GeneticGenetic mapping mapping InvitationInvitation Genetic mapping in polyploids Genetic mapping in polyploids in polyploidsin polyploids You are cordiallyYou are invitedcordially to invited to attend theattend public the defense public defense of my PhDof thesis my PhD entitled: thesis entitled: GeneticGenetic mapping mapping in polyploidsin polyploids on Fridayon 15 Fridayth June 152018th June 2018 at 11:00 in at the 11:00 Aula in ofthe Aula of WageningenWageningen University, University, Generaal GeneraalFoulkesweg Foulkesweg 1, 1, Wageningen.Wageningen. Peter M. Bourke Peter Peter M. Bourke Peter Peter BourkePeter Bourke [email protected]@wur.nl ParanymphsParanymphs Michiel KlaassenMichiel Klaassen Peter PeterM. Bourke M. Bourke [email protected]@wur.nl 2018 2018 Jordi PetitJordi Pedro Petit Pedro [email protected]@wur.nl Propositions 1. Ignoring multivalent pairing during polyploid meiosis simplifies and improves subsequent genetic analyses. (this thesis) 2. Classifying polyploids as either autopolyploid or allopolyploid is both inappropriate and imprecise. (this thesis) 3. The environmental credentials of electric cars are more grey than green. 4. ‘Gene drive’ technologies display once again that humans act more like ecosystem terrorists than ecosystem managers. 5. Heritability is a concept that promises much but delivers little. 6. Awarding patents to cultivars or crop traits is patently wrong. 7. The term “air miles” should refer to one’s lifetime allowance of fossil- fuelled air travel. 8. The Netherlands’ most effective educational tool comes on two wheels with a bell. Propositions belonging to the thesis, entitled “Genetic mapping in polyploids” Peter M. Bourke Wageningen, 15th June 2018 Genetic mapping in polyploids Peter M. Bourke Thesis committee Promotor Prof. Dr R.G.F. Visser Professor of Plant Breeding Wageningen University & Research Co-promotors Dr C.A. Maliepaard Associate professor, Plant Breeding Wageningen University & Research Dr R.E. Voorrips Senior scientist, Plant Breeding Wageningen University & Research Other members Dr J. Endelman, University of Wisconsin-Madison, USA Prof. Dr M.E. Schranz, Wageningen University & Research Dr J.W. van Ooijen, Kyazma B.V., Wageningen Prof. Dr B.J. Zwaan, Wageningen University & Research This research was conducted under the auspices of the Graduate School of Experimental Plant Sciences (EPS) Genetic mapping in polyploids Peter M. Bourke Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus, Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 15 June 2018 at 11 a.m. in the Aula. Peter M. Bourke Genetic mapping in polyploids, 306 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2018) With references, with summary in English ISBN 978-94-6343-846-9 DOI 10.18174/444415 Table of contents Chapter 1 General Introduction 7 Chapter 2 Tools for genetic studies in experimental populations of polyploids 27 Chapter 3 The double reduction landscape in tetraploid potato as revealed by a high-density linkage map 53 Chapter 4 Integrating haplotype-specific linkage maps in tetraploid species using SNP markers 77 Chapter 5 Partial preferential chromosome pairing is genotype dependent in tetraploid rose 109 Chapter 6 polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids 137 Chapter 7 An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis 153 Chapter 8 Quantifying the power and precision of QTL analysis in autopolyploids under bivalent and multivalent genetic models 177 Chapter 9 Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose 209 Chapter 10 polyqtlR – an R package to analyse quantitative trait loci in autopolyploid populations 233 Chapter 11 General Discussion 255 References 277 Summary 297 Acknowledgements 299 About the author 302 List of publications 303 Education certificate 304 Chapter 1 General Introduction 7 ___________________________________________________________________________________General introduction Molecular markers and Mendel’s missing caveat It is only relatively recently that the terms “marker” and “molecular marker” have been taken to be synonymous. In his pioneering experiments with peas, Mendel was already studying the transmission and inheritance of a now-famous set of genetic “markers” (Mendel, 1866), with the physical expression of seven different traits (what we term “phenotypes”) being the marker set itself. It took almost fifty years before it was realised that these morphological markers also represented specific locations on chromosomes which were either transmitted together (due to genetic linkage) or independently (due to lack of linkage) (Morgan, 1911). Curiously, Mendel had selected only unlinked traits for his study of peas (whether this was by accident or by design we do not know). His second law, the law of independent assortment, states that alleles of one gene sort into gametes independently of the alleles of another gene. However, because chromosomes and their connection to inheritance had not yet been discovered, Mendel missed one vital caveat to this law, namely that independence only occurs if such genes are located on separate chromosomes (or perhaps at opposite ends of a single long chromosome). Most of what follows in this thesis is based on this non-independent segregation of linked loci. One of the major milestones in genetics was the realisation that a collection of linked markers could be arranged in a linear fashion, with distances between their positions estimated from the counts of co-inherited markers (Sturtevant, 1913). In his demonstration of this fact using six linked morphological markers of the common fruit fly Drosophila melanogaster, Sturtevant created the world’s first genetic linkage map (Sturtevant, 1913;Van Ooijen and Jansen, 2013). Nowadays, we generally rely on DNA markers (a.k.a. molecular markers) to identify positions on chromosomes. In this thesis we exclusively present data on single nucleotide polymorphism (SNP) markers. These are nucleotide positions which generally differ in the individuals being screened and are usually selected to be “bi-allelic” (i.e. alternating between two possible nucleotides in the material under study). However, the methods we develop are general to any bi-allelic marker system for which marker “dosage” counts can be accurately estimated. The term “dosage” is less commonly used in diploid studies, but is a very important concept in genetic analyses of polyploids. Dosage is generally understood to be the number of copies of the alternative allele carried by an individual at a particular locus. An illustration of the possible marker dosage scores in a tetraploid and hexaploid are shown in Figure 1. 8 ___________________________________________________________________________________Chapter 1 Linkage mapping and QTL analysis – part I The principal aim of this thesis is the development and exploration of methods and tools to create linkage maps and perform quantitative trait locus (QTL) analysis in polyploids. Both of these activities combined can conveniently be termed “genetic mapping” as the title of this thesis suggests. These are not new activities – as already mentioned, the first linkage map was constructed in 1913, and the first QTL analysis was arguably conducted a decade later (Sax, 1923). The novelty of this work lies in its application to polyploids, a group of organisms that possess much more complex genomes than their diploid counterparts, and in its use of modern genotyping data which often consists of many tens of thousands of markers. a. 0 1 2 3 4 b. 0 1 2 3 4 5 6 Figure 1. Representation of the possible marker dosage scores, for a. Tetraploid (ploidy = 4) and b. Hexaploid (ploidy = 6). In general, there are ploidy + 1 possible dosage classes at a bi- allelic marker position, here shown in blue / red. The convention for assigning dosage scores is to count the number of copies of the alternative allele (coloured red), with the reference allele count (in blue) given by ploidy – dosage. Modern plant and animal breeding has benefitted from the use of molecular markers, allowing specific traits of interest to be predicted without having to necessarily grow a plant to maturity and test the trait directly. This can have many advantages, for example by allowing a greater number of traits to be more cost-effectively combined, allowing selection among multiple progenies, or in material for which phenotyping is difficult 9 ___________________________________________________________________________________General introduction or expensive etc. At least, that is the intention of marker-assisted selection (MAS). In practice, MAS has met with mixed success in plant breeding programs (Collard and Mackill, 2008;Hospital, 2009). In the autotetraploid crop potato (Solanum tuberosum L.), markers have been demonstrated to be useful for certain disease resistances (e.g. potato cyst nematode (Schultz et al., 2012)) and have been shown to be a cost-effective proposition if deployed appropriately in a breeding program (Slater et al., 2013). However, in order to use markers effectively, we need to develop models to capture the relationship between a plant’s genotype and its phenotype. For polyploids, modelling these