A high-resolution comparative map of porcine chromosome 4 (SSC4)

J. G. Ma, T. C. Chang, H. Yasue, A. D. Farmer, J. A. Crow, K. Eyer, H. Hiraiwa, T. Shimogiri, S. N. Meyers, J. E. Beever, L. B. Schook, E. F. Retzel, C. W. Beattie, W. S. Liu

Research output: Contribution to journalArticle

Abstract

We used the IMNpRH2 12 000-rad RH and IMpRH 7 000-rad panels to integrate 2019 transcriptome (RNA-seq)-generated contigs with markers from the porcine genetic and radiation hybrid (RH) maps and bacterial artificial chromosome finger-printed contigs, into 1) parallel framework maps (LOD ≥ 10) on both panels for swine chromosome (SSC) 4, and 2) a high-resolution comparative map of SSC4, thus and human chromosomes (HSA) 1 and 8. A total of 573 loci were anchored and ordered on SSC4 closing gaps identified in the porcine sequence assembly Sscrofa9. Alignment of the SSC4 RH with the genetic map identified five microsatellites incorrectly mapped around the centromeric region in the genetic map. Further alignment of the RH and comparative maps with the genome sequence identified four additional regions of discrepancy that are also suggestive of errors in assembly, three of which were resolved through conserved synteny with blocks on HSA1 and HSA8.

Original languageEnglish (US)
Pages (from-to)440-444
Number of pages5
JournalAnimal genetics
Volume42
Issue number4
DOIs
StatePublished - Aug 1 2011

Keywords

  • comparative map
  • radiation hybrid map
  • RNA-seq
  • sequence assembly
  • SSC4
  • swine

ASJC Scopus subject areas

  • Genetics
  • Animal Science and Zoology

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    Ma, J. G., Chang, T. C., Yasue, H., Farmer, A. D., Crow, J. A., Eyer, K., Hiraiwa, H., Shimogiri, T., Meyers, S. N., Beever, J. E., Schook, L. B., Retzel, E. F., Beattie, C. W., & Liu, W. S. (2011). A high-resolution comparative map of porcine chromosome 4 (SSC4). Animal genetics, 42(4), 440-444. https://doi.org/10.1111/j.1365-2052.2010.02140.x