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 realise 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/packages=polymapR.

The identification of allelic variation in potato

“…In this study we made use of existing haplotype data that was generated using sequencing data (Chapter 3), or by means of haplotype inference on bi-allelic SNP markers obtained from SNP array data (Chapter 4, 5). In contrast, phasing in the tetraploid full-sib population was achieved by traditional linkage mapping (Bourke et al 2016;Bourke et al 2018), followed by phase reconstruction within each tetraploid progeny (Zheng et al 2016). The accuracy of haplotype imputation depends on how well these original haplotypes were estimated, which might depend on marker density, relatedness, sample size and demographic history of each allele.…”

“…In this study, we applied Poly-Imputer to 231 full-sib offspring of a cross between two tetraploid potato varieties. As parental haplotypes are phased during linkage mapping (Bourke et al 2016), and for each segment of 1 cM, the transmission of alleles to offspring is known, the expected allele frequencies across the 231 progeny could be calculated. We compared these results to the ground-truth as provided by tetraOrigin-based phases in all progenies.…”

“…F1 population: The offspring of a full-sib population with 233 individuals, previously genotyped with a SNP array and originating from the cross between 'Altus' and 'Colomba' was used for imputation. This population was previously used to generate a high-density linkage map (Bourke et al 2016). For each progeny linkage phase was reconstructed using tetraorigin (Zheng et al 2016).…”

“…For outbreeding autopolyploid crops such as potato (Vos et al 2015;Hamilton, 2011;Felcher et al 2012) chrysanthemum (van Geest et al 2017) and rose (Vukosavljev et al 2016) high-density SNP genotyping platforms are being adopted quickly. This is coupled with the development of tools to accommodate these high marker densities for use in linkage map construction (Hackett et al 2003;Bourke et al 2016), QTL mapping (Bourke et al 2018), or genome-wide association studies (Rosyara et al 2016). Likewise, in recent years a shift can be seen from the use of bi-allelic markers towards the adoption of haplotype markers in genetic analysis.…”

The recombination landscape and multiple QTL mapping in aSolanum tuberosumcv. ‘Atlantic’-derived F1population

“…Along with the development of an array that uses dosage-sensitive SNPs, new analytical methods have recently been developed to effectively utilize this information in reconstructing linkage maps (Hackett et al, 2014;Bourke et al, 2018;Mollinari and Garcia, 2019) and mapping QTL Chen et al, 2018) in autotetraploid species.…”