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:10.1093/bioinformatics/bty371

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^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

45 Citations (Scopus)

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 realize 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/package=polymapR.

Supplementary information: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	3496-3502
Journal	Bioinformatics
Volume	34
Issue number	20
DOIs	https://doi.org/10.1093/bioinformatics/bty371
Publication status	Published - 15 Oct 2018

Access to Document

10.1093/bioinformatics/bty371Licence: CC BY-NC

45 Citations
1 Comment/Letter to the editor

Corrigendum: PolymapR - Linkage analysis and genetic map construction from F 1 populations of outcrossing polyploids
Bourke, P. M., Van Geest, G., Voorrips, R. E., Jansen, J., Kranenburg, T., Shahin, A., Visser, R. G. F., Arens, P., Smulders, M. J. M. & Maliepaard, C., 15 Oct 2018, In: Bioinformatics. 35, 3, p. 540-540
Research output: Contribution to journal › Comment/Letter to the editor › Academic

Open Access

2 Finished

KV 1605-020 Novel genetic and genomic tools polyploid crops (BO-68-001-001, BO-50-002-022, BO-26.03-009-004)
Arens, P.
1/01/17 → 31/12/20
Project: EZproject
H263 A genetic analysis pipeline for polyploids (BO-26.03-003-003, BO-26.03-002-001)
Arens, P.
1/01/13 → 31/12/16
Project: EZproject

Cite this

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title = "PolymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids",

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 realize 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/package=polymapR.Supplementary information: Supplementary data are available at Bioinformatics online.",

author = "Bourke, {Peter M.} and {van Geest}, Geert and Voorrips, {Roeland E.} and Johannes Jansen and Twan Kranenburg and Arwa Shahin and Visser, {Richard G.F.} and Paul Arens and Smulders, {Marinus J.M.} and Chris Maliepaard",

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AU - Bourke, Peter M.

AU - van Geest, Geert

AU - Voorrips, Roeland E.

AU - Jansen, Johannes

AU - Kranenburg, Twan

AU - Shahin, Arwa

AU - Visser, Richard G.F.

AU - Arens, Paul

AU - Smulders, Marinus J.M.

AU - Maliepaard, Chris

PY - 2018/10/15

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N2 - 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 realize 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/package=polymapR.Supplementary information: Supplementary data are available at Bioinformatics online.

AB - 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 realize 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/package=polymapR.Supplementary information: Supplementary data are available at Bioinformatics online.

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JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 20

ER -

PolymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

Abstract

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Research output

Corrigendum: PolymapR - Linkage analysis and genetic map construction from F 1 populations of outcrossing polyploids

Projects

KV 1605-020 Novel genetic and genomic tools polyploid crops (BO-68-001-001, BO-50-002-022, BO-26.03-009-004)

H263 A genetic analysis pipeline for polyploids (BO-26.03-003-003, BO-26.03-002-001)

Cite this