SLA-1 Genetic Diversity in Pigs: Extensive Analysis of Copy Number Variation, Heterozygosity, Expression, and Breed Specificity

Le, Minh-Tri; Choi, Hojun; Lee, Hyejeong; Le, Van Chanh Quy; Ahn, Byeongyong; Ho, Chak-Sum; Hong, Kwonho; Song, Hyuk; Kim, Jin‐Hoi; Park, Chankyu

doi:10.1038/s41598-020-57712-5

Cited by 13 publications

(34 citation statements)

References 49 publications

(71 reference statements)

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“…Noteworthily, Lr-4.0 was present at a limited frequency in population without Duroc such as the German Landrace (11) or even absent in Austrian Pietrain (17). A recent study reporting high frequency of SLA-1 * 04:XX (Lr-4.0) in Duroc and SLA-1 * 08:XX (Lr-22.0) in purebred Yorkshire and Landrace, also supports this observation (36).…”

Section: Discussionmentioning

confidence: 66%

“…The dominant Lr-4.2 haplotype observed in Thai Duroc boars was not found in the study conducted in a selected Japanese Duroc line (10). The absence of this haplotype in the Japanese study suggests a highly unique genetic background of the population, as this haplotype is commonly present in swine breeds worldwide (8,12,21,23,36). Therefore, further study conducted in a larger population of Duroc from different sources is required to confirm the presence of Lr-4.2 haplotype reported in this study.…”

Section: Discussionmentioning

confidence: 70%

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Diversity of the Swine Leukocyte Antigen Class I and II in Commercial Pig Populations

et al. 2021

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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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Section: Discussionmentioning

confidence: 66%

Section: Discussionmentioning

confidence: 70%

Diversity of the Swine Leukocyte Antigen Class I and II in Commercial Pig Populations

et al. 2021

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“…So far, genetic discrimination between domestic pigs and wild boar has been challenging since there have been only few genetic markers identified to distinguish between domestic pigs and wild boar [ 33 ], and even immunogenetic investigation of domestic pigs and wild boar could not identify any statistically significant differences in allele frequency and heterozygosity across SNPs [ 34 ]. However, very recently SLA-1 diversity was investigated in different domestic pig breeds showing significant distribution of SLA-1 alleles among pig breeds which could explain differences in the immune response [ 35 ]. This has not been done for wild boar so far and underlines the necessity of further investigation.…”

Section: Discussionmentioning

confidence: 99%

Comparative Pathology of Domestic Pigs and Wild Boar Infected with the Moderately Virulent African Swine Fever Virus Strain “Estonia 2014”

et al. 2020

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Endemically infected European wild boar are considered a major reservoir of African swine fever virus in Europe. While high lethality was observed in the majority of field cases, strains of moderate virulence occurred in the Baltic States. One of these, “Estonia 2014”, led to a higher number of clinically healthy, antibody-positive animals in the hunting bag of North-Eastern Estonia. Experimental characterization showed high virulence in wild boar but moderate virulence in domestic pigs. Putative pathogenic differences between wild boar and domestic pigs are unresolved and comparative pathological studies are limited. We here report on a kinetic experiment in both subspecies. Three animals each were euthanized at 4, 7, and 10 days post infection (dpi). Clinical data confirmed higher virulence in wild boar although macroscopy and viral genome load in blood and tissues were comparable in both subspecies. The percentage of viral antigen positive myeloid cells tested by flow cytometry did not differ significantly in most tissues. Only immunohistochemistry revealed consistently higher viral antigen loads in wild boar tissues in particular 7 dpi, whereas domestic pigs already eliminated the virus. The moderate virulence in domestic pigs could be explained by a more effective viral clearance.

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“…In pigs, the major histocompatibility complex (MHC in pigs) and the swine leukocyte antigen (SLA) have an important role mediating cellular immunity, which can eliminate viruses and recognize other antigens in pigs. However, this allele is highly polymorphic, which can cause difficulties for the detection of epitopes suitable for a vaccine, That is why the SLA-1 04:01 and SLA-1 08:01 alleles were used for the analysis of antigenic determinants, which have been reported as alleles with a wide distribution in pigs [ 57 , 58 ]. The NetMHCpan 4.0 and Class I Immunogenicity server are widely used tools for the design of vaccines with the possibility of activating the host cellular response mediated by MHC I.…”

Section: Discussionmentioning

confidence: 99%

Immunoinformatics approach for predicting epitopes in HN and F proteins of Porcine rubulavirus

et al. 2020

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Porcine rubulavirus (PRV), which belongs to the family Paramyxoviridae, causes blue eye disease in pigs, characterized by encephalitis and reproductive failure in newborn and adult pigs, respectively. There is no effective treatment against PRV and no information on the effectiveness of the available vaccines. Continuous outbreaks have occurred in Mexico since the early 1980s, which have caused serious economic losses to pig producers. Vaccination can be used to control this disease. Searching for effective antigen candidates against PRV, we first sequenced the PAC1 F protein, then we used various immunoinformatics tools to predict antigenic determinants of B-cells and T-cells against the two glycoproteins of the virus (HN and F proteins). Finally, we used AutoDock Vina to determine the binding energies. We obtained the F gene sequence of a PRV strain collected in the early 1990s in Mexico and compared its amino acid profile with previous and more recent strains, obtaining an identity similarity of 97.78 to 99.26%. For the F proteins, seven linear B-cell epitopes, six conformational B-cell epitopes and twenty-nine T-cell MHC class I epitopes were predicted. For the HN proteins, sixteen linear B-cell epitopes, seven conformational B-cell epitopes and thirty-four T-cell MHC class I epitopes were predicted. The ATRSETDYY and AAYTTTTCF epitopes of the HN protein might be important for neutralizing the viral infection. We determined the in silico binding energy between the predicted epitopes on the F and HN proteins and swine MHC-I molecules. The binding energy of these epitopes ranged from-5.8 to-7.8 kcal/mol. The present study aimed to assess the use of HN and F proteins as antigens, either as recombinant proteins or as a series of peptides that could activate different responses of the immune system. This may help identify relevant immunogens, saving time and costs in the development of new vaccines or diagnostic tools.

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SLA-1 Genetic Diversity in Pigs: Extensive Analysis of Copy Number Variation, Heterozygosity, Expression, and Breed Specificity

Cited by 13 publications

References 49 publications

Diversity of the Swine Leukocyte Antigen Class I and II in Commercial Pig Populations

Diversity of the Swine Leukocyte Antigen Class I and II in Commercial Pig Populations

Comparative Pathology of Domestic Pigs and Wild Boar Infected with the Moderately Virulent African Swine Fever Virus Strain “Estonia 2014”

Immunoinformatics approach for predicting epitopes in HN and F proteins of Porcine rubulavirus

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