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Uncovering the molecular basis of cellular memory in plants

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

Co-supervisor: Prof. Lorenzo Frigerio, School of Life Sciences, Warwick

PhD project title: Uncovering the molecular basis of cellular memory in plants

University of Registration: University of Warwick


Project outline:

Compared to animals, somatic cells of plants can be much more easily reprogrammed to regenerate whole new organs and, sometimes, entire individuals. This unique biological property has enabled plants to reproduce either sexually or asexually according to their habitat. The ability of plant cells to readily acquire a totipotent state has been attributed to their flexible epigenetic states. As a result, plant totipotency has been traditionally exploited by humans for the clonal propagation and genetic manipulation of economically important species. However, regenerated plants are not always phenotypically identical to their parents, a phenomenon known as somaclonal variation. This form of phenotypic variation has been linked to the accumulation of random genetic mutations and stochastic epigenetic modifications after regeneration; though the precise mechanisms are not well understood. The aim of this project is to (i) define the molecular basis of cellular memory in plants and (ii) define the impact of cloning in genetic and epigenetic variation.

Key experimental skills involved:

The student will investigate the molecular changes taking place during cellular de/re-differentiation in plants using a multidisciplinary approach (microscopy, next-generation-sequencing, computational data analysis and genome editing). The groups of JGM and LF have developed all the material and methodology required for his analysis. The student will also use customized computational models (machine learning) to enable the high-throughput analysis of cellular de/re-differentiation.

Lab-Techniques: Confocal Microscopy, cell culture, genome sequencing.

Computational-techniques: computational tools for image data and genomic analysis.

References:

Wibowo, A., Becker, C., Durr, J., Price, J., Papareddy, R., Saintain, Q., Spaepen, S., Hilton, S., Bending.,G., Schulze-Lefert, P., Weigel., D. and Gutierrez-Marcos J.F. (2018) Incomplete reprogramming of cell-specific epigenetic marks during asexual reproduction leads to heritable phenotypic variation in plants PNAS 116:8037-8042.
 

BBSRC Strategic Research Priority: Sustainable Agriculture and Food.

Techniques that will be undertaken during the project:

The student will use a wide range of molecular, histological and computational techniques including: Genomic and Epigenomic analysis using Next Generation Sequencing data and customised computational analysis. Genetic analysis using classic and newly engineered mutants. Confocal microscopy analysis and cellular modelling.

Contact: Dr. Jose Gutierrez-Marcos