Master student in ecological genomics

Master student in ecological genomics

Terrestrial Ecology

Suitable for Msc thesis, at least six months

Evidence is accumulating that epigenetic mechanisms can affect heritable phenotypic traits and thus, may play a role in plant adaptation. However, little is known about the magnitude and relevance of functional epi-allelic variation in natural plant populations.

Our aim is to gain better insight into epi-allelic variants within natural apomictic lineages of the common dandelion. Apomictic dandelions are triploid and reproduce via clonal seed. Many different apomictic genotypes exist and some have widespread occurrence through North-Western Europe, representing an excellent system to evaluate natural epigenetic variation in a single genetic background. Previous studies showed that heritable DNA methylation changes are triggered by environmental stresses in apomictic dandelions, and preliminary screening revealed significant levels of heritable phenotypic and DNA methylation variation within one widespread apomictic lineage.

This may hint at an epigenetic contribution to within-lineage trait variation. However, it is undemonstrated how much of this methylation variation has functional relevance. To further zoom in on this question, we conducted a RNA-Seq study to detect heritable gene expression differences between plants from one clonal lineage grown in a common greenhouse and an experimental garden. Differentially expressed genes (DEG) identified might be a consequence of genetic mutations, epi-alleles or both. The objective of proposed Master project is to unravel these two options. The student will be in charge of performing experimental drug de-methylation treatments to evaluate demethylation effects on expression of selected genes (using real time quantitative PCR): if expression variation between individuals is sensitive to demethylation then, this might imply the presence of epi-allelic variation.

Your profile:

  • Highly motivated candidate with a strong interest in ecological genomics
  • Experience in molecular biology
  • English skills and working within an interdisciplinary team

For further information, please contact:

Dr. Julie Ferreira de Carvalho, Dr. Koen Verhoeven
Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
Tel. 0031 (0)  3 17 47 34 16

Send your application to:

Dr. Julie Ferreira de Carvalho