RP12: Epigenetic response to stress in natural variants of pennycress (Thlaspi arvense)

  • PhD Supervisor(s): Claude Becker, Ortrun Mittelsten Scheid
  • Host Institution: Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
  • Duration: 36 months
  • Fixed start date: 1 April 2018
  • Planned secondment(s): Institute of Applied Genomics - Technology Services, Udine (IT); Eberhard Karls University Tübingen (GE); University of Leipzig (GE)

Pennycress (Thlaspi arvense) is a member of the Brassicaceae family; it is a selfing diploid that is widespread in Europe, and can be found in natural, agricultural, and disturbed sites. T. arvense is of dual interest to us: on the one hand, as a weed it infests agricultural areas and causes losses in agricultural production. On the other hand, it has recently been established as a promising biofuel crop. Its close relatedness to the well-studied model plant A. thaliana and other well-characterised Brassica species makes it amenable to genomic enquiries at the whole-genome level.

In this project we ask how natural epigenetic variation in T. arvense influences the plant’s response to short- and long-term exposure to abiotic and biotic stress. Objectives are: (1) identifying genomic loci that change their epigenetic configuration upon drought treatment; (2) determining the transgenerational stability of stress-induced changes in dependence of the duration, intensity and frequency of the stress; (3) assessing the contribution of epigenetic stress-regulated loci to the physiological stress response of the plant. The project builds on our year-long expertise in the analysis of whole-genome DNA methylation profiles and is carried out in close collaboration with Oliver Bossdorf at the University of Tübingen, Germany. The PhD student will gain experience in complex experimental design, state of the art whole-genome profiling techniques using next-generation sequencing technology, and computational analysis of whole-genome data.

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