Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

Peter M. Bourke, Geert van Geest, Roeland E. Voorrips, Johannes Jansen, Twan Kranenburg, Arwa Shahin, Richard G. F. Visser, Paul Arens, Marinus J. M. Smulders, Chris Maliepaard
doi: https://doi.org/10.1101/228817
Peter M. Bourke
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Geert van Geest
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.Horticulture and Product Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roeland E. Voorrips
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: chris.maliepaard@wur.nl roeland.voorrips@wur.nl
Johannes Jansen
Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Twan Kranenburg
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Arwa Shahin
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.Van Zanten Breeding B. V., Lavendelweg 15, 1435 EW, Rijsenhout, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard G. F. Visser
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul Arens
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marinus J. M. Smulders
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chris Maliepaard
Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: chris.maliepaard@wur.nl roeland.voorrips@wur.nl
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Motivation Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.

Results polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.

Availability and Implementation polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/packages=polymapR.

Contact Chris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted December 04, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
Peter M. Bourke, Geert van Geest, Roeland E. Voorrips, Johannes Jansen, Twan Kranenburg, Arwa Shahin, Richard G. F. Visser, Paul Arens, Marinus J. M. Smulders, Chris Maliepaard
bioRxiv 228817; doi: https://doi.org/10.1101/228817
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
Peter M. Bourke, Geert van Geest, Roeland E. Voorrips, Johannes Jansen, Twan Kranenburg, Arwa Shahin, Richard G. F. Visser, Paul Arens, Marinus J. M. Smulders, Chris Maliepaard
bioRxiv 228817; doi: https://doi.org/10.1101/228817

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genetics
Subject Areas
All Articles
  • Animal Behavior and Cognition (1533)
  • Biochemistry (2491)
  • Bioengineering (1747)
  • Bioinformatics (9700)
  • Biophysics (3915)
  • Cancer Biology (2978)
  • Cell Biology (4213)
  • Clinical Trials (135)
  • Developmental Biology (2639)
  • Ecology (4108)
  • Epidemiology (2033)
  • Evolutionary Biology (6911)
  • Genetics (5224)
  • Genomics (6519)
  • Immunology (2193)
  • Microbiology (6972)
  • Molecular Biology (2765)
  • Neuroscience (17348)
  • Paleontology (126)
  • Pathology (430)
  • Pharmacology and Toxicology (709)
  • Physiology (1062)
  • Plant Biology (2498)
  • Scientific Communication and Education (646)
  • Synthetic Biology (832)
  • Systems Biology (2691)
  • Zoology (433)