Genetics of insect resistance to plant defence Kim M. C. A. Vermeer Thesis committee Promotor Prof. Dr M. Dicke Professor of Entomology Wageningen University Co-promotor Dr P.W. de Jong Assistant professor, Laboratory of Entomology Wageningen University Other members Prof. Dr B.J. Zwaan, Wageningen University Prof. Dr M.E. Schranz, Wageningen University Dr A. Biere, Netherlands Institute of Ecology (NIOO KNAW), Wageningen Dr K. Vrieling, Leiden University This research was conducted under the auspices of the C.T de Wit Graduate School for Pro- duction Ecology and Resource Conservation. Genetics of insect resistance to plant defence Kim M. C. A. Vermeer Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 18 February 2014 at 11 a.m. in the Aula. Kim M. C. A. Vermeer Genetics of insect resistance to plant defence 200 pages. PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in Dutch and English ISBN 978-94-6173-836-3 CONTENTS 1 General introduction 7 2 The potential of a population genomics approach to analyse geographic 25 mosaics of plant-insect coevolution 3 Identification of a saponin degrading β-glucosidase from the flea beetle 43 Phyllotreta nemorum 4 Changes in frequencies of genes that enable Phyllotreta nemorum to utilize 61 its host plant, Barbarea vulgaris, vary in magnitude and direction as much within as between seasons 5 Natural selection against resistance of a flea beetle to host plant defences 75 6 Evaluation of a candidate resistance gene underlying flea beetle resistance 107 to host plant defence with a population genomics approach 7 General discussion 133 References 153 Summary 171 Samenvatting 177 Acknowledgements 183 Curicullum vitae 185 Publications 187 Supplementary 189 5 CHAPTER 1 General introduction Kim M. C. A. Vermeer Chapter 1 This general introduction will provide the reader with background information of the studied system needed to understand the presented work. First, I will provide a general background of plant-insect interactions involving secondary metabolites. Subsequently, I will introduce the study species and give the rationale for using it as the study organism in this research. This is followed by an introduction of the most important concepts and models used in this thesis. Lastly, I will give the aims of the thesis and present a brief overview of the following chapters. SCIENTIFIC BACKGROUND AND RELEVANCE We live on a Green Planet. Without plants we would not refer to the earth as being green. Plants are abundant, despite being the primary food source of many other creatures that roam the same planet and despite being nearly completely immobile. Somehow plants manage to not become completely consumed, as the green color of the earth demon- strates. Different mechanisms of plant defences account for this. Plant defence mecha- nisms can be mechanical like thorns or wax layers. In addition, the plant can also be chemi- cally defended by secondary metabolites (Fraenkel 1953). These chemical compounds de- fend the plant against potential herbivores by e.g. repellence, toxicity, or reduction of the digestibility by the attacker. A plant usually contains a variety of these secondary com- pounds (Schoonhoven et al. 2005) and they have different effects on different herbivores; some herbivores are attracted by the same compound that repels others. A well-known ex- ample of compounds that attract or repel herbivores are glucosinolates and their breakdown products in Cruciferae (Brassicaceae)(Verschaffelt 1910; Fraenkel 1959; Feeny 1977; Chew 1988). Glucosinolates reduce the performance of many generalist herbivores on the plant. For specialist insects that have adapted to this plant however, these glucosinolates can be a feeding and oviposition stimulant (Verschaffelt 1910; Thorsteinson 1953; Fraenkel 1959; Whittaker and Feeny 1971; Nielsen 1978; Renwick 2002). Where glucosinolates act as a first line of defence against generalists here, the plant can subsequently develop a second line of defence that wards off specialists (e.g. in Feeny 1977; Nielsen 1978; Sachdevgupta et al. 1993a; Sachdevgupta et al. 1993b; Shriver et al. 1993). For example, not the presence of glucosinolates but the presence of cardenolides explain rejection of the plant Erysimum cheiranthoides by the cabbage butterfly (Sachdevgupta et al. 1993b). The evolution of defences against herbivorous insects may occurs under selection pressure from these herbivores (Rausher 1996). This selection pressure may vary in time and space, as influenced by the composition of the community (Thompson 2005). Plant defences may also differ in constitutive and induced defences, meaning that the defence is present re- gardless of a herbivore being present or not, and that the defence will be initiated only when the herbivore attacks the plant, respectively. Even within a plant species, genotypes may differ in defence strategies against insects (e.g. Nielsen 1997b; Jander et al. 2001). Herbi- vores in their turn, can also evolve mechanisms to avoid, tolerate or resist the plant’s sec- ond line of defence (Schoonhoven et al. 2005; Despres et al. 2007). The dynamic interplay between plant and herbivorous insects is also known as a (co)evolutionary ‘arms race’ be- 9 General introduction tween plant and insect and is be- Glossary lieved to have led to the variety of Adaptation: the process that traits evolve by natural chemical compounds we find in selection that influence the organism’s fitness. plants (Ehrlich and Raven 1964). Bottleneck: In population genetics a bottleneck re- Implications of the evolution of fers to a sudden and large decrease in population plant-insect interactions and re- size. sistance development concern agri- Gene flow: the exchange of genetic information be- cultural and environmental issues. tween (sub)populations (Endler 1977). Gene flow is Highly invasive cruciferous weeds not the same as migration as migration does not have can, for example, be controlled with to lead to genetic exchange. specialist insects (Jolivet et al. 1988). Moreover, plants that are Genetic drift: the change in allelic composition of high in oviposition stimulants but populations caused by random sampling. The smaller on which larvae cannot survive, the population, the bigger the effect of genetic drift is can be planted near crops to serve expected to be. as a “dead-end” trap for pest in- sects (Renwick 2002; Shelton and Genome: all the genetic information of an individual. Nault 2004). Barbarea vulgaris, for Glucosinolates: organic compounds that contain example, can be used in integrated sulphur and nitrogen and glucose unit(s). We know pest management against the dia- them probably best from the sharp taste of mustard mond back moth (DBM), a notori- seeds. ous pest of various cultivated cruci- fers (Talekar and Shelton 1993; Maladaptation: a trait evolved by natural selection Idris and Grafius 1996; Shelton that used to be advantageous but now negatively in- and Nault 2004; Badenes-Perez et fluences the organism’s fitness. al. 2010). Furthermore, deterrents, repellents, and feeding inhibitors of secondary Metabolites: organic compounds that are certain plants can be incorporated not directly involved in the primary metabolism of an into crops to increase their re- organism. sistance to pest insects. For the Metapopulation: a collection of (sub)populations that development of such applications undergo extinction and recolonization events that af- and for them to remain successful, fect genetic variation and evolution among this collec- we need a better understanding of tion of subpopulations (Hanski 1998). insect resistance mechanisms and how insect resistance evolves. Neutral theory: Most polymorphisms are hardly or This knowledge may also add to not at all under selection and are therefore mainly the prevention of resistance devel- under influence of genetic drift and dispersal (Kimura opment by pest insects. In natural 1983). systems, the occurrence, intensity and direction of selection on the Panmictic population: a population where random herbivore may vary among locali- mating occurs. Each individual has an equal chance ties and through time. The speed of mating with another individual from that population. of insect resistance development is 10 Chapter 1 influenced by variation in plant defenses over time, although there is no real consensus as to whether it may increase or delay the process (Gardner et al. 1998; Gardner and Agrawal 2002; Renwick 2002). Seasonal variation in plant defences may offer a window of oppor- tunity for insects to evolve resistance. On the other hand, temporal variation in the plant de- fence may reduce the intensity of the selection pressure on insect resistance. Geographical variation in plant defence and host plant range also influences the outcome of insect re- sistance development, as does the distributional range of the insect and the level of insect mobility. The spatial structure of a plant-insect interaction should therefore not be ignored when studying insect resistance in a natural system. Different components influencing pop- ulation structure such as gene flow, genetic drift and strength of selection need to be taken into account for a better understanding of the evolution of local adaptation (as already acknowledged by Wright (1931)). Consequently,