fisher's exact test and Cochran Mantel Haenszel (CMH) correction test. Sequence-based typing of the BoLA-DRB3.2 gene identified 43 alleles (27 previously reported alleles and 16 novel alleles) across the two cattle breeds. Alignment analysis of the 16 novel alleles revealed 90.7-95.8% and 85-92% nucleotide and amino acid identities, with the reference allele, BoLA-DRB3*016:01 cDNA clone NR-1. BoLA-DRB3*009:02 (25.6%) and BoLA-DRB3*036:01 (36%) were the most frequent alleles in KKB and Bali cattle, respectively. In KKB cattle, BoLA-DRB3*020:02:01 was significantly associated with resistance to T. orientalis whereas *007:01 and *009:02 were significantly associated with resistance to C. Mycoplasma haemobos. Also, DRB3*017:01 was associated with susceptibility to T. orientalis in KKB cattle. In the Bali cattle, BoLA-DRB3*015:01 was found to be a genetic marker of susceptibility to C. Mycoplasma haemobos infection. Therefore, this study identified BoLA-DRB3.2 alleles associated with resistance and susceptibility to T. orientalis infection in KKB cattle and susceptibility to C. Mycoplasma haemobos infection in Bali cattle for the first time. Therefore, this study suggests that these BoLA-DRB3 resistance alleles could be used as candidate markers for selection, whereas susceptibility alleles could be used as candidate markers for culling in the beef industry.
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Affiliation(s)
- Onyinyechukwu Ada Agina
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
| | - Mohd Rosly Shaari
- Animal Science Research Centre, Malaysian Agricultural Research and Developmental Institute, Serdang Selangor 43400, Headquarters, Malaysia
| | - Nur Mahiza Md Isa
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mokrish Ajat
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Zamri-Saad
- Research Centre for Ruminant Diseases, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Hazilawati Hamzah
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Bishnoi S, Jyotsana B, Kumar V, Prakash V, Ranjan R, Narnaware SD, Pannu U. Toll like receptor 4 (TLR4) gene polymorphism and its association with somatic cell score and milk production traits in Indian dromedary camels. Anim Biotechnol 2024; 35:2331642. [PMID: 38520296 DOI: 10.1080/10495398.2024.2331642] [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: 03/25/2024]
Abstract
Our study aimed to explore the genetic variation in the Toll-like receptor 4 (TLR4) gene and establish its association with somatic cell score (SCS) and milk production traits in four Indian camel breeds namely Bikaneri, Kachchhi, Jaisalmeri and Mewari. TLR4 gene fragment of 573 bp spanning 5' UTR, exon-1 and partial intron-1 region was amplified and genotyped using the PCR-sequence based typing method. Only one SNP located at position C472T was identified. Genotyping revealed two alleles (C and T) and three genotypes: CC, CT and TT. The genotype frequencies for CC, CT and TT were 0.116, 0.326 and 0.558 and allele frequencies for C and T alleles were 0.279 and 0.721, respectively. Association study inferred that the effect of genotype on SCS, lactation yield (LY) and peak yield (PY) was non-significant however heterozygote (CT) genotypes recorded lower SCS and higher LY and PY. It can be concluded that the TLR4 gene possesses limited genetic variation, depicting polymorphism at a single locus in Indian camel breeds with a predominance of the TT genotype. The association study indicated that heterozygote animals possess better udder health and production performance, the statistical significance of which needs to be established using a large data set.
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Affiliation(s)
- Seema Bishnoi
- CVAS, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan, India
| | - Basanti Jyotsana
- ICAR - National Research Centre on Camel, Bikaner, Rajasthan, India
| | - Virendra Kumar
- CVAS, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan, India
| | - Ved Prakash
- ICAR - National Research Centre on Camel, Bikaner, Rajasthan, India
| | - Rakesh Ranjan
- ICAR - National Research Centre on Camel, Bikaner, Rajasthan, India
| | | | - Urmila Pannu
- CVAS, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan, India
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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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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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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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Lo CW, Takeshima SN, Wada S, Matsumoto Y, Aida Y. Bovine major histocompatibility complex (BoLA) heterozygote advantage against the outcome of bovine leukemia virus infection. HLA 2021; 98:132-139. [PMID: 33896123 DOI: 10.1111/tan.14285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/31/2022]
Abstract
Bovine leukemia virus (BLV) causes enzootic bovine leucosis. Host genetic heterozygosity at the major histocompatibility complex can enhance the ability to combat infectious diseases. However, heterozygote advantage is loci specific and depends on disease type. Bovine leukocyte antigen (BoLA)-DRB3 polymorphisms are related with BLV-infection outcome; however, whether BoLA-DRB3 heterozygotes have an advantage against BLV-induced lymphoma and proviral load (PVL) remains unclear. By analyzing 1567 BLV-infected individuals, we found that BoLA-DRB3 heterozygous status was significantly associated with lymphoma resistance irrespective of cattle breeds (p < 0.0001). Similarly, decreased PVL was observed in BoLA-DRB3 heterozygotes (p = 0.0407 for Holstein cows; p = 0.0889 for Japanese Black cattle). Our report provides first evidence of BoLA-DRB3 heterozygote advantage against BLV infection outcome.
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Affiliation(s)
- Chieh-Wen Lo
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Global Animal Resource Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shin-Nosuke Takeshima
- Department of Food and Nutrition, Jumonji University, Saitama, Japan.,Viral Infectious Diseases Unit, RIKEN, Saitama, Japan
| | - Satoshi Wada
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako, Japan
| | - Yasunobu Matsumoto
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Global Animal Resource Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoko Aida
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Global Animal Resource Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Viral Infectious Diseases Unit, RIKEN, Saitama, Japan
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Fisch A, Reynisson B, Benedictus L, Nicastri A, Vasoya D, Morrison I, Buus S, Ferreira BR, Kinney Ferreira de Miranda Santos I, Ternette N, Connelley T, Nielsen M. Integral Use of Immunopeptidomics and Immunoinformatics for the Characterization of Antigen Presentation and Rational Identification of BoLA-DR-Presented Peptides and Epitopes. THE JOURNAL OF IMMUNOLOGY 2021; 206:2489-2497. [PMID: 33789985 DOI: 10.4049/jimmunol.2001409] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 02/04/2023]
Abstract
MHC peptide binding and presentation is the most selective event defining the landscape of T cell epitopes. Consequently, understanding the diversity of MHC alleles in a given population and the parameters that define the set of ligands that can be bound and presented by each of these alleles (the immunopeptidome) has an enormous impact on our capacity to predict and manipulate the potential of protein Ags to elicit functional T cell responses. Liquid chromatography-mass spectrometry analysis of MHC-eluted ligand data has proven to be a powerful technique for identifying such peptidomes, and methods integrating such data for prediction of Ag presentation have reached a high level of accuracy for both MHC class I and class II. In this study, we demonstrate how these techniques and prediction methods can be readily extended to the bovine leukocyte Ag class II DR locus (BoLA-DR). BoLA-DR binding motifs were characterized by eluted ligand data derived from bovine cell lines expressing a range of DRB3 alleles prevalent in Holstein-Friesian populations. The model generated (NetBoLAIIpan, available as a Web server at www.cbs.dtu.dk/services/NetBoLAIIpan) was shown to have unprecedented predictive power to identify known BoLA-DR-restricted CD4 epitopes. In summary, the results demonstrate the power of an integrated approach combining advanced mass spectrometry peptidomics with immunoinformatics for characterization of the BoLA-DR Ag presentation system and provide a prediction tool that can be used to assist in rational evaluation and selection of bovine CD4 T cell epitopes.
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Affiliation(s)
- Andressa Fisch
- Ribeirão Preto College of Nursing, University of São Paulo, Av Bandeirantes, Ribeirão Preto, Brazil
| | - Birkir Reynisson
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, Oxford, United Kingdom
| | - Deepali Vasoya
- The Roslin Institute, Edinburgh, Midlothian, United Kingdom
| | - Ivan Morrison
- The Roslin Institute, Edinburgh, Midlothian, United Kingdom
| | - Søren Buus
- Laboratory of Experimental Immunology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, Oxford, United Kingdom
| | - Tim Connelley
- The Roslin Institute, Edinburgh, Midlothian, United Kingdom
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark .,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina
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Inagaki Y, Kobayashi T, Suda Y, Kusama K, Imakawa K. Genetic variation in Japanese Holstein cattle for EBL development. BMC Vet Res 2020; 16:407. [PMID: 33115449 PMCID: PMC7594299 DOI: 10.1186/s12917-020-02625-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infection with bovine leukemia virus (BLV), the causative agent for enzootic bovine leukosis (EBL), is increasing in dairy farms of Japan. The tendency of tumor development following BLV infection in certain cow families and bull lines has previously been described. We therefore hypothesized the existence of a genetic component which differentiates cattle susceptibility to the disease. RESULTS We analyzed routinely collected large-scale data including postmortem inspection data, which were combined with pedigree information and epidemiological data of BLV infection. A total of 6,022 postmortem inspection records of Holstein cattle, raised on 226 farms served by a regional abattoir over 10 years from 2004 to 2015, were analyzed for associations between sire information and EBL development. We then identified statistically the relative susceptibility to EBL development for the progeny of specific sires and paternal grandsires (PGSs). The heritability of EBL development was calculated as 0.19. Similarly, proviral loads (PVLs) of progeny from identified sires and PGSs were analyzed, but no significant differences were found. CONCLUSIONS These observations suggest that because EBL development in our Holstein population is, at least in part, influenced by genetic factors independent of PVL levels, genetic improvement for lower incidence of EBL development in cattle notwithstanding BLV infection is possible.
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Affiliation(s)
- Yasuko Inagaki
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 243-0034, Atsugi, Kanagawa, Japan
| | - Tomoko Kobayashi
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 243-0034, Atsugi, Kanagawa, Japan
| | - Yoshihito Suda
- Department of Food, Agriculture and Environment, Miyagi University, 982-0215, Sendai, Miyagi, Japan
| | - Kazuya Kusama
- Department of Endocrine Pharmacology, Tokyo University of Pharmacy and Life Sciences, 192-0392, Tokyo, Japan
| | - Kazuhiko Imakawa
- Laboratory of Molecular Reproduction, Research Institute of Agriculture, Tokai University, 862-8652, Kumamoto, Japan.
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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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10
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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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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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12
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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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13
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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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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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Baltian LR, Ripoli MV, Sanfilippo S, Takeshima SN, Aida Y, Giovambattista G. Association between BoLA-DRB3 and somatic cell count in Holstein cattle from Argentina. Mol Biol Rep 2012; 39:7215-20. [DOI: 10.1007/s11033-012-1526-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 01/24/2012] [Indexed: 11/27/2022]
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16
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Takeshima SN, Matsumoto Y, Miyasaka T, Arainga-Ramirez M, Saito H, Onuma M, Aida Y. A new method for typing bovine major histocompatibility complex class II DRB3 alleles by combining two established PCR sequence-based techniques. ACTA ACUST UNITED AC 2011; 78:208-13. [PMID: 21623735 DOI: 10.1111/j.1399-0039.2011.01708.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, two polymerase chain reaction sequence-based typing (PCR-SBT) methods were reported for the genotyping of the bovine leukocyte antigen (BoLA)-DRB3. One technique is a single PCR-SBT (sPCR-SBT) method that generates heterozygous sequences that are subsequently analyzed by the haplofinder program, while the other technique is a nested PCR-SBT (nPCR-SBT) method that allows the analysis of heterozygous sequences using the assign 400ATF software. In this study, these techniques were compared and then integrated to produce an improved genotyping method. The primer set used for sPCR-SBT was more accurate than those used for nPCR-SBT. Combining sPCR-SBT with the assign 400ATF software previously reported for nPCR-SBT enables rapid and accurate genotyping of a large number of DNA samples.
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Affiliation(s)
- S-N Takeshima
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
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Miyasaka T, Takeshima SN, Matsumoto Y, Kobayashi N, Matsuhashi T, Miyazaki Y, Tanabe Y, Ishibashi K, Sentsui H, Aida Y. The diversity of bovine MHC class II DRB3 and DQA1 alleles in different herds of Japanese Black and Holstein cattle in Japan. Gene 2011; 472:42-9. [DOI: 10.1016/j.gene.2010.10.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 10/08/2010] [Accepted: 10/09/2010] [Indexed: 11/16/2022]
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Zhu BF, Yang G, Shen CM, Qin HX, Liu SZ, Deng YJ, Fan SL, Deng LB, Chen F, Zhang P, Fang J, Chen LP, Wang HD, Wang ZY, Lucas R. Distributions of HLA-A and -B alleles and haplotypes in the Yi ethnic minority of Yunnan, China: relationship to other populations. J Zhejiang Univ Sci B 2010; 11:127-35. [PMID: 20104647 PMCID: PMC2816316 DOI: 10.1631/jzus.b0900232] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and -B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and -B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and -B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm. Results: A total of 17 HLA-A and 38 HLA-B alleles were found in the Yi population. The most frequent alleles were A*2402 (32.46%), A*1101 (26.32%), and A*0203 (10.09%) at the HLA-A locus and B*4601 (12.28%), B*1525 (10.09%), B*4001 (8.77%), and B*3802 (7.89%) at the HLA-B locus. The predominant HLA-A-B haplotypes were A*2402-B*1525 (7.86%) and A*0203-B*3802 (5.64%), followed by A*1101-B*4001 (4.69%). Phylogenetic analysis indicates that the Yi population in the Honghe, Yunnan Province of China basically belongs to groups of southeastern Asian origin, but shares some characteristics with northeastern Asian groups. Conclusion: The present study may add to the understanding of HLA polymorphism in the Yi ethnic group that was poorly defined previously, and provide useful information for bone marrow transplantation, anthropological research, and forensic sciences as well as for disease-association studies.
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Affiliation(s)
- Bo-feng Zhu
- Department of Forensic Medicine, School of Medicine, Xi'an Jiaotong University, Xi'an 710061, China
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