Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR

P.M. Bourke*, R.E. Voorrips, Christine A. Hackett, G.A. van Geest, J.H. Willemsen, P.F.P. Arens, M.J.M. Smulders, R.G.F. Visser, C.A. Maliepaard*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

13 Citations (Scopus)



The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialized tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement.

Here, we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualization tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed.
Original languageEnglish
Article numberbtab574
Pages (from-to)3822-3829
Number of pages7
JournalBioinformatics (Oxford, England)
Issue number21
Early online date6 Aug 2021
Publication statusPublished - 2021


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