Epigenetic and transcriptomic mechanisms of polyphenism in an aphid model

Polyphenism is the ability of an organism's genotype to produce multiple discrete phenotypes when exposed to environmental stress. Polyphenism is very important to organisms as it allows them to react quickly to changes in environmental stress and therefore increase their chance of survival in the changing environment. There are many different types of polyphenism, including phase polyphenism, wing polyphenism and others. Aphids are one of the key model organisms used in studying polyphenism. Under normal conditions, aphids reproduce asexually and all the offsprings are essentially clones of the mother. However, upon exposure to environmental stress such as crowding, predation, and depletion of food resources, aphids exhibit wing polyphenism whereby the offspring from the next generation will develop wings, which allows them to escape from poor environmental conditions. Even though the aphid model has been used to investigate polyphenism, the underlying mechanisms in regulating such wing polyphenism remain unclear. The main experiment in this thesis involved exposing two different aphid genotypes (N116 and N127) to crowding conditions to trigger alternative morph production and the degree and number of adult alternative morphs were recorded (mesocosm experiment). Next, we carried out two transfer experiments to investigate the possibility of trade-offs between dispersal and reproduction. At the end of this mesocosm experiment, five 4th instar nymphs of each morph were transferred to individual plants to allow them to reproduce for another 12 days (Transfer experiment 1). The total number of offspring produced by each morph was recorded. At the end of transfer experiment 1, five 4th instar nymphs produced by each morph were transferred to another individual plant and allowed to reproduce for another 12 days and the total number of the population was recorded. The adult morphs collected from the mesocosm experiment were used to investigate the underlying mechanisms of wing polyphenism in aphids and the role of epigenetics mechanisms in regulating pea aphid wing polyphenisms through different techniques: qPCR, RNA-seq, MBD-seq, pyrosequencing and mIRNA-seq. 25 The two aphid genotypes reacted very differently to starvation conditions with N116 producing winged offspring in the next generation while N127 changed their body colour from red to pale. In addition, N127 also produced a higher percentage of alternative morphs compared to N116. We found that in both transfer experiments the dispersal morphs have lower reproduction compared to the wild type. This suggests a possible trade-off between dispersal and reproduction and such a trade-off could last for more than one generation. Our RNA-seq and qPCR identify several genes that could be involved in regulating wing development, reproduction and stress response in the pea aphid. Pyrosequencing revealed that among the genes that were differentially expressed between morphs only a few were differentially methylated. Further, our MBD-seq shows that the pea aphid has the highest methylation in the gene body region. However, integrating the MBD-seq and RNA-seq suggests that there was no clear correlation between DNA methylation and gene expression but some genotypes and morphs show stronger positive trends. In addition, we found that many conserved and some novel miRNAs were differentially expressed between the aphid morphs. Target gene prediction results from these miRNAs suggest that they target many genes that were involved in wing development, reproduction and wing development. Together the results from this thesis provide insight into genes that could be regulating wing polyphenism, stress response and reproduction in pea aphids and the role of different epigenetic mechanisms in regulating this polyphenism.