Pedimap
Software for the visualization of genetic and phenotypic data in pedigrees
Roeland E. Voorrips, Wageningen UR – Plant Breeding
Pedimap is a tool for exploring and visualizing the flow of phenotypes and alleles (observed or based on Identity-by-Descent calculations) through pedigrees. It has tools for the manual and automatic selection of parts of the pedigree based on criteria such as ancestors and/or progeny to a specified number of generations, along the maternal, paternal or both lines, sibs etc. For each selection multiple views can be generated to display different linkage groups, phenotypic traits etc. Once a view is created for one selection, it can be automatically recreated for any other selection. Pedimap can deal with numeric as well as textual phenotypic scores, and with polyploids as well as diploids. The genetic information can be displayed according to genetic linkage maps, hence the name.
Pedimap is available for the Windows platform (all 32-bit or 64-bit versions, Windows98 up to Windows7). Pedimap can be downloaded here.
Screenshots:
Part of an apple pedigree, with individuals colored according to crispness.
Part of the user interface with the subpopulations panel (top left), information panel (bottom left) and the pedigree view (right) showing both crispness values ( as colors), and SSR alleles for chromosome 1.
Part of an apple pedigree showing Identity-by-Descent probabilities for chromosome 1. Each color represents a different founder allele. The two rectangles in each individual represent the maternally and paternally inherited chromosome. The vertical dimension of each rectangle corresponds to the positions along the linkage map, while the width of a color at particular height reflects the probability that the corresponding founder allele is present at that locus on the map.
Pedimap is a useful stand-alone tool to check marker data and to understand the relation between phenotype and genotype. Further, Pedimap can be used to display the results calculated by the FlexQTL (www.flexqtl.nl) software developed by Dr Marco Bink of Wageningen UR – Biometris. Pedimap can quickly highlight problematic marker scores and display the calculated Identity-by-Descent information. Pedimap and FlexQTL are designed to work together.
In order to facilitate the import of large amounts of SNP data from Illumina’s GenomeStudio software, an R script was developed that can be downloaded here.
Pedimap is being developed at Wageningen UR – Plant Breeding. Its development was started in the framework of the European HiDRAS (www.hidras.unimi.it) project. Currently development of Pedimap takes place within USDA-NIFA1 RosBREED (www.rosbreed.org) and EU-FruitBreedomics (www.fruitbreedomics.com) projects.
For questions, contact Roeland voorrips AT wur.nl.
1 Funding for "RosBREED: Enabling marker-assisted breeding in Rosaceae" was provided by the Specialty Crop Research Initiative Competitive Grant 2009-51181-05808 of the USDA's National Institute of Food and Agriculture.
