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Plasil M, Oppelt J, Klumplerova M, Bubenikova J, Vychodilova L, Janova E, Stejskalova K, Futas J, Knoll A, Leblond A, Mihalca AD, Horin P. Newly identified variability of the antigen binding site coding sequences of the equine major histocompatibility complex class I and class II genes. HLA 2023; 102:489-500. [PMID: 37106476 DOI: 10.1111/tan.15078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/21/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
The major histocompatibility complex (MHC) with its class I and II genes plays a crucial role in the immune response to pathogens by presenting oligopeptide antigens to various immune response effector cells. In order to counteract the vast variability of infectious agents, MHC class I and II genes usually retain high levels of SNPs mainly concentrated in the exons encoding the antigen binding sites. The aim of the study was to reveal new variability of selected MHC genes with a special focus on MHC class I physical haplotypes. Long-range NGS to was used to identify exon 2-exon 3 alleles in three genetically distinct horse breeds. A total of 116 allelic variants were found in the MHC class I genes Eqca-1, Eqca-2, Eqca-7 and Eqca-Ψ, 112 of which were novel. The MHC class II DRA locus was confirmed to comprise five exon 2 alleles, and no new sequences were observed. Additional variability in terms of 15 novel exon 2 alleles was identified in the DQA1 locus. Extensive overall variability across the entire MHC region was confirmed by an analysis of MHC-linked microsatellite loci. Both diversifying and purifying selection were detected within the MHC class I and II loci analyzed.
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Affiliation(s)
- Martin Plasil
- Research group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Jan Oppelt
- Research group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Marie Klumplerova
- Research group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Jana Bubenikova
- Research group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Leona Vychodilova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
| | - Eva Janova
- Research group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Karla Stejskalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
| | - Jan Futas
- Research group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Ales Knoll
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czechia
| | - Agnes Leblond
- Clinical Department of Companion, Leisure & Sport Animals, INRAE-VetAgro Sup, Campus vétérinaire de Lyon, Marcy L'Etoile, France
| | - Andrei D Mihalca
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Petr Horin
- Research group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
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Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics 2020; 21:677. [PMID: 32998693 PMCID: PMC7525986 DOI: 10.1186/s12864-020-07089-6] [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: 04/29/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
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Affiliation(s)
- Marie Klumplerova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Petra Splichalova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Jan Oppelt
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.,Ceitec MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jan Futas
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Aneta Kohutova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Petra Musilova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Roman Vodicka
- Zoo Prague, U Trojského zámku 120/3, 171 00, Praha 7, Czech Republic
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Petr Horin
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic. .,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
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Brosnahan MM. Genetics, Evolution, and Physiology of Donkeys and Mules. Vet Clin North Am Equine Pract 2019; 35:457-467. [PMID: 31672199 DOI: 10.1016/j.cveq.2019.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The genus Equus is made up of donkeys, horses, and zebras. Despite significant variation in chromosome number across these species, interspecies breeding results in healthy, although infertile, hybrid offspring. Most notable among these are the horse-donkey hybrids, the mule and hinny. Donkeys presently are used for everything from companion animals to beasts of burden. Although closely related from an evolutionary standpoint, differences in anatomy and physiology preclude the assumption that they can be treated identically to the domestic horse. Veterinarians should be aware of these differences and adjust their practice accordingly.
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Affiliation(s)
- Margaret M Brosnahan
- College of Veterinary Medicine, Midwestern University, 19555 North 59th Avenue, Cactus Wren Hall 336-P, Glendale, AZ 85308, USA.
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Horecky C, Horecka E, Futas J, Janova E, Horin P, Knoll A. Microsatellite markers for evaluating the diversity of the natural killer complex and major histocompatibility complex genomic regions in domestic horses. HLA 2018; 91:271-279. [PMID: 29341455 DOI: 10.1111/tan.13211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/05/2017] [Accepted: 01/14/2018] [Indexed: 01/06/2023]
Abstract
Genotyping microsatellite markers represents a standard, relatively easy, and inexpensive method of assessing genetic diversity of complex genomic regions in various animal species, such as the major histocompatibility complex (MHC) and/or natural killer cell receptor (NKR) genes. MHC-linked microsatellite markers have been identified and some of them were used for characterizing MHC polymorphism in various species, including horses. However, most of those were MHC class II markers, while MHC class I and III sub-regions were less well covered. No tools for studying genetic diversity of NKR complex genomic regions are available in horses. Therefore, the aims of this work were to establish a panel of markers suitable for analyzing genetic diversity of the natural killer complex (NKC), and to develop additional microsatellite markers of the MHC class I and class III genomic sub-regions in horses. Nine polymorphic microsatellite loci were newly identified in the equine NKC. Along with two previously reported microsatellites flanking this region, they constituted a panel of 11 loci allowing to characterize genetic variation in this functionally important part of the horse genome. Four newly described MHC class I/III-linked markers were added to 11 known microsatellites to establish a panel of 15 MHC markers with a better coverage of the class I and class III sub-regions. Major characteristics of the two panels produced on a group of 65 horses of 13 breeds and on five Przewalski's horses showed that they do reflect genetic variation within the horse species.
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Affiliation(s)
- C Horecky
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic.,CEITEC-MENDELU, Mendel University in Brno, Brno, Czech Republic
| | - E Horecka
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic.,CEITEC-MENDELU, Mendel University in Brno, Brno, Czech Republic
| | - J Futas
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - E Janova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - P Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - A Knoll
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic.,CEITEC-MENDELU, Mendel University in Brno, Brno, Czech Republic
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5
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Putnová L, Štohl R, Vrtková I. Genetic monitoring of horses in the Czech Republic: A large-scale study with a focus on the Czech autochthonous breeds. J Anim Breed Genet 2018; 135:73-83. [PMID: 29345072 DOI: 10.1111/jbg.12313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
Abstract
We propose the first comprehensive in-depth study monitoring horses in the Czech Republic. We scanned 9,289 animals from 44 populations for 17 equine STRs. Other equids analysed involved Equus przewalskii and Equus asinus. The total of 228 different alleles were detected, with the mean number of 13.4 per locus. The highest allelic richness (AR) was found in the Welsh Part Bred (6.01), followed by the Camargue (5.93) and Czech Sport Pony (5.91), whereas the Friesian exhibited the lowest AR (3.06). Interpopulation differences explained approximately nine per cent of the total genetic diversity. Reynold's genetic distance ranged from 0.003 between the Czech Warmblood and the Slovak Warmblood to 0.404 between the Friesian and donkeys. Close genetic proximity between the Silesian Noriker and Noriker was revealed. The Moravian Warmblood was better differentiated and more distant from the Czech Warmblood than the Kinsky Horse and retained the original genes of the old Austro-Hungarian tribes. A high gene flow level and a lack of genetic structure were found in the seven studied populations. Despite the historical bottlenecks and previous inbreeding, the Czech-Moravian Belgian Horse, Hucul, Old Kladruber Horse and Silesian Noriker did not suffer a serious loss of genetic diversity due to genetic drift/low effective population size. A NeighborNet dendrogram revealed breeds not classified in their groups according to the nomenclature (the Friesian, Hafling and Merens).
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Affiliation(s)
- L Putnová
- Laboratory of Agrogenomics, Department of Morphology, Physiology and Animal Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic
| | - R Štohl
- Department of Control and Instrumentation, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - I Vrtková
- Laboratory of Agrogenomics, Department of Morphology, Physiology and Animal Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic
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Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Miller DC, Antczak DF. MHC haplotype diversity in Persian Arabian horses determined using polymorphic microsatellites. Immunogenetics 2017; 70:305-315. [PMID: 29170799 DOI: 10.1007/s00251-017-1039-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/19/2017] [Indexed: 01/15/2023]
Abstract
Previous research on the equine major histocompatibility complex (MHC) demonstrated strong correlations between haplotypes defined by polymorphic intra-MHC microsatellites and haplotypes defined using classical serology. Here, we estimated MHC diversity in a sample of 124 Arabian horses from an endangered strain native to Iran (Persian Asil Arabians), using a validated 10-marker microsatellite panel. In a group of 66 horses related as parent-offspring pairs or half-sibling groups, we defined 51 MHC haplotypes, 49 of which were new. In 47 of the remaining 58 unrelated horses, we could assign one previously identified MHC haplotype, and by default, we gave provisional haplotype status to the remaining constellation of microsatellite alleles. In these horses, we found 21 haplotypes that we had previously defined and 31 provisional haplotypes, two of which had been identified in an earlier study. This gave a total of 78 new MHC haplotypes. The final 11 horses were MHC heterozygotes that we could not phase using information from any of the previously validated or provisional haplotypes. However, we could determine that these horses carried a total of 22 different undefined haplotypes. In the overall population sample, we detected three homozygous horses and one maternally inherited recombinant from 21 informative segregations. Virtually all of the horses tested were MHC heterozygotes, and most unrelated horses (98%) were heterozygous for rare microsatellite-defined haplotypes found less than three times in the sampled horses. This is evidence for a very high level of MHC haplotype variation in the Persian Asil Arabian horse.
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Affiliation(s)
- R Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Animal Science, University of Tehran, Karaj, 4111, Iran
| | | | | | - D C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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7
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Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes. Immunogenetics 2016; 69:145-156. [PMID: 27889800 DOI: 10.1007/s00251-016-0964-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/19/2016] [Indexed: 12/16/2022]
Abstract
The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next generation sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse.
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Bartolomé Del Pino LE, Roberto N, Vincenzo V, Francesca I, Antonella C, Luca AG, Francesco B, Teresa SM. Babesia caballi and Theileria equi infections in horses in Central-Southern Italy: Sero-molecular survey and associated risk factors. Ticks Tick Borne Dis 2016; 7:462-9. [DOI: 10.1016/j.ttbdis.2016.01.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 01/12/2016] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
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9
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Oduori DO, Onyango SC, Kimari JN, MacLeod ET. A field survey for the seroprevalence of Theileria equi and Babesia caballi in donkeys from Nuu Division, Kenya. Ticks Tick Borne Dis 2015; 6:683-8. [PMID: 26072000 DOI: 10.1016/j.ttbdis.2015.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/22/2015] [Accepted: 05/31/2015] [Indexed: 11/25/2022]
Abstract
Equine piroplasmosis is one of the most significant tick-borne disease of equids. The prevalence of this disease in donkeys of semi-arid Kenya remains largely unexplored. The primary objective of this study was to demonstrate the extent to which donkeys in Nuu division, Kenya have been exposed to the haemoprotozoans Babesia caballi and Theileria equi, the causative agents of equine piroplasmosis. The study also assessed the effect of age and sex on seroprevalence. A stratified sampling approach was used and three hundred and fourteen donkeys were sampled across nine sub-locations in Nuu division, Mwingi district. Serodiagnosis was via competitive inhibition enzyme linked immunosorbent assays (cELISA). The seroprevalence of T. equi was 81.2% (95% CI: 76.4-85.4). There was no significant difference in sub-location seropositivity, gender seropositivity or age related seropositivity. Antibodies against B. caballi were not detected (95% CI: 0-1.2). Findings from this study suggest that T. equi infection is endemic in Nuu division, Mwingi where it exists in a state of endemic stability. Existence of the infection should be communicated to animal health practitioners and donkey owning communities in the area.
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Affiliation(s)
- David O Oduori
- The Donkey Sanctuary Kenya, P.O. Box 24203-00502, Nairobi, Kenya; The University of Edinburgh, Division of Infection and Pathway Medicine, College of Medicine and Veterinary Medicine Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom.
| | | | | | - Ewan T MacLeod
- The University of Edinburgh, Division of Infection and Pathway Medicine, College of Medicine and Veterinary Medicine Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom
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10
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Sun Y, Zhang X, Xi D, Li G, Wang L, Zheng H, Du M, Gu Z, Yang Y, Yang Y. Isolation and cDNA characteristics of MHC-DRA genes from gayal ( Bos frontalis) and gaytle ( Bos frontalis × Bos taurus). BIOTECHNOL BIOTEC EQ 2015; 29:33-39. [PMID: 26019617 PMCID: PMC4434052 DOI: 10.1080/13102818.2014.986128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 10/13/2014] [Indexed: 11/12/2022] Open
Abstract
The mammalian major histocompatibility complex (MHC) plays important roles in pathogen recognition and disease resistance. In the present study, the coding sequence and the 5′- and 3′-untranslated regions of MHC class II DR alpha chain (the DRA gene) from rare gayal and gaytle were cloned and analyzed to dissect structural and functional variations. The nucleotide and amino acid sequences for the DRA genes in gayal (Bofr-DRA) and gaytle (Bofr × BoLA-DRA) were almost identical to those for cattle and yak (99%). Compared to yak, two amino acids substitutions in the signal peptide (SP) domain for gayal were found within all Bos animals. Except for only one replacement in the amino acid within the α2 domain of the DRA protein in gayal, the additional residues were highly conserved across the species investigated. The 20 peptide-binding sites (PBS) of Bofr-DRA and Bofr × BoLA-DRA were essentially reserved in the α1 domain among all species investigated. The lesser degree of substitution in Bofr-DRA is concordant with the concept that the DRA gene is highly conserved among all mammals. The very high degree of conservativity of the DRA gene among ruminants, including gayal, suggests its recent evolutionary separation.
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Affiliation(s)
- Yongke Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Xiaomin Zhang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Guozhi Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Liping Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Huanli Zheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Min Du
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Zhaobing Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Yulin Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Yuai Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
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11
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Sun Y, Zheng H, Xi D, Zhang X, Du M, Pu L, Lin M, Yang Y. Molecular characteristics of the MHC-DRA genes from yak (Bos grunniens) and Chinese yakow (Bos grunniens × Bos taurus). Int J Immunogenet 2013; 41:69-73. [PMID: 23815277 DOI: 10.1111/iji.12072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/23/2013] [Accepted: 06/02/2013] [Indexed: 11/28/2022]
Abstract
Two full-length cDNAs (762 bp) of the DRA gene from yak and Chinese yakow were isolated and analysed to identify structural and functional variations. The sequences for DRA in yak (Bogr-DRA) and Chinese yakow (Bogr × BoLA-DRA) were essentially identical to those for cattle (99%) and buffalo (97%). Except for two substitutions in the amino acids comprising the domain for signal peptide (SP) in yak, the additional residues were highly conserved across the species investigated. Peptide-binding site (PBS) of Bogr-DRA and Bogr × BoLA-DRA was highly reserved in the α1 domain among all species investigated. The lack of mutation in Bogr-DRA is consistent with the conception that the gene is highly conserved among all mammalian species. The very high conservation of the DRA gene among ruminants, including yak, may be due to its recent evolutionary detachment.
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Affiliation(s)
- Y Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
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12
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Kamath PL, Getz WM. Unraveling the effects of selection and demography on immune gene variation in free-ranging plains zebra (Equus quagga) populations. PLoS One 2012; 7:e50971. [PMID: 23251409 PMCID: PMC3522668 DOI: 10.1371/journal.pone.0050971] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
Demography, migration and natural selection are predominant processes affecting the distribution of genetic variation among natural populations. Many studies use neutral genetic markers to make inferences about population history. However, the investigation of functional coding loci, which directly reflect fitness, is critical to our understanding of species' ecology and evolution. Immune genes, such as those of the Major Histocompatibility Complex (MHC), play an important role in pathogen recognition and provide a potent model system for studying selection. We contrasted diversity patterns of neutral data with MHC loci, ELA-DRA and -DQA, in two southern African plains zebra (Equus quagga) populations: Etosha National Park, Namibia, and Kruger National Park, South Africa. Results from neutrality tests, along with observations of elevated diversity and low differentiation across populations, supported previous genus-level evidence for balancing selection at these loci. Despite being low, MHC divergence across populations was significant and may be attributed to drift effects typical of geographically separated populations experiencing little to no gene flow, or alternatively to shifting allele frequency distributions driven by spatially variable and fluctuating pathogen communities. At the DRA, zebra exhibited geographic differentiation concordant with microsatellites and reduced levels of diversity in Etosha due to highly skewed allele frequencies that could not be explained by demography, suggestive of spatially heterogeneous selection and local adaptation. This study highlights the complexity in which selection affects immune gene diversity and warrants the need for further research on the ecological mechanisms shaping patterns of adaptive variation among natural populations.
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Affiliation(s)
- Pauline L Kamath
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America.
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13
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Colli L, Perrotta G, Negrini R, Bomba L, Bigi D, Zambonelli P, Verini Supplizi A, Liotta L, Ajmone-Marsan P. Detecting population structure and recent demographic history in endangered livestock breeds: the case of the Italian autochthonous donkeys. Anim Genet 2012; 44:69-78. [DOI: 10.1111/j.1365-2052.2012.02356.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2012] [Indexed: 11/29/2022]
Affiliation(s)
- L. Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - G. Perrotta
- Laboratorio di Genetica e Servizi L.G.S.; I-26100; Cremona; Italy
| | - R. Negrini
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - L. Bomba
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - D. Bigi
- Dipartimento di Protezione e Valorizzazione Agro-Alimentare; Università di Bologna - Sede di Reggio Emilia; I-42123; Reggio Emilia; Italy
| | - P. Zambonelli
- Dipartimento di Protezione e Valorizzazione Agro-Alimentare; Università di Bologna - Sede di Reggio Emilia; I-42123; Reggio Emilia; Italy
| | - A. Verini Supplizi
- Dipartimento di Patologia; Diagnostica e Clinica Veterinaria; Università di Perugia; I-06126; Perugia; Italy
| | - L. Liotta
- Dipartimento di Morfologia, Biochimica; Fisiologia e Produzioni Animali; Università di Messina; I-98168; Messina; Italy
| | - P. Ajmone-Marsan
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
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