title: gsrc: an R package for genome structure rearrangement calling.
abstract: Genome structure rearrangements are a common phenomenon in allopolyploid species. Deletions, duplications and homeologous non-reciprocal translocations (HNRT) between the highly similar subgenomes can be observed, which are known to have a large impact on phenotypic traits. Current research is limited because these rearrangements can be located genome wide only by cost intensive sequencing approaches and not reliably in high-density array genotyping data. We developed gsrc, an R-package to detect genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. We exemplarily apply gsrc to a publicly available Brassica napus dataset.
  
  
  
  The compiled R-package and source code are available at http://cran.r-project.org/web/packages/gsrc/ .
  
  
  
  birgit.samans@uni-giessen.de.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany.
authors: Fabian
authors: F
authors: Grandke
authors: Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany.
authors: Rod
authors: R
authors: Snowdon
authors: Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany.
authors: Birgit
authors: B
authors: Samans
mesh_terms: D029688:Brassica napus / Q000235:genetics; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D011123:Polyploidy; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software