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IVO MOES Unraveling the Genetics of Lifespan in Nasonia Using GWAS in an Inbred Line Panel

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IVO MOES Unraveling the Genetics of Lifespan in Nasonia Using GWAS in an Inbred Line Panel UNRAVELING THE GENETICS OF LIFESPAN IN NASONIA USING GENOME WIDE ASSOCIATION ANALYSIS IN AN INBRED LINE PANEL IVO MOES Unraveling the genetics of lifespan in Nasonia using GWAS in an inbred line panel MSc Thesis Report By Ivo V. Moes Registration number: 910306576010 Chair group: Laboratory of Genetics Course code: GEN-70424 Supervisor: Bart Pannebakker, Laboratory of Genetics, Wageningen UR Examiner: Bas Zwaan, Laboratory of Genetics, Wageningen UR Date: 4-9-2015 Wageningen UR Ivo Moes | Laboratory of Genetics | Wageningen UR 2015 Abstract An important part of our understanding of the genetics underlying lifespan and ageing is generated through research in model organisms. The parasitoid wasp Nasonia vitripennis has been subject of research for decades. This model organism possesses many favorable characteristics, such as a short generation time and a haplodipolid sex determination system. This, and the increasing availability of next generation sequencing techniques, has made Nasonia re-emerge as a model organism in the field of genetics. In this study, a sequenced line panel of 34 inbred lines of Nasonia is used to identify genes associated with lifespan. A genome wide association study (GWAS) has been performed, which led to the selection of two candidate genes: beta-syntrophin 1 and neurogenic locus protein delta. In addition to the GWAS, a linkage analysis of the single nucleotide polymorphisms (SNPs) has been used to define haplotype blocks. These blocks have also been subjected to an association analysis, in order to support the GWAS results. Relative expression levels of the candidate genes have been measured with quantitative PCR, which showed a trend, but yielded no significant results. Although the principal aim of this study was to elucidate the genetic basis of lifespan, a pipeline for phenotype- genotype associations in the inbred line panel has been developed in the process. The effectiveness of this pipeline is demonstrated here, facilitating its use for research of other traits. Ivo Moes | Laboratory of Genetics | Wageningen UR 2015 Contents Introduction ............................................................................................................................................1 Longevity and ageing ...........................................................................................................................1 Nasonia vitripennis: the model organism .............................................................................................1 GWAS and haplotyping .......................................................................................................................2 Methods ...................................................................................................................................................4 Hvrx inbred line panel ..........................................................................................................................4 Genotyping ...........................................................................................................................................4 GWAS ..................................................................................................................................................4 Haplotype analysis................................................................................................................................5 Quantitative PCR ..................................................................................................................................6 Statistical analysis ................................................................................................................................6 Results .....................................................................................................................................................7 Genome Wide Association Study .........................................................................................................7 Haplotype analysis................................................................................................................................8 Candidate genes ....................................................................................................................................9 Quantitative PCR ................................................................................................................................10 Discussion ..............................................................................................................................................10 Genome Wide Association Study .......................................................................................................10 Neurogenic locus protein delta ..........................................................................................................11 Beta-1-Syntrophin...............................................................................................................................12 Recommendations for future research ................................................................................................13 Conclusion ..........................................................................................................................................14 Acknowledgements ...............................................................................................................................15 References .............................................................................................................................................16 Appendix ...............................................................................................................................................18 Ivo Moes | Laboratory of Genetics | Wageningen UR 2015 1. Introduction Longevity and ageing Our understanding of the biological phenomenon of ageing and the factors determining lifespan have given rise to a lively field of research, where the mechanistic causes of ageing seem to be gradually elucidated. However, there remains a lack of consensus concerning its evolutionary causes. Ageing might be the result of pleiotropic mutations, affecting multiple traits in different stages of life (Jones and Rando 2011). This antagonistic pleiotropy theory is based around the idea that expression of a certain gene could increase fitness in one stage of life, while causing pathologies in another. According to this theory, ageing is not an evolutionary adaptation, but merely a by-product of fitness optimization during the fertile period. Tumour suppressor genes, such as p53, can be seen as an example of this in mammals: they induce senescence in cells displaying abnormal proliferation, but also interfere with the proliferation of stem cells resulting in tissue degeneration (Ungewitter and Scrable 2009). Another theory for an evolutionary basis of ageing is found in the apparent trade-off between growth and reproduction, and lifespan: caloric restriction has, for instance, proven to be correlated with a significant increase in lifespan in many animal species. Furthermore, the number of offspring has shown to be inversely correlated with lifespan in some mammals (Gems 2015). An example can also be found in the yeast Saccharomyces cerevisiae. In times of nutrient abundance, a yeast cell would exploit the situation by prioritizing maturation and reproduction over somatic maintenance and proliferation. In times of scarcity, the organism would either be unable to mature and reproduce, or the offspring would be unlikely to do so. Individual proliferation is preferred in this situation: sporulation is induced, making cells durable and lowering metabolic rate to a minimum, ready to ‘switch back’ when circumstance are more favourable (Gems and Partridge 2013). Such evolutionary adaptations are engraved in molecular pathways that would allow for the switching as a result of environmental cues. Two of these highly conserved signalling cascades that have proven to affect lifespan in a range of model organisms are the Insulin/Insulin Like Growth Factor I signalling (IIS) pathway and the mammalian target of rapamycin (mTOR) signalling pathway. Interventions in different parts of these pathways have led to significant changes in lifespan in a range of organisms and strongly effects incidence of age related pathologies such as cancer and Alzheimer’s disease (Barbieri, Bonafe et al. 2003). Homology of longevity-associated genetic pathways between flagship model organisms such as Caenorhabiditis elegans and Drosophila melangoster has previously shown to uncover conserved molecular pathways in higher animals (Gems and Partridge 2013). In recent years, driven by the development of next generation sequencing, Nasonia vitripennis has re-emerged as a model organism in genetic research, and it might be a valuable addition to the arsenal of organisms used in lifespan research. Nasonia vitripennis: the model organism The parasitoid wasps of the genus Nasonia have been studied for decades as model species (Whiting 1967). The genus consists of four species, of which Nasonia vitripennis has been studied most extensively. Crossing between the species is restricted by the presence of the endosymbiotic bacteria Wolbachia, which causes cytoplasmic incompatibility (Bordenstein, O'Hara et al. 2001). Antibiotic curing from the bacteria leads to inter-fertility of the species. The female wasp lays the eggs on the surface of the host, generally larvae of other dipterans, after which venoms
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