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Mishra SK, Niranjan SK, Singh R, Kumar P, Kumar SL, Banerjee B, Kataria RS. Diversity analysis at MHC class II DQA locus in buffalo (Bubalus bubalis) indicates extensive duplication and trans-species evolution. Genomics 2020; 112:4417-4426. [PMID: 32738270 DOI: 10.1016/j.ygeno.2020.07.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/06/2020] [Accepted: 07/26/2020] [Indexed: 12/15/2022]
Abstract
Variation at MHC Class II-DQA locus in riverine and swamp buffaloes (Bubu) has been explored in this study. Through sequencing of buffalo DQA, 48 nucleotide variants identified from 17 individuals, reporting 42 novel alleles, including one pseudogene. Individual animal displayed two to seven variants, suggesting the presence of more than two Bubu-DQA loci, as an evidence of extensive duplication. dN values were found to be higher than dS values at peptide binding sites, separately for riverine and swamp buffaloes, indicating locus being under positive selection. Evolutionary analysis revealed numerous trans-species polymorphism with alleles from water buffalo assigned to at least three different loci (Bubu-DQA1, DQA2, DQA3). Alleles of both the sub-species intermixed within the cluster, showing convergent evolution of MHC alleles in bovines. The results thus suggest that both riverine and swamp buffaloes share con-current arrangement of DQA region, comparable to cattle in terms of copy number and population polymorphism.
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Affiliation(s)
- Shailendra Kumar Mishra
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India; School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India.
| | - Ravinder Singh
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - Prem Kumar
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - S Lava Kumar
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - Bhaswati Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201310, India
| | - Ranjit Singh Kataria
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India.
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2
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Zhang Z, Sun X, Chen M, Li L, Ren W, Xu S, Yang G. Genomic Organization and Phylogeny of MHC Class II Loci in Cetaceans. J Hered 2019; 110:332-339. [PMID: 30844043 DOI: 10.1093/jhered/esz005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 01/26/2019] [Indexed: 01/01/2023] Open
Abstract
Cetaceans are a suborder of secondarily adapted aquatic mammals with an enigmatic history involving a transition from land to sea approximately 55 Mya. During the transition period, cetaceans would have faced many new pathogen challenges, but limited information is available about the adaptive immune system of these mammals. The major histocompatibility complex (MHC) family plays a key role in antigen recognition and presentation in adaptive immunity, which is believed to have evolved in response to pathogens. In the present study, MHC class II loci were characterized in 7 published cetacean genome assemblies and the genomic organization of cetaceans was compared with that of their terrestrial relatives, the cow, sheep, and pig. A total of 9 MHC class II loci were identified in the cetacean genomes: DRA, DRB, DQA, DQB, DPB, DOA, DOB, DMA, and DMB. Sequences from 8 of the 9 genes included intact coding regions and were presumably functional. The organization of the MHC class II loci was conserved across the examined mammalian species, whereas the orientation and number of the alpha and beta genes varied among the species. The phylogenetic reconstruction of all MHC genes from Cetartiodactyla suggested that alpha and beta genes had different topologies. Additionally, based on a phylogenetic reconstruction of the multi-locus DRB, 2 (DRB1 and DRB2) of the 4 putative gene copies were hypothesized to have duplicated and evolved during the radiation of cetaceans.
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Affiliation(s)
- Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaohui Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Meixiu Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lili Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Mishra SK, Gonge DS, Behl J, Biswas TK, Sivalingam J, Kataria RS, Niranjan SK. Allelic diversity and locus duplication at the MHC Class II DQ sub-region in the Indian yak population. Anim Genet 2018; 50:112-113. [PMID: 30378694 DOI: 10.1111/age.12737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Shailendra K Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India
| | - Dimpee S Gonge
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India
| | - Jyotsna Behl
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India
| | - Tapas K Biswas
- ICAR-National Research Centre on Yak, Dirang, Arunachal Pradesh, 790 101, India
| | - Jayakumar Sivalingam
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India
| | - Ranjit S Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India
| | - Saket K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India
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High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes. Immunogenetics 2016; 68:439-447. [DOI: 10.1007/s00251-016-0915-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
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Sun Y, Xi D, Li G, Hao T, Chen Y, Yang Y. Genetic characterization of MHC class II DQB exon 2 variants in gayal ( Bos frontalis). BIOTECHNOL BIOTEC EQ 2014; 28:827-833. [PMID: 26019566 PMCID: PMC4434113 DOI: 10.1080/13102818.2014.960787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/07/2014] [Indexed: 11/20/2022] Open
Abstract
In the present study, exon 2 of major histocompatibility complex (MHC) class II DQB gene from 39 gayals (Bos frontalis) was isolated, characterized and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 36 DQB exon 2 variants among 39 gayals. These variants exhibited a high degree of nucleotide and amino acid substitutions with most amino acid variations occurring at positions forming the peptide-binding sites (PBS). The DQB loci were analysed for patterns of synonymous (dS) and non-synonymous (dN) substitution. The gayals were observed to be under strong balancing selection in the DQB exon 2 PBS (dN = 0.094, P = 0.001). It appears that this variability among gayals could confer the ability to mount immune responses to a wide variety of peptides or pathogens.
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Affiliation(s)
- Yongke Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Guozhi Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Tiantian Hao
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Yuhan Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Yuai Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
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Xi D, Hao T, He Y, Leng J, Sun Y, Yang Y, Mao H, Deng W. Nucleotide sequence and polymorphism of MHC class IIDQBexon 2 alleles in Chinese yakow (Bos grunniens × Bos taurus). Int J Immunogenet 2014; 41:269-75. [DOI: 10.1111/iji.12109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 11/26/2013] [Accepted: 12/22/2013] [Indexed: 11/28/2022]
Affiliation(s)
- D. Xi
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - T. Hao
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - Y. He
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - J. Leng
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - Y. Sun
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - Y. Yang
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - H. Mao
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - W. Deng
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
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O'Toole D, Li H. The pathology of malignant catarrhal fever, with an emphasis on ovine herpesvirus 2. Vet Pathol 2014; 51:437-52. [PMID: 24503439 DOI: 10.1177/0300985813520435] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The enigmatic pathogenesis of malignant catarrhal fever (MCF) involves dysregulated immune responses in susceptible ruminant species. Economically important outbreaks of MCF are due to 2 of the 10 viruses currently comprising the malignant catarrhal fever virus group: ovine herpesvirus 2 (OvHV-2) and alcelaphine herpesvirus 1 (AlHV-1). Attempts to develop effective vaccines for this group of viruses in the 1970s were sufficiently discouraging that they were temporarily abandoned. This review focuses on recent efforts to understand the pathogenesis of MCF, particularly the sheep-associated form of the disease, with the goal of developing rational control methods, including vaccination. The past 2 decades have seen several advances, including recognition of new members of the MCF virus group, better diagnostic assays, induction of disease by a natural route (aerosol), and clearer understanding of OvHV-2's shedding patterns by domestic sheep. A consistent theme in experimental studies of OvHV-2 in susceptible species is that there are 2 peaks of OvHV-2 gene expression: a preclinical peak involving the respiratory tract and a second in multiple organ systems leading to clinical disease. Latent and lytic gene expression may coexist in tissues during clinical stages in symptomatic animals.
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Affiliation(s)
- D O'Toole
- Wyoming State Veterinary Laboratory, University of Wyoming, 1174 Snowy Range Rd, Laramie, Wyoming 82070, USA.
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Genetic variability of MHC class II DQB exon 2 alleles in yak (Bos grunniens). Mol Biol Rep 2014; 41:2199-206. [PMID: 24430299 DOI: 10.1007/s11033-014-3071-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 01/04/2014] [Indexed: 11/26/2022]
Abstract
The major histocompatibility class (MHC) DQ molecules are dimeric glycoproteins revealing antigen presentation to CD(4+) T cells. In the present study, the exon 2 of the MHC class II DQB gene from 32 yaks (Bos grunniens) was cloned, sequenced and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 25 DQB exon 2 alleles among 32 yaks, all alleles are found to belong to DQB1 loci. These alleles exhibited a high degree of nucleotide and amino acid polymorphisms with most amino acid variations occurring at positions forming the peptide-binding sites. The DQB loci were analyzed for patterns of synonymous (d S) and non-synonymous (d N) substitution. The yak was observed to be under strong positive selection in the DQB exon 2 peptide-binding sites (d N = 0.15, P < 0.001). It appears that this variability among yaks confers the ability to mount immune responses to a wide variety of peptides or pathogens.
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Mitochondrial DNA haplotype analysis of liver fluke in bison from Bialowieza Primaeval Forest indicates domestic cattle as the likely source of infection. Vet Parasitol 2013; 191:161-4. [DOI: 10.1016/j.vetpar.2012.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 06/12/2012] [Accepted: 08/02/2012] [Indexed: 11/22/2022]
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Wu HL, Tong CC, Li E, Luo TL. Insight into gene evolution within Cervidae and Bovidae through genetic variation in MHC-DQA in the black muntjac (Muntiacus crinifrons). GENETICS AND MOLECULAR RESEARCH 2012; 11:2888-98. [PMID: 22653641 DOI: 10.4238/2012.may.15.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The critical role that the major histocompatibility complex plays in the immune recognition of parasites and pathogens makes its evolutionary dynamics exceptionally relevant to ecology, population biology, and conservation studies. The black muntjac is a rare deer endemic to a small mountainous region in eastern China. We found that this species has two DQA loci through cDNA expression and sequence variation analysis. The level of variation at both DQA loci was found to be extremely low (three alleles for DQA1 and four alleles for DQA2), possibly because of past bottlenecks and the species' relatively solitary behavior pattern. The ratio of d(N)/d(S) in the putative peptide binding region of the DQA2 locus (13.36, P = 0.012) was significantly larger than one but not that of DQA1 (0.94, P = 0.95), suggesting strong positive selection at the DQA2 but not at the DQA1 locus. This difference might reflect different sets of evolutionary selection pressures acting on the two loci. The phylogenetic tree showed that DQA1 alleles from two species of Cervidae and two of Bovidae grouped together, as did the DQA2 alleles. However, different genes from the four species were located in separate branches. These results lead us to suggest that these DQA alleles are derived from primordial DQA genes from a common ancestor and are maintained in Cervidae and Bovidae since their divergence around 25.5-27.8 million years ago.
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Affiliation(s)
- H-L Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China.
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11
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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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Niranjan SK, Deb SM, Kumar S, Mitra A, Naskar S, Sharma A. Genetic characterisation of buffalo MHC ( Bubu)-DQB cDNA molecule. JOURNAL OF APPLIED ANIMAL RESEARCH 2011. [DOI: 10.1080/09712119.2011.565191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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TOKARSKA M, PERTOLDI C, KOWALCZYK R, PERZANOWSKI K. Genetic status of the European bison Bison bonasus after extinction in the wild and subsequent recovery. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2010.00178.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Yasukochi Y, Kurosaki T, Yoneda M, Koike H. Identification of the expressed MHC class II DQB gene of the Asiatic black bear, Ursus thibetanus, in Japan. Genes Genet Syst 2010; 85:147-55. [PMID: 20558901 DOI: 10.1266/ggs.85.147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genetic diversity estimation of the major histocompatibility complex (MHC) gene may be an important tool in the assessment of immune response ability against infectious disease. We were able to identify a near full-length expressed DQB sequence by RACE-PCR method from the Asiatic black bear, Ursus thibetanus in Japan. This is the first such full length expression in the Ursidae. The bear had at least one functional DQB locus. In phylogenetic tree analysis its DQB amino acid sequence formed a monophyletic group with DQB sequences from members of the order Carnivora and had a 90% nucleotide sequence similarity with the DQB allele of the California sea lion, Zalophus californianus. We compared the DQB amino acid composition of U. thibetanus with those of several other mammalian species including Homo sapiens. Amino acid residues known to be functionally important for human MHC genes, tended to be also conserved among other mammalian species while PBRs in the beta1 domain were heterogeneous among mammalian species. The DQB sequence obtained from the bear had not only no putative frameshifts or deletions but also no abnormal amino acid mutations such as had been observed in human DQB molecules. This suggests that the bear DQB sequence was an apparently functional DQB allele. As a preliminary study, we sequenced the exon 2 region of DQB alleles from genomic DNA, and succeeded to amplify the exon 2 of DQB loci. Our study will provide useful information for conservation genetics of the U. thibetanus as well as more generally regarding the mammalian MHC region.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Biosystems Science, the Graduate University for Advanced Studies, Hayama.
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Niranjan SK, Deb SM, Kumar S, Mitra A, Sharma A, Sakaram D, Naskar S, Sharma D, Sharma SR. Allelic diversity at MHC class II DQ loci in buffalo (Bubalus bubalis): evidence for duplication. Vet Immunol Immunopathol 2010; 138:206-12. [PMID: 20724005 DOI: 10.1016/j.vetimm.2010.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 07/15/2010] [Accepted: 07/21/2010] [Indexed: 10/19/2022]
Abstract
The genetic diversity of MHC class II DQ genes was investigated in riverine buffalo (Bubalus bubalis) by PCR-RFLP and sequencing. Highly variable regions (exons 2-3) of DQ genes were amplified from 152 buffaloes and genotyped by PCR-RFLP. Alleles identified by differential restriction patterns were sequenced for the characterization. PCR-RFLP was a rapid method to discriminate between DQA1 and duplicated DQA2 genes in buffalo, however, the method appeared to be inadequate for determining the more complicated DQB genotypes. A total of 7 and 10 alleles were identified for DQA and DQB loci, respectively. Nucleotide as well as amino acid variations among DQ alleles particularly at peptide binding regions were high. Such variations were as expected higher in DQB than DQA alleles. The phylogenetic analysis for both genes revealed the grouping of alleles into two major sub-groups with higher genetic divergence. High divergence among DQ allelic families and the isolation of two diverse DQA and DQB sequences from individual samples indicated duplication of DQ loci was similar in buffalo to other ruminants.
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Affiliation(s)
- Saket K Niranjan
- Animal Genetics Division, Indian Veterinary Research Institute, Izatnagar, UP 243122, India.
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Brinkmeyer-Langford CL, Childers CP, Fritz KL, Gustafson-Seabury AL, Cothran M, Raudsepp T, Womack JE, Skow LC. A high resolution RH map of the bovine major histocompatibility complex. BMC Genomics 2009; 10:182. [PMID: 19393056 PMCID: PMC2682492 DOI: 10.1186/1471-2164-10-182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 04/24/2009] [Indexed: 11/10/2022] Open
Abstract
Background The cattle MHC is termed the bovine leukocyte antigen (BoLA) and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence information are critical to the study of the BoLA region. The bovine genome sequencing project has produced two assemblies (Btau_3.1 and 4.0) that differ substantially from each other and from conventional gene maps in the BoLA region. To independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of BoLA using a 12,000rad radiation hybrid panel. Seventy-seven unique sequence tagged site (STS) markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000rad bovine radiation hybrid (RH) panel to evaluate the different assemblies of the bovine genome sequence. Results Analysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, most could be attributed to closely spaced markers that could not be precisely ordered in the RH panel. One probable incorrectly-assembled sequence and three missing sequences were noted in the Btau_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36) when reordered to account for the ancestral inversion in the ruminant MHC. Conclusion These results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.
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Affiliation(s)
- Candice L Brinkmeyer-Langford
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843-4458, USA.
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Takeshima S, Chen S, Miki M, Kado M, Aida Y. Distribution and origin of bovine major histocompatibility complex class IIDQA1genes in Japan. ACTA ACUST UNITED AC 2008; 72:195-205. [DOI: 10.1111/j.1399-0039.2008.01092.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Alvarez-Busto J, García-Etxebarria K, Herrero J, Garin I, Jugo BM. Diversity and evolution of the Mhc-DRB1 gene in the two endemic Iberian subspecies of Pyrenean chamois, Rupicapra pyrenaica. Heredity (Edinb) 2007; 99:406-13. [PMID: 17551521 DOI: 10.1038/sj.hdy.6801016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Major histocompatibility complex class II locus DRB variation was investigated by single-strand conformation polymorphism analysis and sequence analysis in the two subspecies of Pyrenean chamois (Rupicapra pyrenaica) endemic to the Iberian Peninsula. Low levels of genetic variation were detected in both subspecies, with seven different alleles in R. p. pyrenaica and only three in the R. p. parva. After applying the rarefaction method to cope with the differences in sample size, the low allele number of parva was highlighted. The low allelic repertoire of the R. p. parva subspecies is most likely the result of bottlenecks caused by hunting pressure and recent parasitic infections by sarcoptic mange. A phylogenetic analysis of both Pyrenean chamois and DRB alleles from 10 different caprinid species revealed that the chamois alleles form two monophyletic groups. In comparison with other Caprinae DRB sequences, the Rupicapra alleles displayed a species-specific clustering that reflects a large temporal divergence of the chamois from other caprinids, as well as a possible difference in the selective environment for these species.
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Affiliation(s)
- J Alvarez-Busto
- Genetika, Antropologia Fisikoa eta Animali Fisiologia Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Bilbao, Spain
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Radwan J, Kawałko A, Wójcik JM, Babik W. MHC-DRB3 variation in a free-living population of the European bison, Bison bonasus. Mol Ecol 2007; 16:531-40. [PMID: 17257111 DOI: 10.1111/j.1365-294x.2006.03179.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
MHC genes play a crucial role in pathogen recognition and are the most polymorphic genes in vertebrates. Loss of variation in these genes in bottlenecked species is thought to put their survival at risk. We examined variation at the MHC II DRB3 locus in the European bison, Bison bonasus, a species that has undergone an extreme bottleneck: the current population originated from only 12 founders. We also tested for the association of DRB3 genes with the incidence of posthitis, a disease affecting the reproductive organs of bulls and posing a new threat to the survival of the species. We found very limited MHC diversity, with only four alleles segregating in a sample of 172 individuals from a free-ranging Białowieza population. The alleles were highly divergent and revealed the hallmark of positive selection acting on them in the past, that is, a significant excess of nonsynonymous substitutions. This excess was concentrated in putative antigen-binding sites, suggesting that selection was driven by pathogens. However, we did not observe departures from Hardy-Weinberg equilibrium, an indicator of strong ongoing selection. Neither have we found a significant association between DRB3 alleles or genotypes and susceptibility to posthitis. Alleles conferring resistance to males may have been lost during the extreme bottleneck the species had undergone.
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Affiliation(s)
- J Radwan
- Institute of Nature Conservation, Polish Academy of Sciences, A. Mickiewicza 33, 31-120 Kraków, Poland
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Traul DL, Li H, Dasgupta N, O'Toole D, Eldridge JA, Besser TE, Davies CJ. Resistance to malignant catarrhal fever in American bison (Bison bison) is associated with MHC class IIa polymorphisms. Anim Genet 2007; 38:141-6. [PMID: 17326800 DOI: 10.1111/j.1365-2052.2007.01575.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Rhadinovirus ovine herpesvirus-2 (OvHV-2) is the most common causative agent of malignant catarrhal fever (MCF) in clinically susceptible ruminants including cattle and bison. American bison (Bison bison) are highly susceptible to clinical MCF. Nevertheless, approximately 20% of bison on ranches or in feedlots become infected with the virus without developing clinical disease. Defining the genetic basis for differences in susceptibility between bison could facilitate development of improved control strategies for MCF. One genetic region that influences susceptibility to infectious diseases is the major histocompatibility complex (MHC). In this study, a Bison bison (Bibi) DRB3 oligonucleotide microarray was used to type 189 bison from 10 herds where MCF outbreaks had occurred. Binary logistic regression was used to classify DRB3 alleles as resistant (R), susceptible (S) or neutral (N). Animals were reclassified using six DRB3 genotype categories: N/N, N/R, N/S, R/S, R/R and S/S. Analysis of homogeneity across herds showed that there was a herd effect. Consequently, a penalized logistic regression model was run with herd and genotype categories as the explanatory variables. The R/R genotype was associated with resistance to MCF (P = 0.0327), while the S/S genotype was associated with clinical MCF (P = 0.0069). This is the first evidence that MHC class IIa polymorphism is associated with resistance or susceptibility to OvHV-2-induced MCF.
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Affiliation(s)
- D L Traul
- Animal Disease Research Unit, USDA-Agricultural Research Service, Washington State University, Pullman, WA 99164-6630, USA
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