Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17

D. J. Sidjanin, B. Miller, J. Kijas, J. McElwee, J. Pillardy, Joel Malek, G. Pai, T. Feldblyum, C. Fraser, G. Acland, G. Aguirre

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Abstract

Progressive rod-cone degeneration (prcd) is a canine retinal disease that maps to the centromeric end of CFA9 in a region of synteny with the distal part of HSA17q. As such, prcd has been postulated as the only animal model of RP17, a human retinitis pigmentosa locus that maps to 17q22. In an effort to establish more detailed regions of synteny between dog CFA9 and the HSA17q-ter region, we created a robust gene-enriched CFA9-RH083000 map with 34 gene-based markers and 12 microsatellites, with the highest resolution and number of markers for the centromeric end of CFA9. Furthermore, we built an approximately 1.5-Mb physical map containing both GRB2 and GALK1, genes so far identified by meiotic linkage analysis as being closest to the prcd locus, and generated about 1.2 Mb low-pass (3.2×) canine sequence. Canine to human comparative sequence analysis identified 49 transcripts that had been previously mapped to the HSA17q25 region. The generated low-pass canine sequence was annotated with a working draft of human sequence from HSA17q25, and we used this scaffold to order and orient the canine sequence against human. This order and orientation are preliminary, as high-throughput genomic sequencing of HSA17q-ter has not been fully completed.

Original languageEnglish
Pages (from-to)138-148
Number of pages11
JournalGenomics
Volume81
Issue number2
DOIs
Publication statusPublished - 1 Feb 2003
Externally publishedYes

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Keywords

  • Bacterial artificial chromosome
  • Contig mapping
  • Dog
  • Genome sequencing
  • Nucleotide sequence
  • Physical mapping
  • Progressive retinal atrophy
  • Progressive rod-cone degeneration
  • Radiation hybrid mapping
  • Retinitis pigmentosa
  • Rod photoreceptors
  • Synteny

ASJC Scopus subject areas

  • Genetics

Cite this

Sidjanin, D. J., Miller, B., Kijas, J., McElwee, J., Pillardy, J., Malek, J., Pai, G., Feldblyum, T., Fraser, C., Acland, G., & Aguirre, G. (2003). Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17. Genomics, 81(2), 138-148. https://doi.org/10.1016/S0888-7543(02)00028-9