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A new 4016-marker radiation hybrid map for porcine-human genome analysis

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Abstract

We constructed a 5000-rad comprehensive radiation hybrid (RH) map of the porcine (Sus scrofa) genome and compared the results with the human genome. Of 4475 typed markers, 4016 (89.7%) had LOD >5 compared with the markers used in our previous RH map by means of two-point analysis and were grouped onto the 19 porcine chromosomes (SSCs). All mapped markers had LOD >3 as determined by RHMAPPER analysis. The current map comprised 430 microsatellite (MS) framework markers, 914 other MS markers, and 2672 expressed sequence tags (ESTs). The whole-genome map was 8822.1 cR in length, giving an average marker density of 0.342 Mb/cR. The average retention frequency was 35.8%. Using BLAST searches of porcine ESTs against the RefSeq human nucleotide and amino acid sequences (release 22), we constructed high-resolution comparative maps of each SSC and each human chromosome (HSA). The average distance between ESTs in the human genome was 1.38 Mb. SSC contained 50 human chromosomal syntenic groups, and SSC11, SSC12, and SSC16 were only derived from the HSA13q, HSA17, and HSA5 regions, respectively. Among 38 porcine terminal regions, we found that at least 20 regions have been conserved between the porcine and human genomes; we also found four paralogous regions for the major histocompatibility complex (MHC) on SSC7, SSC2, SSC4, and SSC1.

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Acknowledgments

The authors thank Ms. Y. Mizuide and E. Odajima (STAFF-Institute) for their technical assistance. An Animal Genome Project grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan funded this study.

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Authors and Affiliations

  1. Animal Genome Research Program (AGP), Society for Techno-Innovation of Agriculture, Forestry and Fisheries (STAFF) Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Noriyuki Hamasima, Ayumi Mikawa, Hideaki Suzuki, Kohei Suzuki, Hirohide Uenishi & Takashi Awata

  2. Society for Techno-Innovation of Agriculture, Forestry and Fisheries (STAFF) Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Ayumi Mikawa, Hideaki Suzuki & Kohei Suzuki

  3. Animal Genome Research Program (AGP), Division of Animal Sciences, National Institute of Agrobiological Sciences (STAFF), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Noriyuki Hamasima, Hirohide Uenishi & Takashi Awata

Authors
  1. Noriyuki Hamasima
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  2. Ayumi Mikawa
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  3. Hideaki Suzuki
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  4. Kohei Suzuki
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  5. Hirohide Uenishi
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  6. Takashi Awata
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Correspondence to Noriyuki Hamasima.

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Hamasima, N., Mikawa, A., Suzuki, H. et al. A new 4016-marker radiation hybrid map for porcine-human genome analysis. Mamm Genome 19, 51–60 (2008). https://doi.org/10.1007/s00335-007-9081-x

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  • DOI: https://doi.org/10.1007/s00335-007-9081-x

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