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Ando A, Matsubara T, Suzuki S, Imaeda N, Takasu M, Shigenari A, Miyamoto A, Ohshima S, Kametani Y, Shiina T, Kulski JK, Kitagawa H. Genetic Links between Reproductive Traits and Amino Acid Pairwise Distances of Swine Leukocyte Antigen Alleles among Mating Partners in Microminipigs. Int J Mol Sci 2024; 25:7362. [PMID: 39000468 PMCID: PMC11242825 DOI: 10.3390/ijms25137362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/23/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Previously, we found that a greater dissimilarity in swine leukocyte antigen (SLA) class I and class II alleles between mating partners resulted in increased farrowing rates in a highly inbred population of Microminipigs (MMPs). In this follow-up study, we have analyzed the effects of dissimilarity in SLA alleles between mating partners for seven different reproductive traits, including litter size and the number of stillborn and live or dead weaned piglets. We determined the relationships among reproductive traits within each mating event and the amino acid distances of SLA alleles as markers of diversity between mating partners. Our results indicate that mating partners with greater amino acid pairwise genetic distances in the SLA-1 class I gene or DQB1 class II gene alleles were associated with significantly larger litter sizes and higher numbers of live piglets at birth and weaning. Also, partners with greater pairwise distances in the SLA-2 class I gene alleles exhibited fewer pre-weaning deaths. These findings suggest that the dissimilarity in SLA class I and class II alleles between mating partners may affect not only farrowing rates but also other key reproductive traits such as litter size and improved piglet survival rates. Consequently, SLA alleles could serve as valuable genetic markers for selecting mating partners in breeding programs and for conducting epistatic studies on various reproductive traits in MMPs.
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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, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
| | - Tatsuya Matsubara
- Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (T.M.); (N.I.)
| | - Shingo Suzuki
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
| | - Noriaki Imaeda
- Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (T.M.); (N.I.)
| | - Masaki Takasu
- Gifu University Institute for Advanced Study, Gifu University, Gifu 501-1193, Japan;
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu 501-1193, Japan
| | - Atsuko Shigenari
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
| | - Asuka Miyamoto
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
| | - Shino Ohshima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
| | - Yoshie Kametani
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
| | - Jerzy K. Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.S.); (A.S.); (A.M.); (S.O.); (Y.K.); (T.S.); or (J.K.K.)
- Faculty of Health and Medical Sciences, School of Biomedical Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Hitoshi Kitagawa
- Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (T.M.); (N.I.)
- Laboratory of Veterinary Internal Medicine, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Ehime 794-8555, Japan
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Ando A, Matsubara T, Suzuki S, Imaeda N, Takasu M, Shigenari A, Miyamoto A, Ohshima S, Kametani Y, Shiina T, Kulski JK, Kitagawa H. Genetic Association between Farrowing Rates and Swine Leukocyte Antigen Alleles or Haplotypes in Microminipigs. Cells 2022; 11:3138. [PMID: 36231100 PMCID: PMC9563624 DOI: 10.3390/cells11193138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 11/16/2022] Open
Abstract
We have previously reported specific swine leukocyte antigen (SLA) haplotype associations with significant effects on several reproduction performance traits in a highly inbred miniature pig population of Microminipigs (MMPs). In this study, to clarify the effects on farrowing rates of SLA similarity between mating partners in the MMP population, we compared the farrowing rates as a measure of reproductive success after 1063-cumulative matings among the following three groups of mating partners: (1) completely sharing SLA class I or class II haplotypes or alleles between partners (CS), (2) only one sharing the haplotypes or alleles (OS), and (3) non-sharing the haplotypes or alleles (NS). Average farrowing rates in CS groups consisting of completely sharing SLA class II haplotypes or DRBI and DQB1 alleles were lowest in the three groups. Moreover, lower farrowing rates were indicated in mating pairs with smaller amino acid pairwise genetic distances of SLA-1, SLA-3, DRB1 and DQB1 alleles between the pairs. These results suggested that the dissimilarity of SLA class I and class II alleles between mating partners markedly improved reproductive performance; therefore, SLA alleles or haplotypes are potentially useful genetic markers for the selection of mating pairs in breeding programs and epistatic studies of reproductive traits of MMPs.
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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, Isehara 259-1193, Japan
| | - Tatsuya Matsubara
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Noriaki Imaeda
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Atsuko Shigenari
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Asuka Miyamoto
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Shino Ohshima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Yoshie Kametani
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Jerzy K. Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Hitoshi Kitagawa
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
- Laboratory of Veterinary Internal Medicine, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari 794-8555, Japan
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Imaeda N, Ando A, Matsubara T, Takasu M, Nishii N, Miyamoto A, Ohshima S, Kametani Y, Suzuki S, Shiina T, Ono T, Kulski JK, Kitagawa H. Stillbirth rates and their association with swine leucocyte antigen class II haplotypes in Microminipigs. Anim Biosci 2021; 34:1749-1756. [PMID: 34237925 PMCID: PMC8563260 DOI: 10.5713/ab.20.0763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/16/2021] [Accepted: 05/11/2021] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE Microminipig (MMP) is a miniature pig with an extra small body size for experimental use. In the present study, the occurrence of stillbirths and their genetic association with swine leukocyte antigen (SLA) class II haplotypes were evaluated in a population of MMPs. METHODS The occurrences of stillbirth and genetic association with SLA class II haplotypes using 483 stillborn and 2,246 live piglets, and their parents were compared among the three groups of newborn piglet litters; an all stillborn (AS) group consisting of only stillborn piglet litters, a partial stillborn (PS) group consisting of stillborn and live piglet litters, and an all alive (AA) group consisting of only live piglet litters. RESULTS The incidence of stillborn piglets was 483/2,729 (17.7%). Distributions of litter sizes, numbers of stillborn piglets in a litter, parities, and gestation periods were distinct among the three groups. The frequencies of low resolution haplotype (Lr)-0.7 or Lr-0.23 were higher in the AS group than in the PS or AA groups. In sires, the frequency of Lr-0.7 associated with the AS group was significantly higher in the AS group than with the AA group. In dams, the frequency of Lr-0.23 was significantly higher in the AS group than in the PS or AA groups, whereas the frequency of Lr-0.7 was not significantly different. CONCLUSION The incidence of stillborn piglets in MMPs appears to be higher than those in other pig breeds. Several traits related with stillbirths such as the number of stillborn piglets and parities of the AS group were different from those of the PS and AA groups. Specific SLA class II haplotypes were associated significantly with a high incidence of stillbirths and could be used as genetic markers to adopt breeding strategies to lower the rate of stillbirth in MMPs.
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Affiliation(s)
- Noriaki Imaeda
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193,
Japan
| | - Asako Ando
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193,
Japan
| | - Tatsuya Matsubara
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193,
Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193,
Japan
| | - Naohito Nishii
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193,
Japan
| | - Asuka Miyamoto
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193,
Japan
| | - Shino Ohshima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193,
Japan
| | - Yoshie Kametani
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193,
Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193,
Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193,
Japan
| | - Tetsushi Ono
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Okayama University of Science, Imabari 794-8555,
Japan
| | - Jerzy K. Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193,
Japan
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA 6009,
Australia
| | - Hitoshi Kitagawa
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193,
Japan
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Okayama University of Science, Imabari 794-8555,
Japan
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Kulski JK, Suzuki S, Shiina T. Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region. Front Genet 2021; 12:665899. [PMID: 34122517 PMCID: PMC8193847 DOI: 10.3389/fgene.2021.665899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
The major histocompatibility complex (MHC) on chromosome 6p21 is one of the most single-nucleotide polymorphism (SNP)-dense regions of the human genome and a prime model for the study and understanding of conserved sequence polymorphisms and structural diversity of ancestral haplotypes/conserved extended haplotypes. This study aimed to follow up on a previous analysis of the MHC class I region by using the same set of 95 MHC haplotype sequences downloaded from a publicly available BioProject database at the National Center for Biotechnology Information to identify and characterize the polymorphic human leukocyte antigen (HLA)-class II genes, the MTCO3P1 pseudogene alleles, the indels of transposable elements as haplotypic lineage markers, and SNP-density crossover (XO) loci at haplotype junctions in DNA sequence alignments of different haplotypes across the extended class II region (∼1 Mb) from the telomeric PRRT1 gene in class III to the COL11A2 gene at the centromeric end of class II. We identified 42 haplotypic indels (20 Alu, 7 SVA, 13 LTR or MERs, and 2 indels composed of a mosaic of different transposable elements) linked to particular HLA-class II alleles. Comparative sequence analyses of 136 haplotype pairs revealed 98 unique XO sites between SNP-poor and SNP-rich genomic segments with considerable haplotype shuffling located in the proximity of putative recombination hotspots. The majority of XO sites occurred across various regions including in the vicinity of MTCO3P1 between HLA-DQB1 and HLA-DQB3, between HLA-DQB2 and HLA-DOB, between DOB and TAP2, and between HLA-DOA and HLA-DPA1, where most XOs were within a HERVK22 sequence. We also determined the genomic positions of the PRDM9-recombination suppression sequence motif ATCCATG/CATGGAT and the PRDM9 recombination activation partial binding motif CCTCCCCT/AGGGGAG in the class II region of the human reference genome (NC_ 000006) relative to published meiotic recombination positions. Both the recombination and anti-recombination PRDM9 binding motifs were widely distributed throughout the class II genomic regions with 50% or more found within repeat elements; the anti-recombination motifs were found mostly in L1 fragmented repeats. This study shows substantial haplotype shuffling between different polymorphic blocks and confirms the presence of numerous putative ancestral recombination sites across the class II region between various HLA class II genes.
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Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia.,Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Shiina
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
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Techakriengkrai N, Nedumpun T, Golde WT, Suradhat S. Diversity of the Swine Leukocyte Antigen Class I and II in Commercial Pig Populations. Front Vet Sci 2021; 8:637682. [PMID: 33996967 PMCID: PMC8121083 DOI: 10.3389/fvets.2021.637682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Among swine genetic markers, the highly polymorphic swine leukocyte antigen (SLA) is one of the key determinants, associated with not only immune responses but also reproductive performance and meat quality. The objective of this study was to characterize the SLA class I and II diversities in the commercial pig populations. In this study, a total number of 158 pigs (126 gilts and 32 boars) were randomly selected from different breeding herds of five major pig-producing companies, which covered ~70% of Thai swine production. The results indicate that a moderate level of SLA diversity was maintained in the Thai swine population, despite the performance-oriented breeding scheme. The highly common SLA class I alleles were SLA-1*08:XX, SLA-2*02:XX, and SLA-3*04:XX at a combined frequency of 30.1, 18.4, and 34.5%, respectively, whereas DRB1*04:XX, DQB1*02:XX and DQA*02:XX were the common class II alleles at 22.8, 33.3, and 38.6%, respectively. The haplotype Lr-32.0 (SLA-1*07:XX, SLA-2*02:XX, and SLA-3*04:XX) and Lr-0.23 (DRB1*10:XX, DQB1*06:XX, DQA* 01:XX) was the most common SLA class I and II haplotype, at 15.5 and 14.6%, respectively. Common class I and II haplotypes were also observed, which Lr-22.15 was the most predominant at 11.1%, followed by Lr-32.12 and Lr-4.2 at 10.8 and 7.9%, respectively. To our knowledge, this is the first report of SLA class I and II diversities in the commercial pigs in Southeast Asia. The information of the common SLA allele(s) in the population could facilitate swine genetic improvement and future vaccine design.
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Affiliation(s)
- Navapon Techakriengkrai
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Diagnosis and Monitoring of Animal Pathogens Research Unit, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
| | - Teerawut Nedumpun
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
| | - William T Golde
- Department of Vaccines and Diagnostics, Moredun Research Institute, Penicuik, United Kingdom
| | - Sanipa Suradhat
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
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A comparative analysis of SLA-DRB1 genetic diversity in Colombian (creoles and commercial line) and worldwide swine populations. Sci Rep 2021; 11:4340. [PMID: 33619347 PMCID: PMC7900169 DOI: 10.1038/s41598-021-83637-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/18/2021] [Indexed: 12/30/2022] Open
Abstract
Analysing pig class II mayor histocompatibility complex (MHC) molecules is mainly related to antigen presentation. Identifying frequently-occurring alleles in pig populations is an important aspect to be considered when developing peptide-based vaccines. Colombian creole pig populations have had to adapt to local conditions since entering Colombia; a recent census has shown low amounts of pigs which is why they are considered protected by the Colombian government. Commercial hybrids are more attractive regarding production. This research has been aimed at describing the allele distribution of Colombian pigs from diverse genetic backgrounds and comparing Colombian SLA-DRB1 locus diversity to that of internationally reported populations. Twenty SLA-DRB1 alleles were identified in the six populations analysed here using sequence-based typing. The amount of alleles ranged from six (Manta and Casco Mula) to nine (San Pedreño). Only one allele (01:02) having > 5% frequency was shared by all three commercial line populations. Allele 02:01:01 was shared by five populations (around > 5% frequency). Global FST indicated that pig populations were clearly structured, as 20.6% of total allele frequency variation was explained by differences between populations (FST = 0.206). This study’s results confirmed that the greatest diversity occurred in wild boars, thereby contrasting with low diversity in domestic pig populations.
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Nishi K, Iwai S, Tajima K, Okano S, Sano M, Kobayashi E. Prevention of Chronic Rejection of Marginal Kidney Graft by Using a Hydrogen Gas-Containing Preservation Solution and Adequate Immunosuppression in a Miniature Pig Model. Front Immunol 2021; 11:626295. [PMID: 33679720 PMCID: PMC7925892 DOI: 10.3389/fimmu.2020.626295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022] Open
Abstract
In clinical kidney transplantation, the marginal kidney donors are known to develop chronic allograft rejection more frequently than living kidney donors. In our previous study, we have reported that the hydrogen gas-containing organ preservation solution prevented the development of acute injuries in the kidney of the donor after cardiac death by using preclinical miniature pig model. In the present study, we verified the impact of hydrogen gas treatment in transplantation with the optimal immunosuppressive protocol based on human clinical setting by using the miniature pig model. Marginal kidney processed by hydrogen gas-containing preservation solution has been engrafted for long-term (longer than 100 days). A few cases showed chronic rejection reaction; however, most were found to be free of chronic rejection such as graft tissue fibrosis or renal vasculitis. We concluded that marginal kidney graft from donor after cardiac death is an acceptable model for chronic rejection and that if the transplantation is carried out using a strict immunosuppressive protocol, chronic rejection may be alleviated even with the marginal kidney.
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Affiliation(s)
- Kotaro Nishi
- Laboratory of Small Animal Surgery 2, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Satomi Iwai
- Laboratory of Small Animal Surgery 2, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Kazuki Tajima
- Laboratory of Small Animal Internal Medicine 2, School of Veterinary Medicine, Kitasato University, Towada, Japan
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shozo Okano
- Laboratory of Small Animal Surgery 2, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Motoaki Sano
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
| | - Eiji Kobayashi
- Department of Organ Fabrication, Keio University School of Medicine, Tokyo, Japan
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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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Genomic Diversity of the Major Histocompatibility Complex in Health and Disease. Cells 2019; 8:cells8101270. [PMID: 31627481 PMCID: PMC6830316 DOI: 10.3390/cells8101270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022] Open
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