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

Anim Genet. 2011 Aug;42(4):440-4. doi: 10.1111/j.1365-2052.2010.02140.x. Epub 2010 Dec 1.

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromosome Mapping / methods*
  • Chromosomes, Artificial, Bacterial
  • Chromosomes, Mammalian / genetics*
  • Focal Adhesion Kinase 1 / genetics
  • Gene Expression Profiling / methods*
  • Humans
  • Likelihood Functions
  • Microsatellite Repeats / genetics
  • Radiation Hybrid Mapping
  • Species Specificity
  • Swine / genetics*
  • Synteny / genetics

Substances

  • Focal Adhesion Kinase 1
  • PTK2 protein, human