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Enhancing stress resistance in plants by targeted epigenome manipulation

Principal Supervisor: Dr Jose Gutierrez-Marcos - School of Life Sciences

Co-supervisor: Dr Guy Barker - School of Life Sciences

PhD project title: Enhancing stress resistance in plants by targeted epigenome manipulation

University of Registration: Warwick

Project outline:

Plants are sessile organisms that are known for their adaptive plasticity to the changing environment. Environmental changes cannot only influence gene expression patterns but also affect the stability of the genome. Both of these responses seem to involve epigenetic mechanisms. We have discovered that environmental signals, in addition to the direct influence on plant growth, can also cause phenotypic changes that can be transmitted to the progeny, and sometimes remaining stable for several generations.

Environmental stress has a major influence on plant growth and survival, limiting the geographical distribution of natural species and the yield and growing season of agricultural crops. The natural priming response can be elicited experimentally by exposing plants to a short period of extreme abiotic and biotic stress. Using this strategy we have identified regions of the Arabidopsis genome sensitive to epigenetic modification in response to stress that modulate the expression of neighboring genes. However, the precise mechanisms implicated in this process and the phenotypic consequences remain unknown.

Specific objectives: 

  1. Identification of genome regions targeted epigenetically by stress. This objective will use whole-genome sequencing to identify sequences undergoing epigenetic modification.
  2. Functional characterization of epigenetically targeted genome regions. This objective will use CRISPR/Cas9 genome editing tools to direct genetic and epigenetic changes and assess their effects in gene expression.
  3. Phenotypic characterization of engineer genome modification. This objective will develop methodology for the high-throughput phenotypic analysis of engineered plants.

Key experimental skills involved:

The student will gain skills in molecular biology, gene expression and DNA methylation coupled to next-generation sequencing (NGS). In addition, the student is expected to develop computational skills for the analysis of NGS data using support present in both groups.

References:

  1. Wibowo A., Becker B., Marconi G., Durr J., Price J., Hagmann J., Papareddy R., Kageyama J., Becker J., Weigel D., and Gutierrez-Marcos JF. Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and restricted in the male germline by DNA glycosylase activity (2016). eLife 5:e13546

BBSRC Strategic Research Priority: Food Security

Techniques that will be undertaken during the project:

  • Plant genetic engineering
  • CRISPR/cas9 genome engineering
  • High-throughput phenotypic analysis
  • NGS library preparation and sequencing
  • Computational analysis of epigenomic data

Contact: Dr Jose Gutierrez Marcos, University of Warwick