Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C. polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.
Bioinformatics 2019;
34:3496-3502. [PMID:
29722786 PMCID:
PMC6184683 DOI:
10.1093/bioinformatics/bty371]
[Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
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.
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