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Vasoya D, Connelley T, Tzelos T, Todd H, Ballingall KT. Large scale transcriptional analysis of MHC class I haplotype diversity in sheep. HLA 2024; 103:e15356. [PMID: 38304958 DOI: 10.1111/tan.15356] [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: 10/25/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.
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Affiliation(s)
- Deepali Vasoya
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Thomas Tzelos
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
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2
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Usai MG, Casu S, Sechi T, Salaris SL, Miari S, Mulas G, Cancedda MG, Ligios C, Carta A. Advances in understanding the genetic architecture of antibody response to paratuberculosis in sheep by heritability estimate and LDLA mapping analyses and investigation of candidate regions using sequence-based data. Genet Sel Evol 2024; 56:5. [PMID: 38200416 PMCID: PMC10777618 DOI: 10.1186/s12711-023-00873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Paratuberculosis is a contagious and incurable disease that is caused by Mycobacterium avium subsp. paratuberculosis (MAP) with significant negative effects on animal welfare and farm profitability. Based on a large naturally infected flock over 12 years, we analyzed repeated enzyme-linked immunosorbent assay tests (ELISA), OvineSNP50 BeadChip genotypes and whole-genome sequences imputed from 56 influential animals. The main goals were to estimate the genetic parameters of proxy traits for resistance to MAP, identify genomic regions associated with the host's immune response against MAP and search for candidate genes and causative mutations through association and functional annotation analyses of polymorphisms identified by sequencing. RESULTS Two variables were derived from ELISA tests. The first, a binary variable, assessed the infection status of each animal over the entire productive life, while the second considered the level of antibody recorded over time. Very similar results were obtained for both variables. Heritability estimates of about 0.20 were found and a significant region capturing 18% and 13% of the genetic variance was detected on ovine chromosome 20 by linkage disequilibrium and linkage analysis on OvineSNP50 positions. Functional annotation and association analyses on the imputed sequence polymorphisms that were identified in this region were carried out. No significant variants showed a functional effect on the genes that mapped to this region, most of which belong to the major histocompatibility complex class II (MHC II). However, the conditional analysis led to the identification of two significant polymorphisms that can explain the genetic variance associated with the investigated genomic region. CONCLUSIONS Our results confirm the involvement of the host's genetics in susceptibility to MAP in sheep and suggest that selective breeding may be an option to limit the infection. The estimated heritability is moderate with a relevant portion being due to a highly significant region on ovine chromosome 20. The results of the combined use of sequence-based data and functional analyses suggest several genes belonging to the MHC II as the most likely candidates, although no mutations in their coding regions showed a significant association. Nevertheless, information from genotypes of two highly significant polymorphisms in the region can enhance the efficiency of selective breeding programs.
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Affiliation(s)
- Mario Graziano Usai
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sara Casu
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy.
| | - Tiziana Sechi
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sotero L Salaris
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sabrina Miari
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Giuliana Mulas
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | | | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale Della Sardegna G. Pegreffi, 07100, Sassari, Italy
| | - Antonello Carta
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
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3
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Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Sharma N, Chopra A, Kandalkar Y, Choudhary A, Magotra A. Population-wide genetic analysis of Ovar-DQA1 and DQA2 loci across sheep breeds in India revealed their evolutionary importance and fitness of sheep in a tropical climate. Anim Biotechnol 2023; 34:4645-4657. [PMID: 36847639 DOI: 10.1080/10495398.2023.2180010] [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: 03/01/2023]
Abstract
Genetic variability at the major histocompatibility complex (MHC) is important in any species due to significant role played by MHC for antigen presentation. DQA locus has not been studied for its genetic variability across sheep population in India. In the present study, MHC of sheep at DQA1 and DQA2 loci were evaluated across 17 Indian sheep breeds. Results revealed high degree of heterozygosity (10.34% to 100% for DQA1 and 37.39 to 100% for DQA2). 18 DQA1 alleles and 22 DQA2 alleles were isolated in different breeds. Nucleotide content for DQA region revealed richness of AT content (54.85% for DQA1 and 53.89% for DQA2). DQA1 and DQA2 sequences clustered independently. We could see evidence of divergence of DQA as DQA1 and DQA2 across sheep breeds. Wu-Kabat variability index revealed vast genetic variation across DQA1 and DQA2, specifically at peptide binding sites (PBS) that consisted 21 residues for DQA1 and 17 residues for DQA2. Evolutionary analysis revealed the presence of positive and balancing selection for DQA1 locus, however DQA2 was under purifying selection across sheep breeds. Higher heterozygosity and large diversity at both loci especially at PBS indicated the fitness of the sheep population for evading pathogens and adapt to the harsh tropical climate.
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Affiliation(s)
- G R Gowane
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - S S Misra
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - Rani Alex
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Nikita Sharma
- Animal Health Section, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics and Breeding Division, ICAR-Arid Region Campus, Central Sheep and Wool Research Institute, Bikaner, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | | | - Ankit Magotra
- Animal Genetics and Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
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4
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Lukacs M, Nymo IH, Madslien K, Våge J, Veiberg V, Rolandsen CM, Bøe CA, Sundaram AYM, Grimholt U. Functional immune diversity in reindeer reveals a high Arctic population at risk. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1058674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Climate changes the geographic range of both species as well as pathogens, causing a potential increase in the vulnerability of populations or species with limited genetic diversity. With advances in high throughput sequencing (HTS) technologies, we can now define functional expressed genetic diversity of wild species at a larger scale and identify populations at risk. Previous studies have used genomic DNA to define major histocompatibility complex (MHC) class II diversity in reindeer. Varying numbers of expressed genes found in many ungulates strongly argues for using cDNA in MHC typing strategies to ensure that diversity estimates relate to functional genes. We have used available reindeer genomes to identify candidate genes and established an HTS approach to define expressed MHC class I and class II diversity. To capture a broad diversity we included samples from wild reindeer from Southern Norway, semi-domesticated reindeer from Northern Norway and reindeer from the high Artic archipelago Svalbard. Our data show a medium MHC diversity in semi-domesticated and wild Norwegian mainland reindeer, and low MHC diversity reindeer in Svalbard reindeer. The low immune diversity in Svalbard reindeer provides a potential risk if the pathogenic pressure changes in response to altered environmental conditions due to climate change, or increased human-related activity.
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5
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Dicks KL, Pemberton JM, Ballingall KT, Johnston SE. MHC class IIa haplotypes derived by high-throughput SNP screening in an isolated sheep population. G3-GENES GENOMES GENETICS 2021; 11:6298591. [PMID: 34568908 PMCID: PMC8496268 DOI: 10.1093/g3journal/jkab200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/12/2021] [Indexed: 12/01/2022]
Abstract
Investigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant haplotype affecting only the SNPs downstream of the expressed genes. The panel of 13 SNPs was genotyped in 5951 Soay sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of the recombinant SNP haplotype. This SNP-based method has enabled the rapid generation of locus-specific MHC genotypes for large numbers of Soay sheep. This volume of high-quality genotypes in a well-characterized population of free-living sheep will be valuable for investigating the mechanisms maintaining diversity at the MHC.
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Affiliation(s)
- Kara L Dicks
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Josephine M Pemberton
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Keith T Ballingall
- Moredun Research Institute, Pentlands Science Park, Edinburgh EH26 0PZ, UK
| | - Susan E Johnston
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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6
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Yang H, Yang YL, Li GQ, Yu Q, Yang J. Identifications of immune-responsive genes for adaptative traits by comparative transcriptome analysis of spleen tissue from Kazakh and Suffolk sheep. Sci Rep 2021; 11:3157. [PMID: 33542475 PMCID: PMC7862382 DOI: 10.1038/s41598-021-82878-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
Aridity and heat are significant environmental stressors that affect sheep adaptation and adaptability, thus influencing immunity, growth, reproduction, production performance, and profitability. The aim of this study was to profile mRNA expression levels in the spleen of indigenous Kazakh sheep breed for comparative analysis with the exotic Suffolk breed. Spleen histomorphology was observed in indigenous Kazakh sheep and exotic Suffolk sheep raised in Xinjiang China. Transcriptome sequencing of spleen tissue from the two breeds were performed via Illumina high-throughput sequencing technology and validated by RT-qPCR. Blood cytokine and IgG levels differed between the two breeds and IgG and IL-1β were significantly higher in Kazakh sheep than in Suffolk sheep (p < 0.05), though spleen tissue morphology was the same. A total of 52.04 Gb clean reads were obtained and the clean reads were assembled into 67,271 unigenes using bioinformatics analysis. Profiling analysis of differential gene expression showed that 1158 differentially expressed genes were found when comparing Suffolk with Kazakh sheep, including 246 up-regulated genes and 912 down-regulated genes. Utilizing gene ontology annotation and pathway analysis, 21 immune- responsive genes were identified as spleen-specific genes associated with adaptive traits and were significantly enriched in hematopoietic cell lineage, natural killer cell-mediated cytotoxicity, complement and coagulation cascades, and in the intestinal immune network for IgA production. Four pathways and up-regulated genes associated with immune responses in indigenous sheep played indispensable and promoting roles in arid and hot environments. Overall, this study provides valuable transcriptome data on the immunological mechanisms related to adaptive traits in indigenous and exotic sheep and offers a foundation for research into adaptive evolution.
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Affiliation(s)
- Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Yong-Lin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Guo-Qing Li
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Shihezi, 832000, China.,Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii, Honolulu, HI, 96822, USA.
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7
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Hanks E, Todd H, Palarea-Albaladejo J, McNeilly TN, Britton C, Ballingall KT. A novel technique for retrospective genetic analysis of the response to vaccination or infection using cell-free DNA from archived sheep serum and plasma. Vet Res 2020; 51:9. [PMID: 32024546 PMCID: PMC7003321 DOI: 10.1186/s13567-020-0737-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/16/2020] [Indexed: 12/31/2022] Open
Abstract
Genetic variation is associated with differences in disease resistance and susceptibility among individuals within a population. To date, molecular genetic analyses of host responses have relied on extraction of genomic DNA from whole blood or tissue samples. However, such samples are not routinely collected during large-scale field studies. We demonstrate that cell-free genomic DNA (cfDNA) may be extracted and amplified from archived plasma samples, allowing retrospective analysis of host genetic diversity. This technique was also applicable to archived serum samples up to 35 years old and to different ruminant species. As proof of concept, we used this cfDNA approach to genotype the major histocompatibility complex (MHC) class II DRB1 locus of 224 Merino sheep which had participated in field trials of a commercial Haemonchus contortus vaccine, Barbervax®, in Australia. This identified a total of 51 different DRB1 alleles and their relative frequencies. This is the first study to examine host MHC diversity using DNA extracted from archived plasma samples, an approach that may be applied to retrospective analyses of genetic diversity and responses to vaccination or infection across different species and populations.
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Affiliation(s)
- Eve Hanks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK. .,SAC Consulting: Veterinary Services, SRUC Veterinary Services, Pentland Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK.
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Penicuik, Edinburgh, EH26 0PZ, UK
| | - Javier Palarea-Albaladejo
- Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Penicuik, Edinburgh, EH26 0PZ, UK
| | - Collette Britton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Keith T Ballingall
- Moredun Research Institute, Pentlands Science Park, Penicuik, Edinburgh, EH26 0PZ, UK.
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8
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Stear A, Ali AOA, Brujeni GN, Buitkamp J, Donskow-Łysoniewska K, Fairlie-Clarke K, Groth D, Isa NMM, Stear MJ. Identification of the amino acids in the Major Histocompatibility Complex class II region of Scottish Blackface sheep that are associated with resistance to nematode infection. Int J Parasitol 2019; 49:797-804. [PMID: 31306661 DOI: 10.1016/j.ijpara.2019.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/01/2019] [Accepted: 05/09/2019] [Indexed: 01/25/2023]
Abstract
Lambs with the Major Histocompatibility Complex DRB1*1101 allele have been shown to produce fewer nematode eggs following natural and deliberate infection. These sheep also possess fewer adult Teladorsagia circumcincta than sheep with alternative alleles at the DRB1 locus. However, it is unclear if this allele is responsible for the reduced egg counts or merely acts as a marker for a linked gene. This study defined the MHC haplotypes in a population of naturally infected Scottish Blackface sheep by PCR amplification and sequencing, and examined the associations between MHC haplotypes and faecal egg counts by generalised linear mixed modelling. The DRB1*1101 allele occurred predominately on one haplotype and a comparison of haplotypes indicated that the causal mutation or mutations occurred in or around this locus. Additional comparisons with another resistant haplotype indicated that mutations in or around the DQB2*GU191460 allele were also responsible for resistance to nematode infections. Further analyses identified six amino acid substitutions in the antigen binding site of DRB1*1101 that were significantly associated with reductions in the numbers of adult T. circumcincta.
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Affiliation(s)
- Abigail Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Bearsden Road, Glasgow, Scotland G61 1QH, UK
| | - Alsagher O A Ali
- Animal Medicine Department, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Gholamreza Nikbakht Brujeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Johannes Buitkamp
- Bavarian State Research Center for Agriculture, Institute of Animal Breeding, 85586 Grub, Germany
| | - Katarzyna Donskow-Łysoniewska
- Laboratory of Parasitology, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland; Department of Parasitology, Institute of Zoology, Faculty of Biology, University of Warsaw, ul. Miecznikowa, 02-096 Warsaw, Poland
| | - Karen Fairlie-Clarke
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Bearsden Road, Glasgow, Scotland G61 1QH, UK
| | - David Groth
- School of Pharmacy and Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - N Mahiza Md Isa
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan, Malaysia
| | - Michael J Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Bearsden Road, Glasgow, Scotland G61 1QH, UK; Department of Animal, Plant and Soil Science, Agribio, La Trobe University, Bundoora, VIC 3086, Australia.
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9
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MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites. Genes Immun 2019; 20:660-670. [PMID: 31068686 DOI: 10.1038/s41435-019-0075-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/18/2019] [Indexed: 01/31/2023]
Abstract
The Icelandic horse has been maintained as a closed population in its eponymous homeland for many generations, with no recorded introductions of new horses of any breed since the year 1000 CE. Here we determined the diversity of major histocompatibility complex (MHC) haplotypes in 156 Icelandic horses from two groups, based on a panel of 12 polymorphic intra-MHC microsatellites tested in families of various composition. We identified a total of 79 MHC haplotypes in these two groups, including one documented intra-MHC recombination event from a total of 147 observed meioses. None of these MHC haplotypes have been previously described in any other horse breed. Only one MHC homozygote was found in the entire population studied. These results indicate a very high level of MHC heterozygosity and haplotype diversity in the Icelandic horse. The environment in Iceland is remarkable for its lack of common agents of equine infectious disease, including equine herpesvirus type 1, influenza virus, and streptococcus equi. The driving forces for maintenance of MHC heterozygosity in Icelandic horses must thus be sought outside of these major horse pathogens. Based on our results, we propose that intra-MHC recombination may play a major role in the generation of novel haplotypes.
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10
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Dicks KL, Pemberton JM, Ballingall KT. Characterisation of major histocompatibility complex class IIa haplotypes in an island sheep population. Immunogenetics 2019; 71:383-393. [PMID: 30796497 PMCID: PMC6525122 DOI: 10.1007/s00251-019-01109-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
The ovine MHC class IIa is known to consist of six to eight loci located in close proximity on chromosome 20, forming haplotypes that are typically inherited without recombination. Here, we characterise the class IIa haplotypes within the Soay sheep (Ovis aries) on St. Kilda to assess the diversity present within this unmanaged island population. We used a stepwise sequence-based genotyping strategy to identify alleles at seven polymorphic MHC class IIa loci in a sample of 118 Soay sheep from four cohorts spanning 15 years of the long-term study on St. Kilda. DRB1, the most polymorphic MHC class II locus, was characterised first in all 118 sheep and identified six alleles. Using DRB1 homozygous animals, the DQA (DQA1, DQA2 and DQA2-like) and DQB (DQB1, DQB2 and DQB2-like) loci were sequenced, revealing eight haplotypes. Both DQ1/DQ2 and DQ2/DQ2-like haplotype configurations were identified and a single haplotype carrying three DQB alleles. A test sample of 94 further individuals typed at the DRB1 and DQA loci found no exceptions to the eight identified haplotypes and a haplotype homozygosity of 21.3%. We found evidence of historic positive selection at DRB1, DQA and DQB. The limited variation at MHC class IIa loci in Soay sheep enabled haplotype characterisation but showed that no single locus could capture the full extent of the expressed variation in the region.
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Affiliation(s)
- Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Keith T Ballingall
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 OPZ, UK
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11
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Ballingall KT, Dicks K, Kyriazopoulou P, Herrmann-Hoesing L. Allelic nomenclature for the duplicated MHC class II DQ genes in sheep. Immunogenetics 2018; 71:347-351. [PMID: 30415411 DOI: 10.1007/s00251-018-1096-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
The principal MHC class II molecules involved in the presentation of peptides to the antigen specific receptors on CD4+ T cells genes in sheep are derived from DR and DQ genes. Allelic nomenclature systems for the DRB1 and its partner DRA loci are available for Ovid's; however, no official nomenclature is available for the DQ genes which creates ambiguity within the research community. Ovine MHC haplotypes include at least two pairs of DQA and DQB genes, termed DQA1, DQB1 and DQA2, DQB2 and both sets are polymorphic and both seem to be functional. In a number of haplotypes, the DQA1 locus appears to be absent (DQA1-null) and is replaced by a second locus termed DQA2-like. Here, we identify families of alleles based on sequence similarity and phylogenetic clustering which correspond to each of the DQA and DQB genes identified in previous genomic and transcript analyses of homozygous animals. Using such criteria to cluster sequences, we have named 82 full-length and partial cDNA transcripts derived from domestic sheep (Ovis aries) which correspond to alleles at the Ovar-DQA1, DQA2, DQA2-like, DQB1, DQB2 and DQB2-like genes and provide associated sequence resources available to the research community through the IPD-MHC Database. This sets the basis for naming and annotation of DQ genes within the ovine MHC and may be used as a template for DQ genes in other ruminant species which will ultimately support research in livestock infectious disease.
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Affiliation(s)
| | - Kara Dicks
- The University of Edinburgh, Edinburgh, UK
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12
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Ballingall KT, Bontrop RE, Ellis SA, Grimholt U, Hammond JA, Ho CS, Kaufman J, Kennedy LJ, Maccari G, Miller D, Robinson J, Marsh SGE. Comparative MHC nomenclature: report from the ISAG/IUIS-VIC committee 2018. Immunogenetics 2018; 70:625-632. [PMID: 30039257 DOI: 10.1007/s00251-018-1073-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/13/2018] [Indexed: 12/24/2022]
Abstract
Significant progress has been made over the last decade in defining major histocompatibility complex (MHC) diversity at the nucleotide, allele, haplotype, diplotype, and population levels in many non-human species. Much of this progress has been driven by the increased availability and reduced costs associated with nucleotide sequencing technologies. This report provides an update on the activities of the comparative MHC nomenclature committee which is a standing committee of both the International Society for Animal Genetics (ISAG) and the International Union of Immunological Societies (IUIS) where it operates under the umbrella of the Veterinary Immunology Committee (VIC). A previous report from this committee in 2006 defined the role of the committee in providing guidance in the development of a standardized nomenclature for genes and alleles at MHC loci in non-human species. It described the establishment of the Immuno Polymorphism Database, IPD-MHC, which continues to provide public access to high quality MHC sequence data across a range of species. In this report, guidelines for the continued development of a universal MHC nomenclature framework are described, summarizing the continued development of each species section within the IPD-MHC project.
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Affiliation(s)
- Keith T Ballingall
- Moredun Research Institute, Midlothian, UK and Chair of the Comparative MHC Nomenclature Committee, Edinburgh, Scotland, UK.
| | | | | | | | | | | | | | - Lorna J Kennedy
- Centre for Integrated Genomic Medical Research, Manchester, UK
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, Surrey, UK.,Anthony Nolan Research Institute, London, UK
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - James Robinson
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
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