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

Peter M Bourke,Geert Van Geest,Johan H Willemsen,Roeland E Voorrips,Marinus J M Smulders,Chris Maliepaard,Christine A Hackett,Paul Arens,Richard G F Visser,Russell Schwartz

doi:10.1093/bioinformatics/btab574

Abstract

MotivationThe 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.ResultsHere, 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.Availabilityand implementationpolyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

Polyploids, which carry more than two copies of each chromosome, are an important group of organisms that occur widely among plant species, including several domesticated crops (Salman-Minkov et al, 2016)
We demonstrate the capabilities of polyqtlR with a number of example applications
By fitting various combinations of quantitative trait loci (QTL) as cofactors, we found that the significance of the LG 3, 4 and 6 peaks could be increased, while the peak on LG 2 dropped in significance upon the inclusion of co-factors

Summary

Introduction

Polyploids, which carry more than two copies of each chromosome, are an important group of organisms that occur widely among plant species, including several domesticated crops (Salman-Minkov et al, 2016). Many theories to explain their prevalence among crop species have been proposed, identifying features which may have appealed to early farmers in their domestication of wild species. Such features include their larger organs, such as tubers, fruits or flowers (the so-called ‘gigas’ effect) (Sattler et al, 2016), phenotypic novelty (Udall and Wendel, 2006), their ability to be clonally propagated (Herben et al, 2017), increased seedling and juvenile vigour (Levin, 1983) and the possibility of seedlessness which accompanies odd-numbered ploidies (Bradshaw, 2016). Polyploidy may be induced deliberately [through species hybridization with associated unreduced gametes, or through the use of some chemical cell division inhibitor, such as colchicine (Blakeslee and Avery, 1937)], often to combine properties of parents that could not otherwise be crossed (Van Tuyl and Lim, 2003), or to benefit from some of the other advantages listed above

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Conclusion