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Microsatellite diversity and crossover regions within homozygous and heterozygous SLA haplotypes of different pig breeds

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Abstract

Our aim was to investigate microsatellite (MS) diversity and find crossover regions at 42 polymorphic MS loci in the swine leukocyte antigen (SLA) genomic region of 72 pigs with different well-defined homozygous and heterozygous SLA haplotypes. We analyzed the genetic polymorphisms of 42 MS markers in 23 SLA homozygous–heterozygous, common pig breeds with 12 SLA serological haplotypes and 49 National Institutes of Health (NIH) and Clawn homozygous–heterozygous miniature pigs with nine SLA serological or genotyped haplotypes including four recombinant haplotypes. In comparing the same and different haplotypes, both haplospecific patterns and allelic variations were observed at the MS loci. Some of the shared haplotype blocks extended over 2 Mb suggesting the existence of strong linkage disequilibrium (LD) in the entire SLA region. Crossover regions were easily defined by the MS markers within the class I and/or III region in the NIH and Clawn recombinant haplotypes. The present haplotype comparison shows that our set of MS markers provides a fast and cost-efficient alternative, or complementary, method to the serological or sequence-based determination of the SLA alleles for the characterization of SLA haplotypes and/or the crossover regions between different haplotypes.

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Fig. 1

Abbreviations

HT:

heterozygosity

MHC:

major histocompatibility complex

MS:

microsatellite

SLA:

swine leukocyte antigen

PCR:

polymerase chain reaction

PIC:

polymorphic information content

LD:

linkage disequilibrium

LW:

Large White

LR:

Landrace

PC:

Poland China

M:

Meishan

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Acknowledgements

We wish to thank Drs. Christine Renard (a former researcher in Institut National de la Recherche Agronomique Commissariat à l’énergie atomique), Kouji Tanaka, Yukari M, Shinmura, and Junichi Tottori (Japan Farm CLAWN Institute) for providing us with samples for SLA homozygous–heterozygous pigs and the Clawn miniature pigs, respectively. This study was supported by grants from an arm of the Science and Technology Agency, the Ministry of Education, Science, Sports, and Culture, Japan, the Animal Genome Research Project of the Ministry of Agriculture, Forestry and Fisheries of Japan, and the US Department of Agriculture Agricultural Research Service project funds.

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Authors and Affiliations

  1. Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan

    Asako Ando, Atsuko Shigenari, Jerzy K Kulski & Hidetoshi Inoko

  2. Division of Animal Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Hirohide Uenishi

  3. Animal Genome Research Program (NIAS/STAFF), 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Hirohide Uenishi & Maiko Tanaka-Matsuda

  4. Teaching and Research Support Center, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan

    Hisako Kawata

  5. Second Research Division, STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Maiko Tanaka-Matsuda

  6. INRA, Institut National de la Recherche Agronomique, Laboratoire Mixte de Radiobiologie et d’Etude du Génome; CEA DSV, IRCM, 78352, Jouy-en-Josas, France

    Laurence Flori & Patrick Chardon

  7. Animal Parasitic Diseases Laboratory, ANRI, ARS, USDA, Beltsville, MD, 20705-2350, USA

    Joan K Lunney

  8. Centre for Forensic Science, The University of Western Australia, Nedlands, Western Australia, Australia

    Jerzy K Kulski

Authors
  1. Asako Ando
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  2. Hirohide Uenishi
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  3. Hisako Kawata
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  4. Maiko Tanaka-Matsuda
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  5. Atsuko Shigenari
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  6. Laurence Flori
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  7. Patrick Chardon
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  8. Joan K Lunney
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  9. Jerzy K Kulski
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  10. Hidetoshi Inoko
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Corresponding author

Correspondence to Hidetoshi Inoko.

Electronic supplementary material

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Supplementary Table 1

SLA haplotypes of SLA homozygous–heterozygous common large pig breeds and NIH and Clawn miniature pigs (137 KB)

High resolution image file (TIFF 1.4 MB)

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Ando, A., Uenishi, H., Kawata, H. et al. Microsatellite diversity and crossover regions within homozygous and heterozygous SLA haplotypes of different pig breeds. Immunogenetics 60, 399–407 (2008). https://doi.org/10.1007/s00251-008-0289-z

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  • DOI: https://doi.org/10.1007/s00251-008-0289-z

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