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Song K, Yu JY, Li J, Li M, Peng LY, Yi PF. Astragaloside IV Regulates cGAS-STING Signaling Pathway to Alleviate Immunosuppression Caused by PRRSV Infection. Viruses 2023; 15:1586. [PMID: 37515271 PMCID: PMC10383485 DOI: 10.3390/v15071586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/01/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) poses a global threat to pig health and results in significant economic losses. Impaired innate and adaptive immune responses are evident during PRRSV infection. Cyclic GMP-AMP synthase (cGAS), a classical pattern recognition receptor recognizing mainly intracytoplasmic DNA, induces type I IFN responses through the cGAS-STING signaling pathway. It has also been demonstrated that cGAS-STING is involved in PRRSV infection. This study utilized the qRT-PCR, ELISA, and WB methods to examine the effects of Astragaloside IV (AS-IV) on the regulation of innate immune function and cGAS-STING signaling pathway in porcine alveolar macrophages. The results showed that AS-IV attenuated the decreased innate immune function caused by PRRSV infection, restored the inhibited cGAS-STING signaling pathway, and increased the expression of interferon, ultimately exerting antiviral effects. Moreover, these results suggest that AS-IV may be a promising candidate for a new anti-PRRSV antiviral, and its mechanism of action may provide insights for developing novel antiviral agents.
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Affiliation(s)
- Ke Song
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jia-Ying Yu
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jiang Li
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Miao Li
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Lu-Yuan Peng
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Peng-Fei Yi
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
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2
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Wu J, Liu R, Li H, Yu H, Yang Y. Genetic diversity analysis in Chinese miniature pigs using swine leukocyte antigen complex microsatellites. Anim Biosci 2021; 34:1757-1765. [PMID: 33677912 PMCID: PMC8563246 DOI: 10.5713/ab.20.0637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/11/2021] [Indexed: 11/27/2022] Open
Abstract
Objective The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited. Methods Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds. Results In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively. Conclusion This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.
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Affiliation(s)
- Jinhua Wu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan 528225, China
| | - Ronghui Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan 528225, China.,Agriculture and Rural Affairs Committee of Kaizhou District, Chongqing Municipality, Chongqing 405400, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan 528225, China
| | - Hui Yu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan 528225, China
| | - Yalan Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan 528225, China
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3
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Zhang F, Yang T, Ao H, Zhai L, Tan Z, Wang Y, Xing K, Zhao X, Wang Z, Yu Y, Wang C. Novel nucleotide variants in SLA-DOB and CD4 are associated with immune traits in pregnant sows. Gene 2019; 707:22-29. [PMID: 31026568 DOI: 10.1016/j.gene.2019.04.057] [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: 12/06/2018] [Revised: 03/28/2019] [Accepted: 04/19/2019] [Indexed: 11/17/2022]
Abstract
Reinforcing the immunity of pregnant sows can not only improve their own health condition but also increase the survival rate and healthy status of their piglets. This study aims to find single-nucleotide polymorphism (SNP) and molecular markers that are associated with the immune traits of pregnant sows. SLA-DOB and CD4 were selected as candidate genes, and blood samples were randomly collected from pregnant Landrace sows and used to detect T-lymphocyte subsets, interferon alpha, interleukin 6, Toll-like receptor 3, serum antibody immunoglobulin G, and porcine reproductive and respiratory syndrome virus-specific antibody. Then, association analyses were conducted for the polymorphic sites of candidate genes with immune traits. We found 12 mutations in the two genes and conducted an association study with eight of them. Our results indicated that among the eight mutations, SNP1, SNP2, and SNP3 of the SLA-DOB gene and Ins9, SNP10, and SNP11 in the CD4 gene are newly discovered mutations. Except for SNP1, SNP3, and SNP11, the other five SNPs are associated with at least one immune trait tested. Especially, SNP2 and Ins9 are significantly associated with at least one of the T-lymphocyte subgroups and at least one antibody. These novel mutations have potential important effects on the polymorphic loci of the above immune traits in pregnant sows. The results suggest that the SLA-DOB and CD4 genes and their genetic mutations can be considered as important candidate genes and mutations for the immunity of pregnant sows.
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Affiliation(s)
- Fengxia Zhang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Ting Yang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hong Ao
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Zhai
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zhen Tan
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Yuan Wang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Kai Xing
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xitong Zhao
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zhiquan Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China..
| | - Chuduan Wang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China..
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4
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Gao FS, Feng L, Jiang P, Li ZB, Gao H, Zhai XX, Zhang ZH, Hu X. Expression, purification, crystallization and preliminary X-ray diffraction analysis of swine leukocyte antigen 2 complexed with a CTL epitope AS64 derived from Asia1 serotype of foot-and-mouth disease virus. BMC Vet Res 2018; 14:407. [PMID: 30563524 PMCID: PMC6299498 DOI: 10.1186/s12917-018-1742-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 12/07/2018] [Indexed: 02/05/2023] Open
Abstract
Background Currently, the structural characteristics of the swine major histocompatibility complex (MHC) class I molecule, also named swine leukocyte antigen class I (SLA-I) molecule need to be further clarified. Results A complex of SLA-I constituted by an SLA-2*HB01 molecule with swine β2-microglobulin and a cytotoxic T lymphocyte (CTL) epitope FMDV-AS64 (ALLRSATYY) derived from VP1 protein (residues 64–72) of Asia 1 serotype of foot-and-mouth disease virus (FMDV) was expressed, refolded, purified and crystallized. By preliminary X-ray diffraction analysis, it was shown that the diffraction resolution of the crystal was 2.4 Å and the space group belonged to P212121 with unit cell parameters a = 48.37, b = 97.75, c = 166.163 Å. Conclusion This research will be in favor of illuminating the structural characteristics of an SLA-2 molecule associated with a CTL epitope derived from Asia1 serotype of FMDV.
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Affiliation(s)
- Feng-Shan Gao
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China.
| | - Lei Feng
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Ping Jiang
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Zi-Bin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100094, People's Republic of China
| | - Hua Gao
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Xiao-Xin Zhai
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Zong-Hui Zhang
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
| | - Xiao Hu
- Department of Bioengineering,
- College of Life Science and Technology, Dalian University, Xuefu street 10, Dalian, Liaoning, 116622, People's Republic of China
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5
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Fan S, Wang Y, Wang X, Huang L, Zhang Y, Liu X, Zhu W. Analysis of the affinity of influenza A virus protein epitopes for swine MHC I by a modified in vitro refolding method indicated cross-reactivity between swine and human MHC I specificities. Immunogenetics 2018; 70:671-680. [PMID: 29992375 DOI: 10.1007/s00251-018-1070-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/20/2018] [Indexed: 11/28/2022]
Abstract
In vitro refolding assays can be used to investigate the affinity and stability of the binding of epitope peptides to major histocompatibility complex (MHC) class I molecules, which are key factors in the presentation of peptides to cytotoxic T lymphocytes (CTLs). The recognition of peptide epitopes by CTLs is crucial for protection against influenza A virus (IAV) infection. The peptide-binding motif of the swine SLA-3*hs0202 molecule has been previously reported and partly overlaps with the binding motif of the most abundant human MHC allele, HLA-A*0201. In this study, we screened all the protein sequences of the swine-origin epidemic IAV strain A/Beijing/01/2009 (H1N1), and a total of 73 9-mer epitope peptides were predicted to fit the consensus motif of the swine SLA-3*hs0202 or HLA-A*0201 molecule. Then, 14 peptides were selected, and their affinities to SLA-3*hs0202 were tested by a modified in vitro refolding assay. Our results show that ten epitopes could tolerate gel filtration, indicating that these epitopes formed stable or partly stable complexes with SLA-3*hs0202. Eight out of the ten epitopes have been previously reported as HLA-A2-restricted epitopes, which implied cross-reactivity between swine and human MHC I specificities. Furthermore, the modified mini-system refolding method could be applied for the screening of peptides because the refolding efficiency remained almost unchanged with the positive peptide (HA-KMN9) subjected to size-exclusion chromatography and Resource Q anion-exchange chromatography. The results presented here provide new insight into the development of epitope-based vaccines to control IAV and increase our understanding of swine molecular immunology.
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Affiliation(s)
- Shuhua Fan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, People's Republic of China. .,Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, People's Republic of China.
| | - Yongli Wang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, People's Republic of China
| | - Xian Wang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, People's Republic of China
| | - Li Huang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, People's Republic of China.,Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, People's Republic of China
| | - Yunxia Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, People's Republic of China.,Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, People's Republic of China
| | - Xiaomeng Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, People's Republic of China.,Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, People's Republic of China
| | - Wenshuai Zhu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, People's Republic of China.,Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, People's Republic of China
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6
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Zhang S, Yang J, Wang L, Li Z, Pang P, Li F. SLA-11 mutations are associated with litter size traits in Large White and Chinese DIV pigs. Anim Biotechnol 2018; 30:212-218. [PMID: 29936889 DOI: 10.1080/10495398.2018.1471401] [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] [Indexed: 10/28/2022]
Abstract
Litter size is an important economic traits in pigs. SLA-11 gene is a member of SLA (swine leukocyte antigen) complex. In our previous study, the SLA-11 gene was differentially expressed in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows. Here, we identified two mutations (c.754-132 T > C and c.1421 + 38 T > C) in SLA-11 gene and analyzed the associations of two SNPs with litter size traits in Large White (n = 263) and DIV (n = 117) sows. The results showed that in Large White pigs, SLA-11 c.754-132 CC sows produced 0.74 and 0.87 more pigs per litter for TNB and NBA of all parities than did TT sows (p < .05); In DIV pigs, SLA-11 c.754-132 CC sows produced 1.17 more pigs per litter for TNB of all parities than did TC sows (p < .05). In Large White pigs, SLA-11 c.1421 + 38 CC sows produced 0.9 more pigs per litter for TNB of all parities than did TT sows (p < .05), while in DIV pigs SLA-11 c.1421 + 38 CC sows produced 0.84 and 0.7 less pigs per litter for TNB and NBA of all parities than did TT sows (p < .05). Our research indicated that SLA-11 mutations were potential molecular markers for improving the litter size traits in pigs.
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Affiliation(s)
- Shuna Zhang
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Jiahao Yang
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Lei Wang
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Zhenzhu Li
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Panfei Pang
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Fenge Li
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China.,b The Cooperative Innovation Center for Sustainable Pig Production , Wuhan , PR China
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7
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Fan S, Wang Y, Wang S, Wang X, Wu Y, Li Z, Zhang N, Xia C. Polymorphism and peptide-binding specificities of porcine major histocompatibility complex (MHC) class I molecules. Mol Immunol 2018; 93:236-245. [DOI: 10.1016/j.molimm.2017.06.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/07/2017] [Accepted: 06/10/2017] [Indexed: 10/19/2022]
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8
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Yin XM, Gan LN, Qin WY, Sun SY, Zhu GQ, Wu SL, Bao WB. Differential expression of genes BPI, TAP1, SLA-1 and SLA-3 in Escherichia coli F18-resistant and sensitive Meishan post-weaning piglets. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea. Genes (Basel) 2016; 7:genes7070036. [PMID: 27429004 PMCID: PMC4962006 DOI: 10.3390/genes7070036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 11/16/2022] Open
Abstract
The swine leukocyte antigens (SLAs) are the multigene families related to immune responses. Little is known about the effect of the DRA gene on diarrheal disease. This study reported the genetic diversity of the DRA gene in exons 1, 3 and 4 in 290 Chinese Yantai black pigs. No variation was identified in exon 3. In exon 1, three genotypes and two alleles were identified, generated by two single nucleotide polymorphisms (SNPs). In exon 4, there were eight genotypes and five alleles containing seven SNPs were detected with four SNPs being novel SNPs. The low polymorphism found in swine DRA is consistent with the concept that the DRA gene is highly conserved among all mammalian species. Statistical analyses indicated that the genotypes of exon 1 were not significantly associated with piglet diarrhea (p > 0.05); however, genotypes C₄C₄ (1.80 ± 0.33) and A₄E₄ (1.66 ± 0.25) of exon 4 were significantly susceptible to diarrhea (p < 0.01). These indicate that the particular genotypes of the DRA gene are susceptible to diarrheal disease, which provides valuable information for disease-resistance breeding in swine.
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10
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Ando A, Imaeda N, Ohshima S, Miyamoto A, Kaneko N, Takasu M, Shiina T, Kulski JK, Inoko H, Kitagawa H. Characterization of swine leukocyte antigen alleles and haplotypes on a novel miniature pig line, Microminipig. Anim Genet 2014; 45:791-8. [DOI: 10.1111/age.12199] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2014] [Indexed: 11/29/2022]
Affiliation(s)
- A. Ando
- Department of Molecular Life Science; Division of Basic Medical Science and Molecular Medicine; Tokai University School of Medicine; Isehara 259-1193 Japan
| | - N. Imaeda
- Department of Veterinary Medicine; Faculty of Applied Biological Sciences; Gifu University; Gifu 501-1193 Japan
| | - S. Ohshima
- Department of Molecular Life Science; Division of Basic Medical Science and Molecular Medicine; Tokai University School of Medicine; Isehara 259-1193 Japan
| | - A. Miyamoto
- Department of Molecular Life Science; Division of Basic Medical Science and Molecular Medicine; Tokai University School of Medicine; Isehara 259-1193 Japan
| | - N. Kaneko
- Fuji Micra Inc.; Fujinomiya 418-0005 Japan
| | - M. Takasu
- Department of Veterinary Medicine; Faculty of Applied Biological Sciences; Gifu University; Gifu 501-1193 Japan
| | - T. Shiina
- Department of Molecular Life Science; Division of Basic Medical Science and Molecular Medicine; Tokai University School of Medicine; Isehara 259-1193 Japan
| | - J. K. Kulski
- Department of Molecular Life Science; Division of Basic Medical Science and Molecular Medicine; Tokai University School of Medicine; Isehara 259-1193 Japan
- Centre for Forensic Science; The University of Western Australia; Nedlands WA 6008 Australia
| | - H. Inoko
- Department of Molecular Life Science; Division of Basic Medical Science and Molecular Medicine; Tokai University School of Medicine; Isehara 259-1193 Japan
| | - H. Kitagawa
- Department of Veterinary Medicine; Faculty of Applied Biological Sciences; Gifu University; Gifu 501-1193 Japan
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11
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Gao C, Jiang Q, Guo D, Liu J, Han L, Qu L. Characterization of swine leukocyte antigen (SLA) polymorphism by sequence-based and PCR-SSP methods in Chinese Bama miniature pigs. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 45:87-96. [PMID: 24560654 DOI: 10.1016/j.dci.2014.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 06/03/2023]
Abstract
The highly polymorphic swine leukocyte antigen (SLA) genes have been repeatedly shown to influence swine immune traits, disease resistance, vaccine responsiveness and tumour penetrance. Analysis of the SLA diversity in as many pig breeds as possible is important to clarify the relationships between SLA genes and diseases or traits, and develop these pigs as valuable animal models for biomedical research. The Chinese Bama miniature pig breed is an economically significant breed that is available at several research institutions in China. In this study, we identified a total of 32 alleles at five polymorphic SLA loci (SLA-1, SLA-3, SLA-2, DRB1 and DQB1) representing nine class I and seven class II haplotypes using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. The possible functional sites of the SLA genes were predicted and analyzed by comparison with those of the human and mouse. Based on the sequence information, we subsequently developed a rapid PCR-based typing assay using sequence-specific primers (PCR-SSP) to efficiently follow the SLA types of the progeny. In the studied cohort (2n = 562), the most prevalent Haplotype Hp-35.6 (SLA-1(∗)1201, SLA-1(∗)1301-SLA-3(∗)0502-SLA-2(∗)1001-DRB1(∗)0501-DQB1(∗)0801) was identified in 182 Bama pigs with a frequency of 32.38%. The presence of the duplicated SLA-1 locus was confirmed in five of the class I haplotypes. Moreover, we identified two crossovers within the class I region and one between the class I and class II regions, which corresponded to recombination frequencies of 0.36% and 0.18%, respectively. The information of this study is essential for an understanding of the SLA allelic architecture and diversity, and it will be helpful for studying the adaptive immune response and further developing the more effective vaccines in the context of SLA specificities.
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Affiliation(s)
- Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Qian Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Dongchun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Jiasen Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Liandong Qu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China.
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12
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Le MT, Choi H, Choi MK, Nguyen DT, Kim JH, Seo HG, Cha SY, Seo K, Chun T, Schook LB, Park C. Comprehensive and high-resolution typing of swine leukocyte antigen DQA from genomic DNA and determination of 25 new SLA class II haplotypes. ACTA ACUST UNITED AC 2013; 80:528-35. [PMID: 23137324 DOI: 10.1111/tan.12017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We previously reported the development of genomic-DNA-based high-resolution genotyping methods for SLA-DQB1 and DRB1. Here, we report the successful typing of SLA-DQA using similar methodological principles. We designed a method for comprehensive genotyping of SLA-DQA using intronic sequence information of SLA-DQA exon 2 that we had obtained from 12 animals with different SLA-DQB1 genotypes. We expanded our typing to 76 selected animals with diverse DQB1 and DRB1 genotypes, 140 random animals from 7 pig breeds, and 3 wild boars. This resulted in the identification of 17 DQA alleles with 49 genotypes. Two new alleles were identified from wild boars. Combine with SLA-DQB1, and DRB1 typing results, we identified 34 SLA class II haplotypes including 25 that were previously unreported.
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Affiliation(s)
- M T Le
- Department of Animal Biotechnology, Konkuk University, Seoul, South Korea
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13
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Domestication does not narrow MHC diversity in Sus scrofa. Immunogenetics 2012; 65:195-209. [PMID: 23239371 DOI: 10.1007/s00251-012-0671-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 11/21/2012] [Indexed: 10/27/2022]
Abstract
The Major Histocompatibility Complex (MHC) is a multigene family of outstanding polymorphism. MHC molecules bind antigenic peptides in the peptide-binding region (PBR) that consists of five binding pockets (P). In this study, we compared the genetic diversity of domestic pigs to that of the modern representatives of their wild ancestors, the wild boar, in two MHC loci, the oligomorphic DQA and the polymorphic DRB1. MHC nucleotide polymorphism was compared with the actual functional polymorphism in the PBR and the binding pockets P1, P4, P6, P7, and P9. The analysis of approximately 200 wild boars collected throughout Europe and 120 domestic pigs from four breeds (three pureblood, Pietrain, Leicoma, and Landrace, and one mixed Danbred) revealed that wild boars and domestic pigs share the same levels of nucleotide and amino acid polymorphism, allelic richness, and heterozygosity. Domestication did not appear to act as a bottleneck that would narrow MHC diversity. Although the pattern of polymorphism was uniform between the two loci, the magnitude of polymorphism was different. For both loci, most of the polymorphism was located in the PBR region and the presence of positive selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous substitutions in the PBR. P4 and P6 were the most polymorphic binding pockets. Functional polymorphism, i.e., the number and the distribution of pocket variants within and among populations, was significantly narrower than genetic polymorphism, indicative of a hierarchical action of selection pressures on MHC loci.
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Jung WY, Seo DW, Choi NR, Lee JH, Jin DI, Hwang SS, Yang BC, Chung HJ, Kim KW, Park JK, Lee HC. Investigation of SLA class I and II haplotypes in the NIH miniature pigs. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0136-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ye L, Zi C, Pan ZY, Zhu J, Du ZD, Zhu GQ, Huang XG, Bao WB, Wu SL. Investigation of the relationship between SLA-1 and SLA-3 gene expression and susceptibility to Escherichia coli F18 in post-weaning pigs. Comp Immunol Microbiol Infect Dis 2012; 35:23-30. [PMID: 22019298 DOI: 10.1016/j.cimid.2011.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 09/24/2011] [Accepted: 09/27/2011] [Indexed: 11/18/2022]
Abstract
Porcine post-weaning diarrhea and edema disease are principally caused by Escherichia coli strains that produce F18 adhesin. FUT1 genotyping and receptor binding studies divided piglets into E. coli F18-resistant and -sensitive groups, and the roles of SLA-1 and SLA-3 were investigated. SLA-1 and SLA-3 expression was detected in 11 pig tissues, with higher levels of SLA-1 in lung, immune tissues and gastrointestinal tract, and higher levels of SLA-3 also in lung and lymphoid tissues. Both genes were expressed higher in F18-resistant piglets, and their expression was positively correlated in different tissues; a negative correlation was observed in some tissues of F18-sensitive group, particularly in lung and lymphatic samples. Gene ontology and pathway analyses showed that SLA-1 and SLA-3 were involved in 37 biological processes, including nine pathways related to immune functions. These observations help to elucidate the relationship between SLA class I genes and E. coli F18-related porcine gastrointestinal tract diseases.
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Affiliation(s)
- L Ye
- College of Animal Science and Technology, Yangzhou University, China
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Pan X, Qi J, Zhang N, Li Q, Yin C, Chen R, Gao F, Xia C. Complex assembly, crystallization and preliminary X-ray crystallographic studies of the swine major histocompatibility complex molecule SLA-1*1502. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:568-71. [PMID: 21543863 PMCID: PMC3087642 DOI: 10.1107/s174430911100741x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 02/26/2011] [Indexed: 05/30/2023]
Abstract
In order to illustrate the structure of the swine MHC class I (SLA-I) molecule and to evaluate the cytotoxic T lymphocyte (CTL) response against porcine reproductive and respiratory syndrome virus (PRRSV), the ternary complex of the SLA-I molecule termed SLA-1*1502 with β(2)-microglobulin and the CTL epitope TMPPGFELY (PRRSV-NSP9(TY9)) derived from PRRSV nonstructural protein 9 (residues 198-206) was assembled and crystallized. The crystal diffracted X-rays to 2.2 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 66.1, b = 74.1, c = 98.6 Å; it contained one molecule in the asymmetric unit. The Matthews coefficient and the solvent content were calculated to be 2.74 Å(3) Da(-1) and 55.17%, respectively. The results will be helpful in obtaining insight into the structural basis of the presentation of viral epitopes by SLA-I.
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Affiliation(s)
- Xiaocheng Pan
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Bejing 100094, People’s Republic of China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, People’s Republic of China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Bejing 100094, People’s Republic of China
| | - Qirun Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Bejing 100094, People’s Republic of China
| | - Chunsheng Yin
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Bejing 100094, People’s Republic of China
| | - Rong Chen
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Bejing 100094, People’s Republic of China
| | - Feng Gao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Bejing 100094, People’s Republic of China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, People’s Republic of China
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Chung H, McClure MC. Characterization of microsatellite loci in the SLA class I region. Genomics 2011; 97:223-34. [DOI: 10.1016/j.ygeno.2010.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/16/2010] [Accepted: 12/19/2010] [Indexed: 11/29/2022]
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Grosse-Brinkhaus C, Jonas E, Buschbell H, Phatsara C, Tesfaye D, Jüngst H, Looft C, Schellander K, Tholen E. Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population. Genet Sel Evol 2010; 42:39. [PMID: 20977705 PMCID: PMC2984386 DOI: 10.1186/1297-9686-42-39] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 10/26/2010] [Indexed: 11/10/2022] Open
Abstract
Background Quantitative trait loci (QTL) analyses in pig have revealed numerous individual QTL affecting growth, carcass composition, reproduction and meat quality, indicating a complex genetic architecture. In general, statistical QTL models consider only additive and dominance effects and identification of epistatic effects in livestock is not yet widespread. The aim of this study was to identify and characterize epistatic effects between common and novel QTL regions for carcass composition and meat quality traits in pig. Methods Five hundred and eighty five F2 pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP) spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F2 animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program. Results A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance. Conclusions Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.
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YEOM SC, PARK CG, LEE BC, LEE WJ. SLA typing using the PCR-SSP method and establishment of the SLA homozygote line in pedigreed SNU miniature pigs. Anim Sci J 2010; 81:158-64. [DOI: 10.1111/j.1740-0929.2009.00727.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ho CS, Martens GW, Amoss MS, Gomez-Raya L, Beattie CW, Smith DM. Swine leukocyte antigen (SLA) diversity in Sinclair and Hanford swine. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2010; 34:250-257. [PMID: 19782700 DOI: 10.1016/j.dci.2009.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 09/15/2009] [Accepted: 09/18/2009] [Indexed: 05/28/2023]
Abstract
The swine leukocyte antigen (SLA) haplotype B is associated with increased penetrance of the tumor traits in Sinclair swine cutaneous melanoma (SSCM). We established a series of SinclairxHanford swine crosses to facilitate genetic mapping of the tumor-associated loci. In this study, the SLA diversity in the founding animals was characterized for effective selection of maximum tumor penetrance in the pedigrees. Using the sequence-based typing (SBT) method we identified a total of 29 alleles at five polymorphic SLA loci (SLA-1, SLA-3, SLA-2, DRB1 and DQB1) representing six class I and five class II haplotypes. We subsequently developed a rapid PCR-based typing assay using sequence-specific primers (PCR-SSP) to efficiently follow the SLA types of the crossbred progeny. In a total of 469 animals we identified three crossovers within the class I region and three between the class I and class II regions, which corresponded to recombination frequencies of 0.39% and 0.56%, respectively. We also confirmed the presence of two expressed SLA-1 loci in three of the class I haplotypes and were able to determine the relative chromosomal arrangement of the duplicated loci in two haplotypes. This study furthers our understanding of the allelic architecture and polymorphism of the SLA system and will facilitate the mapping of loci associated with the expression of SSCM.
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Affiliation(s)
- Chak-Sum Ho
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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Pan G, Fu Y, Zuo B, Ren Z, Xu D, Lei M, Zheng R, Xiong YZ. Molecular characterization, expression profile and association analysis with fat deposition traits of the porcine APOM gene. Mol Biol Rep 2009; 37:1363-71. [PMID: 19326253 DOI: 10.1007/s11033-009-9518-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 03/17/2009] [Indexed: 10/21/2022]
Abstract
Apolipoprotein M (APOM), a novel apolipoprotein presented mostly in high-density lipoprotein (HDL) in plasma, is involved in lipid and lipoprotein metabolism. Through comparative mapping, we have mapped this gene to SSC7 p1.1 in which many QTLs affecting fat deposition traits have been reported. As a candidate gene for fat deposition traits, in this study, we obtained the 742-bp mRNA sequence of porcine APOM including the full coding region and encoding a protein of 188 amino acids. The sequence was deposited into the GenBank under the accession no. DQ329240. Semi-quantitative RT-PCR results showed that the porcine APOM gene is expressed predominantly in liver and kidney tissue. The genomic sequence of this gene which contains six exons and five introns, is 3,621 bp in length (DQ272488). Bioinformatic analysis of the 5' regulatory region has revealed that classical TATA-box element and species conserved Hepatocyte nuclear factor-1a (HNF-1alpha) biding site were represented in this region. A G2289C single nucleotide polymorphism (SNP) in the intron 2 of porcine APOM gene detected as an Eco130I PCR-restriction fragment length polymorphism (PCR-RFLP) showed allele frequency differences among three purebreds. Association of the genotypes with fat deposition traits showed that different genotypes of porcine APOM gene were significantly associated with leaf fat weight (P < 0.05), backfat thickness at shoulder (P < 0.05), backfat thickness at thorax-waist (P < 0.05), backfat thickness at buttock (P < 0.01) and average backfat thickness over shoulder, thorax-waist and buttock (P < 0.01).
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Affiliation(s)
- Gang Pan
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
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Lunney JK, Ho CS, Wysocki M, Smith DM. Molecular genetics of the swine major histocompatibility complex, the SLA complex. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2009; 33:362-374. [PMID: 18760302 DOI: 10.1016/j.dci.2008.07.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/10/2008] [Accepted: 07/13/2008] [Indexed: 05/26/2023]
Abstract
The swine major histocompatibility complex (MHC) or swine leukocyte antigen (SLA) complex is one of the most gene-dense regions in the swine genome. It consists of three major gene clusters, the SLA class I, class III and class II regions, that span approximately 1.1, 0.7 and 0.5Mb, respectively, making the swine MHC the smallest among mammalian MHC so far examined and the only one known to span the centromere. This review summarizes recent updates to the Immuno Polymorphism Database-MHC (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla/) which serves as the repository for maintaining a list of all SLA recognized genes and their allelic sequences. It reviews the expression of SLA proteins on cell subsets and their role in antigen presentation and regulating immune responses. It concludes by discussing the role of SLA genes in swine models of transplantation, xenotransplantation, cancer and allergy and in swine production traits and responses to infectious disease and vaccines.
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Dohm JC, Tsend-Ayush E, Reinhardt R, Grützner F, Himmelbauer H. Disruption and pseudoautosomal localization of the major histocompatibility complex in monotremes. Genome Biol 2008; 8:R175. [PMID: 17727704 PMCID: PMC2375005 DOI: 10.1186/gb-2007-8-8-r175] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 08/26/2007] [Accepted: 08/29/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The monotremes, represented by the duck-billed platypus and the echidnas, are the most divergent species within mammals, featuring a flamboyant mix of reptilian, mammalian and specialized characteristics. To understand the evolution of the mammalian major histocompatibility complex (MHC), the analysis of the monotreme genome is vital. RESULTS We characterized several MHC containing bacterial artificial chromosome clones from platypus (Ornithorhynchus anatinus) and the short-beaked echidna (Tachyglossus aculeatus) and mapped them onto chromosomes. We discovered that the MHC of monotremes is not contiguous and locates within pseudoautosomal regions of two pairs of their sex chromosomes. The analysis revealed an MHC core region with class I and class II genes on platypus and echidna X3/Y3. Echidna X4/Y4 and platypus Y4/X5 showed synteny to the human distal class III region and beyond. We discovered an intron-containing class I pseudogene on platypus Y4/X5 at a genomic location equivalent to the human HLA-B,C region, suggesting ancestral synteny of the monotreme MHC. Analysis of male meioses from platypus and echidna showed that MHC chromosomes occupy different positions in the meiotic chains of either species. CONCLUSION Molecular and cytogenetic analyses reveal new insights into the evolution of the mammalian MHC and the multiple sex chromosome system of monotremes. In addition, our data establish the first homology link between chicken microchromosomes and the smallest chromosomes in the monotreme karyotype. Our results further suggest that segments of the monotreme MHC that now reside on separate chromosomes must once have been syntenic and that the complex sex chromosome system of monotremes is dynamic and still evolving.
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Affiliation(s)
- Juliane C Dohm
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Enkhjargal Tsend-Ayush
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide 5005 SA, Australia
| | - Richard Reinhardt
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Frank Grützner
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide 5005 SA, Australia
| | - Heinz Himmelbauer
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
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Reiner G, Kliemt D, Willems H, Berge T, Fischer R, Köhler F, Hepp S, Hertrampf B, Daugschies A, Geldermann H, Mackenstedt U, Zahner H. Mapping of quantitative trait loci affecting resistance/susceptibility to Sarcocystis miescheriana in swine. Genomics 2007; 89:638-46. [PMID: 17336038 DOI: 10.1016/j.ygeno.2007.01.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/15/2007] [Accepted: 01/24/2007] [Indexed: 10/23/2022]
Abstract
The outcome of infectious diseases in vertebrates is under genetic control at least to some extent. In swine, e.g., marked differences in resistance/susceptibility to Sarcocystis miescheriana have been shown between Chinese Meishan and European Pietrain pigs, and these differences are associated with high heritabilities. A first step toward the identification of genes and polymorphisms causal for these differences may be the mapping of quantitative trait loci (QTLs). Considering clinical, immunological, and parasitological traits in the above model system, this survey represents the first QTL study on parasite resistance in pigs. QTL mapping was performed in 139 F(2) pigs of a Meishan/Pietrain family infected with S. miescheriana. Fourteen genome-wide significant QTLs were mapped to several chromosomal areas. Among others, major QTLs were identified for bradyzoite numbers in skeletal muscles (F = 17.4; p < 0.001) and for S. miescheriana-specific plasma IgG(2) levels determined 42 days p.i. (F = 20.9; p < 0.001). The QTLs were mapped to different regions of chromosome 7, i.e., to the region of the major histocompatibility complex (bradyzoites) and to an immunoglobulin heavy chain cluster, respectively. These results provide evidence for a direct and causal role for gene variants within these gene clusters (cis-acting) in differences in resistance to S. miescheriana.
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Affiliation(s)
- Gerald Reiner
- Department of Veterinary Clinical Sciences, University of Giessen, D-35392 Giessen, Germany.
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Ho CS, Rochelle ES, Martens GW, Schook LB, Smith DM. Characterization of swine leukocyte antigen polymorphism by sequence-based and PCR-SSP methods in Meishan pigs. Immunogenetics 2006; 58:873-82. [PMID: 17039361 DOI: 10.1007/s00251-006-0145-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 07/14/2006] [Indexed: 10/24/2022]
Abstract
Resource herds of swine leukocyte antigen (SLA)-characterized pigs are an important tool for the study of immune responses, disease resistance, and production traits. They are also valuable large animal models for biomedical research, such as transplantation. The Meishan breed of pig is an economically significant breed that is available at several research institutions in the United States. We have characterized the SLA polymorphism of the breeding stock in the herd maintained at the University of Illinois and developed a simple assay to SLA type individuals within that herd. We have used a reverse transcription-polymerase chain reaction (RT-PCR)-based SLA typing method to clone and DNA sequence 19 SLA alleles at three SLA class Ia (SLA-1, SLA-2, and SLA-3) and two SLA class II (SLA-DRB1 and SLA-DQB1) loci. Based on this sequence information, a rapid SLA typing assay was developed to discriminate each allele using PCR with sequence-specific primers (PCR-SSP). Using this method, we were able to characterize the entire Meishan breeding stock and identify four SLA haplotypes present in the herd. The combination of SLA typing by cloning and DNA sequencing with PCR-SSP is therefore a valuable tool for the characterization of SLA alleles and haplotypes in resource herds of pigs.
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Affiliation(s)
- Chak-Sum Ho
- Transplant Immunology Laboratory, Department of Pathology, Baylor University Medical Center, 3500 Gaston Avenue, Dallas, TX 75246, USA
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Smith DM, Lunney JK, Ho CS, Martens GW, Ando A, Lee JH, Schook L, Renard C, Chardon P. Nomenclature for factors of the swine leukocyte antigen class II system, 2005. ACTA ACUST UNITED AC 2006; 66:623-39. [PMID: 16305679 DOI: 10.1111/j.1399-0039.2005.00492.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A systematic nomenclature for the genes and alleles of the swine major histocompatibility complex (MHC) is essential to the development and communication of research in swine immunology. The Swine Leukocyte Antigen (SLA) Nomenclature Committee of the International Society for Animal Genetics (ISAG) has reviewed all of the DNA-sequence information for MHC class II genes, available in GenBank/EMBL/DDBJ databases, and the associated published reports to develop such a systematic nomenclature. This article summarizes the proposed nomenclature, which parallels the World Health Organization's nomenclature for factors of the human MHC. The SLA class II genes expressed on the cell membrane will be noted as SLA-DRA, SLA-DRB1, SLA-DQA, and SLA-DQB1. Nomenclature assignments for all SLA class II GenBank sequences are now noted. The committee will add new SLA class II allele designations, as they are discovered, and will maintain a publicly available list of all recognized genes and alleles using the Immuno Polymorphism Database (IPD). The sequences will be available from the IPD-MHC section of the database which contains non-human MHC sequences (http://www.ebi.ac.uk/ipd/mhc/sla/).
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Affiliation(s)
- D M Smith
- Baylor University Medical Center, Dallas, TX, USA.
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Yaden BC, Garcia M, Smith TPL, Rhodes SJ. Two promoters mediate transcription from the human LHX3 gene: involvement of nuclear factor I and specificity protein 1. Endocrinology 2006; 147:324-37. [PMID: 16179410 DOI: 10.1210/en.2005-0970] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The LHX3 transcription factor is required for pituitary and nervous system development in mammals. Mutations in the human gene are associated with hormone-deficiency diseases. The gene generates two mRNAs, hLHX3a and hLHX3b, which encode three proteins with different properties. Here, the cis elements and trans-acting factors that regulate the basal transcription of the two mRNAs are characterized. A comparative approach was taken featuring analysis of seven mammalian Lhx3 genes, with a focus on the human gene. Two conserved, TATA-less, GC-rich promoters that are used to transcribe the mRNAs precede exons 1a and 1b of hLHX3. Transcription start sites were mapped for both promoters. Deletion experiments showed most activity for reporter genes containing the basal promoters in the context of -2.0 kb of hLHX3a and 1.8 kb of intron 1a (hLHX3b). Transfection, site-directed mutation, electrophoretic mobility shift, Southwestern blot, and chromatin immunoprecipitation approaches were used to characterize the interaction of transcription factors with conserved elements in the promoters. Specificity protein 1 is a regulator of both promoters through interaction with GC boxes. In addition, a distal element within intron 1a that is recognized by nuclear factor I is critical for hLHX3b promoter function. We conclude that dual promoters allow regulated production of two hLHX3 mRNAs.
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Affiliation(s)
- Benjamin C Yaden
- Department of Biology (B.C.Y., M.G.), Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
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Ando A, Shigenari A, Kulski JK, Renard C, Chardon P, Shiina T, Inoko H. Genomic sequence analysis of the 238-kb swine segment with a cluster of TRIM and olfactory receptor genes located, but with no class I genes, at the distal end of the SLA class I region. Immunogenetics 2005; 57:864-73. [PMID: 16328468 DOI: 10.1007/s00251-005-0053-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 09/20/2005] [Indexed: 10/25/2022]
Abstract
Continuous genomic sequence has been previously determined for the swine leukocyte antigen (SLA) class I region from the TNF gene cluster at the border between the major histocompatibility complex (MHC) class III and class I regions to the UBD gene at the telomeric end of the classical class I gene cluster (SLA-1 to SLA-5, SLA-9, SLA-11). To complete the genomic sequence of the entire SLA class I genomic region, we have analyzed the genomic sequences of two BAC clones carrying a continuous 237,633-bp-long segment spanning from the TRIM15 gene to the UBD gene located on the telomeric side of the classical SLA class I gene cluster. Fifteen non-class I genes, including the zinc finger and the tripartite motif (TRIM) ring-finger-related family genes and olfactory receptor genes, were identified in the 238-kilobase (kb) segment, and their location in the segment was similar to their apparent human homologs. In contrast, a human segment (alpha block) spanning about 375 kb from the gene ETF1P1 and from the HLA-J to HLA-F genes was absent from the 238-kb swine segment. We conclude that the gene organization of the MHC non-class I genes located in the telomeric side of the classical SLA class I gene cluster is remarkably similar between the swine and the human segments, although the swine lacks a 375-kb segment corresponding to the human alpha block.
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Affiliation(s)
- Asako Ando
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
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Lee JH, Simond D, Hawthorne WJ, Walters SN, Patel AT, Smith DM, O'Connell PJ, Moran C. Characterization of the swine major histocompatibility complex alleles at eight loci in Westran pigs. Xenotransplantation 2005; 12:303-7. [PMID: 15943779 DOI: 10.1111/j.1399-3089.2005.00231.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Pigs are an important large animal model for transplantation and a potential source of xenografts. Swine leukocyte antigen (SLA) molecules are strong mediators of alloreactive and xenoreactive immune responses. We have characterized the SLA alleles of a new pig line bred for transplantation research, the Westran (Westmead Hospital transplantation) pig, described in a companion paper. METHODS Three sixth generation inbred Westran pigs and a Large White pig control were used to assess SLA alleles. We examined the SLA-1, SLA-3, SLA-6, SLA-2, DQA1, DQB1, DRA1 and DRB1 loci using reverse transcription-polymerase chain reaction and sequencing-based method. RESULTS All of the Westran pigs had a single allele at each locus, except for the SLA-1 locus. Typing of the SLA-1 locus in additional animals indicated that this is most likely the result of a duplication of the SLA-1 locus rather than heterozygosity. The lack of SLA heterozygosity is consistent with the previous finding of low microsatellite marker heterozygosity and is the result of both the recent deliberate inbreeding of these pigs and their derivation from a feral stock from Kangaroo Island, South Australia, established by the release of a single pair in 1803. CONCLUSIONS After comparing DNA and protein sequences of the Westran SLA alleles with published GenBank SLA sequences, the SLA class I alleles found in the Westran pigs were all novel, while the SLA-DR and DQB1 alleles have been previously described in other pig breeds. Characterization of the SLA alleles in the Westran pigs has identified novel alleles and will be useful for designing protocols for modulation of immune responses to allografts and xenografts.
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Affiliation(s)
- Jun-Heon Lee
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, NSW, Australia
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Barbosa A, Demeure O, Urien C, Milan D, Chardon P, Renard C. A physical map of large segments of pig chromosome 7q11-q14: comparative analysis with human chromosome 6p21. Mamm Genome 2005; 15:982-95. [PMID: 15599557 DOI: 10.1007/s00335-004-3008-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 07/20/2004] [Indexed: 11/29/2022]
Abstract
The aim of this study was to establish a porcine physical map along the chromosome SSC7q by construction of BAC contigs between microsatellites Sw1409 and S0102. The SLA class II contig, located on SSC7q, was lengthened. Four major BAC contigs and 10 short contigs span a region equivalent to 800 cR measured by IMpRH7000 mapping. The BAC contigs were initiated by PCR screening with primers derived from human orthologous segments, extended by chromosome walking, and controlled and oriented by RH mapping with the two available panels, IMpRH7000Rad and IMNpRH12000Rad. The location of 43 genes was revealed by sequenced segments, either from BAC ends or PCR products from BAC clones. The 220 BAC end sequences (BES) were also used to analyze the different marks of evolution. Comparative mapping analysis between pigs and humans demonstrated that the gene organization on HSA6p21 and on SSC7p11 and q11-q14 segments was conserved during evolution, with the exception of long fragments of HSA6p12 which shuffled and spliced the SLA extended class II region. Additional punctual variations (unique gene insertion/deletion) were observed, even within conserved segments, revealing the evolutionary complexity of this region. In addition, 18 new polymorphic microsatellites have been selected in order to cover the entire SSC7p11-q14 region.
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Affiliation(s)
- Angela Barbosa
- Laboratoire mixte de Radiobiologie et d'Etude du Génome, Institut National de la Recherche Agronomigue et Center d'Energie Atomique, Domaine de Vilvert, 78352, Jouy en Josas cedex, France
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Beck TW, Menninger J, Murphy WJ, Nash WG, O'brien SJ, Yuhki N. The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region. Immunogenetics 2004; 56:702-9. [PMID: 15592824 DOI: 10.1007/s00251-004-0742-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Revised: 10/19/2004] [Indexed: 10/26/2022]
Abstract
In order to determine the genomic organization of the major histocompatibility complex (MHC) of the domestic cat (Felis catus), DNA probes for 61 markers were designed from human MHC reference sequences and used to construct feline MHC BAC contig map spanning ARE1 in the class II region to the olfactory receptor complex in the extended class I region. Selected BAC clones were then used to identify feline-specific probes for the three regions of the mammalian MHC (class II-class III-class I) for radiation hybrid mapping and fluorescent in situ hybridization to refine the organization of the domestic cat MHC. The results not only confirmed that the p-arm of domestic cat B2 is inverted relative to human Chromosome 6, but also demonstrated that one inversion breakpoint localized to the distal segment of the MHC class I between TRIM39 and TRIM26. The inversion thus disjoined the approximately 2.85 Mb of MHC containing class II-class III-class I (proximal region) from the approximately 0.50 Mb of MHC class I/extended class I region, such that TRIM39 is adjacent to the Chromosome B2 centromere and TRIM26 is adjacent to the B2 telomere in the domestic cat.
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Affiliation(s)
- Thomas W Beck
- Basic Research Program, SAIC-Frederick, National Cancer Institute-Frederick, Frederick, MD, 21702-1201, USA.
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Nuñez Y, Ponz F, Gallego FJ. Microsatellite-based genotyping of the swine lymphocyte alloantigens (SLA) in miniature pigs. Res Vet Sci 2004; 77:59-62. [PMID: 15120953 DOI: 10.1016/j.rvsc.2004.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2004] [Indexed: 11/19/2022]
Affiliation(s)
- Y Nuñez
- INIA, Departamento de Biotecnología, Autopista A-6 Km 7, 28040 Madrid, Spain
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35
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Shigenari A, Ando A, Renard C, Chardon P, Shiina T, Kulski JK, Yasue H, Inoko H. Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters. Immunogenetics 2003; 55:695-705. [PMID: 14673549 DOI: 10.1007/s00251-003-0627-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Revised: 11/06/2003] [Indexed: 10/26/2022]
Abstract
Genome analysis of the swine leukocyte antigen ( SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen ( HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.
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Affiliation(s)
- Atsuko Shigenari
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, 259-1193, Kanagawa, Japan
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36
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Yue G, Stratil A, Cepica S, Schroffel J, Schroffelova D, Fontanesi L, Cagnazzo M, Moser G, Bartenschlager H, Reiner G, Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 7. J Anim Breed Genet 2003. [DOI: 10.1046/j.0931-2668.2003.00424.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Tanaka M, Matsumoto T, Yanai S, Domukai M, Toki D, Hayashi T, Kiuchi S, Yasue H, Uenishi H, Kobayashi E, Awata T. Conservation of the syntenies between porcine chromosome 7 and human chromosomes 6, 14 and 15 demonstrated by radiation hybrid mapping and linkage analysis. Anim Genet 2003; 34:255-63. [PMID: 12873213 DOI: 10.1046/j.1365-2052.2003.00999.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Comparative mapping studies facilitate the identification of genes located in quantitative trait locus (QTL) regions in domestic animals by utilizing information from the human genome. Radiation hybrid (RH) mapping is effective for this purpose because of its high resolution in ordered gene mapping on chromosomes. We constructed an RH map of pig chromosome 7, by adding 23 markers associated with genes. This RH map clearly demonstrated the mosaic of homology between pig chromosome 7 (SSC7) and human chromosomes 6, 14 and 15 at a 'gene' level, and was confirmed by linkage analysis. Clarification of the homology of SSC7 to human chromosomes will contribute to the elucidation of the gene(s) responsible for QTL detected on this chromosome.
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Affiliation(s)
- M Tanaka
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
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38
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Campbell EMG, Nonneman D, Rohrer GA. Fine mapping a quantitative trait locus affecting ovulation rate in swine on chromosome 8. J Anim Sci 2003; 81:1706-14. [PMID: 12854806 DOI: 10.2527/2003.8171706x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ovulation rate is an integral component of litter size in swine, but is difficult to directly select for in commercial swine production. Because a QTL has been detected for ovulation rate at the terminal end of chromosome 8p, genetic markers for this QTL would enable direct selection for ovulation rate in both males and females. Eleven genes from human chromosome 4p16-p15, as well as one physiological candidate gene, were genetically mapped in the pig. Large insert swine genomic libraries were screened, clones were isolated and then screened for microsatellite repeats, and informative microsatellite markers were developed for seven genes (GNRHR, IDUA, MAN2B2, MSX1, PDE6B, PPP2R2C, and RGS12). Three genes (LRPAP1, GPRK2L, and FLJ20425) were mapped using genotyping assays developed from single nucleotide polymorphisms. Two genes were assigned since they were present in clones that contained mapped markers (HGFAC and HMX1). The resulting linkage map of pig chromosome 8 contains markers associated with 14 genes in the first 27 cM. One inversion spanning at least 3 Mb in the human genome was detected; all other differences could be explained by resolution of mapping techniques used. Fourteen of the most informative microsatellite markers in the first 27 cM of the map were genotyped across the entire MARC swine resource population, increasing the number of markers typed from 2 to 14 and more than doubling the number ofgenotyped animals with ovulation rate data (295 to 600). Results from the revised data set for the QTL analysis, assuming breed specific QTL alleles, indicated that the most likely position of the QTL resided at 4.85 cM on the new linkage map (F1,592 = 20.5150, genome-wide probability less than 0.015). The updated estimate of the effect of an allele substitution was -1.65 ova for the Meishan allele. The F-ratio peak was closest to markers for MAN2B2 (4.80 cM) and was flanked on the other side by markers for PPP2R2C. Two positional candidate genes included in this study are MAN2B2 and RGS12. These results validate the presence of a QTL affecting ovulation rate on chromosome 8 and facilitate selection of positional candidate genes to be evaluated.
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Affiliation(s)
- E M G Campbell
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
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39
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Kulski JK, Shiina T, Anzai T, Kohara S, Inoko H. Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol Rev 2002; 190:95-122. [PMID: 12493009 DOI: 10.1034/j.1600-065x.2002.19008.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The major histocompatibility complex (MHC) genomic region is composed of a group of linked genes involved functionally with the adaptive and innate immune systems. The class I and class II genes are intrinsic features of the MHC and have been found in all the jawed vertebrates studied so far. The MHC genomic regions of the human and the chicken (B locus) have been fully sequenced and mapped, and the mouse MHC sequence is almost finished. Information on the MHC genomic structures (size, complexity, genic and intergenic composition and organization, gene order and number) of other vertebrates is largely limited or nonexistent. Therefore, we are mapping, sequencing and analyzing the MHC genomic regions of different human haplotypes and at least eight nonhuman species. Here, we review our progress with these sequences and compare the human MHC structure with that of the nonhuman primates (chimpanzee and rhesus macaque), other mammals (pigs, mice and rats) and nonmammalian vertebrates such as birds (chicken and quail), bony fish (medaka, pufferfish and zebrafish) and cartilaginous fish (nurse shark). This comparison reveals a complex MHC structure for mammals and a relatively simpler design for nonmammalian animals with a hypothetical prototypic structure for the shark. In the mammalian MHC, there are two to five different class I duplication blocks embedded within a framework of conserved nonclass I and/or nonclass II genes. With a few exceptions, the class I framework genes are absent from the MHC of birds, bony fish and sharks. Comparative genomics of the MHC reveal a highly plastic region with major structural differences between the mammalian and nonmammalian vertebrates. Additional genomic data are needed on animals of the reptilia, crocodilia and marsupial classes to find the origins of the class I framework genes and examples of structures that may be intermediate between the simple and complex MHC organizations of birds and mammals, respectively.
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Affiliation(s)
- Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
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40
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Jacobs K, Mattheeuws M, Van Poucke M, Van Zeveren A, Peelman LJ. Characterization of the porcine FABGL gene. Anim Genet 2002; 33:220-3. [PMID: 12030927 DOI: 10.1046/j.1365-2052.2002.00849.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The porcine major histocompatibility complex, also called swine lymphocyte antigen (SLA) complex, is of particular interest not only because of its central role in the immune response, but also because of its influence on many traits such as reproduction, fatness and meat quality. The porcine FABGL (FabG (beta-ketoacyl-[acyl-carrierprotein] reductase, Escherichia coli) like) gene, coding for a 17beta-hydroxysteroid dehydrogenase (17beta-HSD), is a candidate gene for these traits. The complete gene was sequenced and compared with human and mouse FABGL sequences. The deduced amino acid sequence showed 85 and 83% sequence identity to human and mouse sequences, respectively. Polymorphicic BbvI and DdeI restriction sites were found in the porcine FABGL gene. The promoter was compared with the promoter regions of human and mouse FABGL sequence in order to identify putative regulatory elements. The transcription profile of the porcine gene was determined and showed a widespread tissue distribution.
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Affiliation(s)
- K Jacobs
- Department of Animal Nutrition, Genetics, Breeding and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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41
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Campbell EM, Fahrenkrug SC, Vallet JL, Smith TP, Rohrer GA. An updated linkage and comparative map of porcine chromosome 18. Anim Genet 2001; 32:375-9. [PMID: 11736809 DOI: 10.1046/j.1365-2052.2001.00782.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Swine chromosome 18 (SSC18) has the poorest marker density in the USDA-MARC porcine linkage map. In order to increase the marker density, seven genes from human chromosome 7 (HSA7) expected to map to SSC18 were selected for marker development. The genes selected were: growth hormone releasing hormone receptor (GHRHR), GLI-Kruppel family member (GLI3), leptin (LEP), capping protein muscle Z-line alpha 2 subunit (CAPZA2), beta A inhibin (INHBA), T-cell receptor beta (TCRB) and T-cell receptor gamma (TCRG). Large-insert clones (YACs, BACs and cosmids) that contained these genes, as well as two previously mapped microsatellite markers (SW1808 and SW1984), were identified and screened for microsatellites. New microsatellite markers were developed from these clones and mapped. Selected clones were also physically assigned by fluorescence in situ hybridization (FISH). Fifteen new microsatellite markers were added to the SSC18 linkage map resulting in a map of 28 markers. Six genes have been included into the genetic map improving the resolution of the SSC18 and HSA7 comparative map. Assignment of TCRG to SSC9 has identified a break in conserved synteny between SSC18 and HSA7.
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Affiliation(s)
- E M Campbell
- USDA, ARS, US Meat Animal Research Center, PO Box 166, Spur 18D, Clay Center, NE 68933-0166, USA
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42
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Wada Y, Akita T, Awata T, Furukawa T, Sugai N, Inage Y, Ishii K, Ito Y, Kobayashi E, Kusumoto H, Matsumoto T, Mikawa S, Miyake M, Murase A, Shimanuki S, Sugiyama T, Uchida Y, Yanai S, Yasue H. Quantitative trait loci (QTL) analysis in a Meishan x Göttingen cross population. Anim Genet 2000; 31:376-84. [PMID: 11167524 DOI: 10.1046/j.1365-2052.2000.00696.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to locate the genetic regions in the swine genome that are responsible for economically important traits, a resource population has been constructed by mating two female Meishan pigs with a male Göttingen miniature pig. In subsequent generations, 265 F2 offspring were produced from two F1 males and 19 F1 females. The F2 offspring were scored for eight traits including growth rate, teat number, vertebra number and backfat thickness, and genotyped for 318 genetic markers spanning the swine genome. Least-square analysis revealed quantitative trait loci (QTL) effects for vertebra number on chromosomes 1 and 2; for teat number on chromosomes 1 and 7; for birth weight on chromosome 1; for average daily gain between 4 and 13 weeks of age on chromosomes 9 and 10; for backfat thickness on chromosome 7; and for backskin thickness on chromosome 3.
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Affiliation(s)
- Y Wada
- Department of Animal Breeding and Genetics, National Institute of Animal Industry, Tsukuba, Ibaraki, Japan
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43
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Huett AS, Innes DA, Moore MJ, Schnieke AE, Shiels PG. Identification of a novel HaeIII PCR-RFLP in the SLA DQB gene. Anim Genet 1999; 30:397. [PMID: 10582301 DOI: 10.1046/j.1365-2052.1999.00526-18.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- A S Huett
- PPL Therapeutics Ltd, Roslin, Edinburgh, UK
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44
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Rohrer GA. Mapping four genes from human chromosome 4 to porcine chromosome 8 further develops the comparative map for an economically important chromosome of the swine genome. Anim Genet 1999; 30:60-2. [PMID: 10050287 DOI: 10.1046/j.1365-2052.1999.00421.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Because porcine chromosome (SSC) 8 has become the focal point of many efforts aimed at identifying quantitative trait loci affecting ovulation rate, genes distributed across human chromosome (HSA) 4 were physically mapped in the pig. A more refined comparative map of this region for these two species was produced. In this study, four genes were selected based on their location in the human genome, the availability of nucleotide sequence and their genomic organization. The genes selected were fibroblast growth factor basic (FGF2; HSA 4q25-27), gonadotropin releasing hormone receptor (GNRHR; HSA 4q13), phosphodiesterase 6 B (PDE6B; HSA 4p16.3) and aminopeptidase S (PEPS; HSA 4p11-q12). Genomic libraries were screened via PCR and clones were physically assigned using fluorescence in situ hybridization (FISH). These four genes from HSA 4 were physically mapped to SSC 8p2.3 (PDE6B), 8p1.1 (PEPS), 8q1.1-1.2 (GNRHR) and 8q2.2-2.4 (FGF2). These assignments provide additional benchmarks for the comparative map and help define the level of gene order conserved between HSA 4 and SSC 8.
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Affiliation(s)
- G A Rohrer
- US Department of Agriculture, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
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45
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Abstract
In swine, the major histocompatibility complex (Mhc) or swine leukocyte antigen (SLA) is located on chromosome 7 and divided by the centromere. Thus, the telomeric class I and more centromeric class III regions are located on the p arm and the class II region is located on the q arm. The SLA region spans about 2 Mb, in which more than 70 genes have so far been characterized. Despite its division by the centromere, the spatial relationships between the genes in the class II and class III regions, and between the well-conserved non-class I genes of the class I region, are similar to those found in the human HLA complex. On the other hand, no orthologous relationships have been found between the Mhc class I genes in man and swine. In swine, the 12 SLA class I sequences constitute two distinct clusters. One cluster comprises six classical class I-related sequences, while the other comprises five class I-distantly related sequences including two swine homologous genes of the HLA Mhc class I chain-related gene (MIC) sequence family. The number of functional SLA classical class I genes, as defined by serology, probably varies from one to four, depending on the haplotype. Some of the SLA class I-distantly related sequences are clearly transcribed. As regards the SLA class II genes, some of them clearly code for at least one functional SLA-DR and one SLA-DQ heterodimer product, but none code for any DP product. The amino acid alignment of the variable domains of 33 SLA classical class I chains, and 62 DR beta and 20 DQ beta chains confirmed the exceptionally polymorphic pattern of these polypeptides. Among the class II genes, the genes are either monomorphic, like the DRA gene, or oligomorphic, like the DQA genes. In contrast, the DRB and DQB genes display considerable polymorphism, which seems more marked in DRB than DQB genes.
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Affiliation(s)
- P Chardon
- Laboratoire mixte INRA-CEA de Radiobiologie Appliquée, Département de Génétique Animale, Jouy-en-Josas, France.
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46
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Velten F, Rogel-Gaillard C, Renard C, Pontarotti P, Tazi-Ahnini R, Vaiman M, Chardon P. A first map of the porcine major histocompatibility complex class I region. TISSUE ANTIGENS 1998; 51:183-94. [PMID: 9510374 DOI: 10.1111/j.1399-0039.1998.tb02963.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A map of the SLA complex, or swine major histocompatibility complex (MHC), class I region was constructed by alignment of yeast artificial chromosomes (YACs) harboring MHC class I genes as well as anchor genes already mapped within the human MHC complex (HLA). Five YACs containing 9 anchor genes built a contig of about 1.0-1.2 Mb between the SLA class III BAT1 locus and the olfactory receptor-like genes OLF42. Ten different SLA class I sequences, including putative allelic forms of published classical and non-classical SLA class I genes, were assigned to the 400-kb enclosing centromeric part of the contig. Three additional YACs comprising the OLF89 genes and two YACs containing the butyrophilin gene were located telomeric to the contig. Comparison between the human and porcine MHC complexes showed a perfect conserved order of anchor genes, whereas no orthologous relationships were found for the class I loci.
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Affiliation(s)
- F Velten
- Laboratoire mixte INRA-CEA de Radiobiologie appliquée, Domaine de Vilvert, Jouy-en-Josas, France
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47
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Yerle M, Lahbib-Mansais Y, Pinton P, Robic A, Goureau A, Milan D, Gellin J. The cytogenetic map of the domestic pig. Mamm Genome 1997; 8:592-607. [PMID: 9250869 DOI: 10.1007/s003359900512] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- M Yerle
- INRA, Laboratoire de Génétique Cellulaire, BP27, 31326 Castanet-Tolosan, France
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48
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Sjöberg A, Peelman LJ, Chowdhary BP. Application of three different methods to analyse fibre-FISH results obtained using four lambda clones from the porcine MHC III region. Chromosome Res 1997; 5:247-53. [PMID: 9244452 DOI: 10.1023/a:1018419619634] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Four lambda clones (lambda G11, lambda C4, lambda G14 and lambda G17) from the porcine MHC class III region were labelled with either biotin-14-dATP or digoxigenin-11-dUTP and hybridized in two different combinations to DNA fibres. The latter were prepared from agarose-embedded porcine peripheral lymphocytes lysed with proteinase K, then spread and fixed on poly-L-lysine-coated slides. Hybridization signals thus obtained confirm the order of the clones previously reported using pulsed-field gel electrophoresis (PFGE). Measurements of probe sizes, gap distances between probes and total length of DNA encompassing the probes were made. Three different methods, namely relative length, Watson-Crick standard and probe size standard-based conversions, were used to estimate the parameters in kilobases. These methods of data conversion were compared with each other and with the available PFGE data, and their utility and accuracy were evaluated.
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Affiliation(s)
- A Sjöberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala
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Smith TP, Lopez-Corrales N, Grosz MD, Beattie CW, Kappes SM. Anchoring of bovine chromosomes 4, 6, 7, 10, and 14 linkage group telomeric ends via FISH analysis of lambda clones. Mamm Genome 1997; 8:333-6. [PMID: 9107677 DOI: 10.1007/s003359900434] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report the placement of 34 new microsatellite (ms) markers, isolated from a lambda phage genomic clone library, on the bovine genetic map by linkage to published markers. Five of these markers lie at or near the ends of linkage groups and are used to establish chromosomal coverage and orientation. Fluorescence in situ hybridization (FISH) analysis demonstrates that the linkage groups on the U.S. Meat Animal Research Center (MARC) map extend to the telomeric region of Chromosomes (Chrs) 7 and 10. Linkage groups on Chrs 4, 6, and 14 appear to be less inclusive.
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Affiliation(s)
- T P Smith
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, Nebraska 68933-0166, USA
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Wilkie PJ, Flickinger GH, Paszek AA, Schook LB. A linkage map of porcine chromosome 7 composed of 19 short tandem repeat polymorphisms. Mamm Genome 1996; 7:631-3. [PMID: 8678995 DOI: 10.1007/s003359900191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- P J Wilkie
- Department of Veterinary PathoBiology, University of Minnesota, St. Paul, Minnesota 55108, USA
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