Principal Supervisors: Dr Jose Gutierrez-Marcos, School of Life Sciences and Professor Detlef Weigel, MPI Tubingen
PhD project title: Molecular basis of environmental stress memory in plants
University of Registration: University of Warwick
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. Recent data suggest that environmental signals, in addition to the direct influence on plant growth, can also cause phenotypic changes that can be transmitted to the progeny, sometimes remaining stable for several generations. In this respect, the formation of environmental epialleles and their maintenance represents an important, yet unexplored, source of variation and adaptive power that can contribute to rapid evolution and more importantly to the improvement of crop plants.
The aim of this project is to investigate (i) how environmental signals are able to modify the epigenome of meristematic cells to facilitate their somatic transmission and (ii) how these environmental imprints are maintained across generations after sexual propagation. Using Arabidopsis as a plant model system, the student will investigate, the inheritance of epigenetic modifications upon environmental stress, use known epigenetic mutants to obtain clues about the genetic pathway(s) implicated and the targeted engineering of identified genomic regions to reveal their function. It is expected that the student will be able to test the different by combining computational and laboratory analyses.
Key Skills involved:
The student will gain skills in single-cell epigenomic analysis (bisulphite sequencing, chromatin mapping and mRNA/small RNA profiling). The student will be able to analyse next-generation sequencing (NGS) data to generate hypothesis that will be tested in the laboratory using established CRISPR/Cas9 genome targeting methods. In addition, the student is expected to obtain basic training on computational and statistical tools for analysis of genome-wide data.
- Wibowo A., et al., 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
- Becker, C., et al., Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature (2011) 480: 245-9.
BBSRC Strategic Research Priority: Food Security
Techniques that will be undertaken during the project:
The student will be working in a multidisciplinary environment: the laboratory of JGM has an international track record in plant epigenetics and the group of DW has an international track record in genetics, development and genomics in plants.
Contact: Dr Jose Gutierrez Marcos, University of Warwick