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Radiation hybrid map of the porcine genome comprising 2035 EST loci

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Abstract

The IMpRH7000-rad radiation hybrid panel was used to map 2035 expressed sequence tags (ESTs) at a minimum LOD score of 4.0. A total of 134 linkage groups covers 57,192 cR or 78% of the predicted size of the porcine and 71% of the human genome, respectively. Approximately 81% (1649) of the porcine ESTs were annotated against the NCBI nonredundant database; 1422 mapped in silico to a location in build 35.1 of the human genome sequence (HGS) and 1185 to a gene and location in build 35.1 HGS. The map revealed 40 major breaks in synteny (1.00e −25 and lower) with the human genome, 37 of which fall within a single chromosome. At this improved level of resolution and coverage, porcine chromosomes (SSC) 2, 5, 6, 7, 12, and 14 remain “gene-rich” and homologous to human chromosomes (HSA) 17, 19, and 22, while SSC 1, 8, 11, and X have been confirmed to correspond to the “gene-deserts” on HSA 18, 4, 13, and X.

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Acknowledgments

The authors thank Dr. Ernie Retzel at the Center for Computational Genomics and Bioinformatics (CCGB), University of Minnesota, for database management and support. This project was supported by USDA NRI-CGP 2003−03686.

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Author notes

  1. Anette Rink & Kimberly J. Priest

    Present address: Animal Disease and Food Safety Laboratory, Nevada Department of Agriculture, Reno, Nevada

Authors and Affiliations

  1. Department of Animal Biotechnology, College of Agriculture, Biotechnology and Natural Resources, University of Nevada, Reno, Nevada, 89557, USA

    Anette Rink, Katie Eyer, Benjamin Roelofs, Kimberly J. Priest, Kathleen J. Sharkey-Brockmeier, Sudkamon Lekhong, Elif K. Karajusuf, Jason Bang, Wan-Sheng Liu & Craig W. Beattie

  2. Laboratorie Genetique et Cytogenetique INRA, Tolosan-Castenet, France

    Martine Yerle & Denis Milan

  3. Department of Animal Biotechnology, College of Agriculture, Biotechnology and Natural Resources (CABNR), University of Nevada, Mail Stop 202, 1664 N. Virginia Street, Reno, NV, 89557, USA

    Craig W. Beattie

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  1. Anette Rink
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  2. Katie Eyer
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Correspondence to Craig W. Beattie.

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Rink, A., Eyer, K., Roelofs, B. et al. Radiation hybrid map of the porcine genome comprising 2035 EST loci. Mamm Genome 17, 878–885 (2006). https://doi.org/10.1007/s00335-005-0121-0

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  • DOI: https://doi.org/10.1007/s00335-005-0121-0

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