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

Abstract

MotivationPolyploid 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.ResultspolymapR 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 implementationpolymapR 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.

High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Megathyrsus maximus)

“…The distribution of the markers with DR between the dosage types was proportional to the number of SNPs with each configuration. DR has been extensively studied using SNPs with dosage data in autotetraploid linkage maps in potato (Hackett et al, 2017;Bourke et al, 2018a). Approximately 6% of markers in potato have DR (Bourke et al, 2015), corroborating our results (9.68%).…”

“…We removed markers with more than 25% missing data and monomorphic markers manually in R software (version 3.5.0) (R Core Team, 2018). Subsequently, we followed Bourke et al (2018a) to ensure the retention of reliable markers. We first verified the shifted markers for the polysomic inheritance model from which SNP markers that did not correspond to an expected segregation type were removed.…”

Mapping a Novel Black Spot Resistance Locus in the Climbing Rose Brite Eyes™ (‘RADbrite’)

“…Markers which did not fit expected segregation ratios for either allotetraploid or autotetraploid inheritance (α = 0.01) were removed from analysis. Mapping was conducted using the R package ‘polymapR’ (v 1.0.13; Bourke et al, 2018 ). Chromosomal linkage groups were established via the “cluster_SN_markers” command using the simplex × nulliplex markers at a LOD of 4.…”

High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

“…Just recently, new methods addressing autotetraploid genetics and higher orders of segregation patterns have been reported. Software such TetraploidSNPmap (Hackett et al, 2017), an updated version of the TetraploidMap (Hackett et al, 2007), polymapR (Bourke et al, 2018), and mappoly ((Mollinari and Garcia, 2019) overcame those limitations and allowed the construction of high-density linkage maps using SNP data and multi-dose markers. Potato (Da Silva et al, 2017), sweetpotato ( Ipomoea batatas L.) (Mollinari et al, 2020) and forage grasses (Ferreira et al, 2019; Deo et al, 2020) are examples of autopolyploid crops that have benefited from the utilization of such modern methodologies in QTL inference and linkage mapping analyses.…”